
                                   -position in query-                             -position in repeat-
          %    %    %    query                         C matching  repeat          (left)  end   begin  linkage
+ score  div. del. ins.  sequence  begin  end  (left)  + repeat    class/family    begin   end   (left) id/graphic

+  298    3.9  9.8  0.0  hg38_dna     14    64 (12853) + L1M5      LINE/L1           3881   3936 (2210)   1

ANNOTATION EVIDENCE:
  298   3.92 9.80 0.00  hg38_dna     14    64   11278 + L1M5_orf2 LINE/L1           1772   1827   1467    
298 3.92 9.80 0.00 hg38_dna 14 64 (11278) L1M5_orf2#LINE/L1 1772 1827 (1467) m_b1s551i0

  hg38_dna              14 AGAAAAGTCATA-----ATCTCAATAGATGCAGAAAAAGCATTTGACAAA 58
                                 i     -----                                 
  L1M5_orf2#LIN       1772 AGAAAAATCATATGATCATCTCAATAGATGCAGAAAAAGCATTTGACAAA 1821

  hg38_dna              59 ATTAAA 64
                              v  
  L1M5_orf2#LIN       1822 ATTCAA 1827

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 4.03
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 5.00 (5 / 1)

+ 5528   16.9  7.7  1.4  hg38_dna     72  1322 (11595) + L1MD3     LINE/L1           6654   7981   (14)   2

ANNOTATION EVIDENCE:
 5528  16.95 7.67 1.43  hg38_dna     72  1322   10020 + L1MD3_3end LINE/L1           1401   2728     14    
5528 16.95 7.67 1.43 hg38_dna 72 1322 (10020) L1MD3_3end#LINE/L1 1401 2728 (14) m_b1s551i1

  hg38_dna              72 TATACGTACATATAACTCCTAGCTCTGTCCAC--AGAGGGCCAAGAAACA 119
                                i        vi              i --        v    i  
  L1MD3_3end#LI       1401 TATACATACATATATTTCCTAGCTCTGTCCGCTGAGAGGGCCTAGAAGCA 1450

  hg38_dna             120 GTATCATCTCAATAGAAGCAAGGACACCTAGCACACAGATTTTGGTTTCT 169
                             iv  i i  i   v i i  v         i v     i         
  L1MD3_3end#LI       1451 GTGACACCCCAGTAGCAACGAGCACACCTAGCGCCCAGATCTTGGTTTCT 1500

  hg38_dna             170 AA-TACCATCCTCCAATAAAAGGAATCAAGACATTTTGGAGAAATGGCTG 218
                             -      i               i  i i vii               
  L1MD3_3end#LI       1501 AAATACCATTCTCCAATAAAAGGAACCAGGGCTCCTTGGAGAAATGGCTG 1550

  hg38_dna             219 ATTCTAAGGTTGGGGAAGGGAAAATACTAAATGAGCCTGGAGCATCTCAT 268
                                 i  i     v           v i                 ii 
  L1MD3_3end#LI       1551 ATTCTAGGGCTGGGGCAGGGAAAATACAAGATGAGCCTGGAGCATCTTGT 1600

  hg38_dna             269 AGTGCCAGACAGTAAGGAAATGATAAAAAAAAAAAAATAAAAATTTTTAA 318
                                    v         i  v v     v    i------------i 
  L1MD3_3end#LI       1601 AGTGCCAGAAAGTAAGGAAGTGCTCAAAAACAAAAG------------GA 1638

  hg38_dna             319 TGGGGACATTTCAAAAGGACAAAAGTACCAACCTGAAAAAA-TCCCAAT- 366
                                i   v           v i vi           i i-       -
  L1MD3_3end#LI       1639 TGGGGGCATGTCAAAAGGACACAGGAGCCAACCTGAAAGAGCTCCCAATG 1688

  hg38_dna             367 GCCAAAGCTGGAACAATTTAAGCAAT-------ATAAAAATGGTATTAGA 409
                                              i     i-------    vi  i     i  
  L1MD3_3end#LI       1689 GCCAAAGCTGGAACAATTTGAGCAACAAAATAAATAACGATAGTATTGGA 1738

  hg38_dna             410 TAATAGCTCAAAGACT-AAATAAATATCCATCAATATACATGGATATAAA 458
                            v   i i     ?v -              v i vi i iv        
  L1MD3_3end#LI       1739 TTATAACCCAAAGNATAAAATAAATATCCATGAGTCCATACTGATATAAA 1788

  hg38_dna             459 TAACTGACTCAAT-AATAAATCAATGGGAAAAAAGGGACCAATCTTTCTT 507
                              v   i v   -       -- v    i  ii ii  v      i   
  L1MD3_3end#LI       1789 TAAATGATTGAATAAATAAAT--AGGGGAGAAGGGAAACAAATCTTCCTT 1836

  hg38_dna             508 AGAGAAGAATTTCTATTAATAAATGTAGAAAGAAGGAAGGAAATGGAAAA 557
                            v         i v ?              i   v  i      i     
  L1MD3_3end#LI       1837 ACAGAAGAATTCCAANTAATAAATGTAGAAGGAATGAGGGAAATAGAAAA 1886

  hg38_dna             558 TCACCATTAGAATACCACAATAATAATTGCTGCAGGCAAGATCCAT---T 604
                                       i      i                         i--- 
  L1MD3_3end#LI       1887 TCACCATTAGAACACCACAGTAATAATTGCTGCAGGCAAGATCCACTGAT 1936

  hg38_dna             605 GAACACTAAAATTATTGGACAAAACTTTAAAGAGAAATAGAATATTTGTA 654
                              ii         v   i i         i      i  i       i 
  L1MD3_3end#LI       1937 GAATGCTAAAATTAGTGGGCGAAACTTTAAGGAGAAACAGGATATTTGCA 1986

  hg38_dna             655 CTACCTCA-------------AAAATATTTATTAATCACTGTGGTGGTTT 691
                           ivi     -------------               i             
  L1MD3_3end#LI       1987 TAGCCTCAAAGTATCTCCCCCAAAATATTTATTAATTACTGTGGTGGTTT 2036

  hg38_dna             692 TAACATATGACCACAAATTATTTGATA----TCCCT-------------- 723
                                    v         v       ----     --------------
  L1MD3_3end#LI       2037 TAACATATGTCCACAAATTCTTTGATACTCCTCCCTCCAGGAGGTGGAGC 2086

  hg38_dna             724 -------CCCTTCCTTTGACTGTG-------------GACTTTCTCCTAA 753
                           -------    i  i    v    -------------    iv  i i  
  L1MD3_3end#LI       2087 TTAATTCCCCTCCCCTTGAGTGTGGGCTGGACTTAGTGACTCGCTTCCAA 2136

  hg38_dna             754 CAAATAGACCATGGAAAGGGGGAAAAAGTAACATTACAAT-AAGAAACCT 802
                           vi      vi          ii   v      v     i -i       -
  L1MD3_3end#LI       2137 AGAATAGAGTATGGAAAGGGAAAAATAGTAACTTTACAGTGGAGAAACC- 2185

  hg38_dna             803 TGCCAGACACCATCTT-GCCATGTGATCAAAGTT---ATCATCAGT---- 844
                             v         i   -i   v        i   ---    i    ----
  L1MD3_3end#LI       2186 TGGCAGACACCACCTTAACCAAGTGATCAAGGTTAACATCACCAGTGATA 2235

  hg38_dna             845 --TGATGTGGCTATCATATGCTGCCATATGTGATACAATGAGAAGGGCAC 892
                           -- v    v v      i i iv  vv  i    i i             
  L1MD3_3end#LI       2236 AGTCATGTTGATATCATGTACCCCCTGATATGATGCGATGAGAAGGGCAC 2285

  hg38_dna             893 AACAGCTCTGCGATATTCTTCTCTCAAAATCCATAATCTCAGTCTAATTG 942
                           vv  v     i i        - i?    i      i i         ii
  L1MD3_3end#LI       2286 TTCACCTCTGTGGTATTCTTC-CCNAAAACCCATAACCCCAGTCTAATCA 2334

  hg38_dna             943 TGAGAAAACATCAGATAAATCCAAATTGAGATGCATTTTACAAAACACAT 992
                                          i   i          ivi    i       i  v 
  L1MD3_3end#LI       2335 TGAGAAAACATCAGACAAACCCAAATTGAGGGACATTCTACAAAATACCT 2384

  hg38_dna             993 AACCAGTACTCTTCAAAAGTGACAAGAT-----------ATGAAAGACTG 1031
                           i                 ?  v    i ----------- v         
  L1MD3_3end#LI       2385 GACCAGTACTCTTCAAAANTGTCAAGGTCATGAAAAACAAGGAAAGACTG 2434

  hg38_dna            1032 AGAAACTGTCACAGATTGGAGTAAACGAGGGAGGCATGAAAACTAAACAC 1081
                                          ii    v i  v i    i     vi      ii 
  L1MD3_3end#LI       2435 AGAAACTGTCACAGACCGGAGGAGACTAAGGAGACATGACGACTAAATGC 2484

  hg38_dna            1082 CATGTGGTAT-ATGGGGTGGATCCTGAAATTAAAAAAAAAGAACATTAGA 1130
                           v         -v   iv         i  i--- i      i       v
  L1MD3_3end#LI       2485 AATGTGGTATCCTGGATTGGATCCTGGAAC---AGAAAAAGGACATTAGT 2531

  hg38_dna            1131 GGGAAAACTGTGGTAATCTGAATAAAGTGTATAGTTTCATTAATACTATT 1180
                             i       vv v    i         v i?     vi      v  ? 
  L1MD3_3end#LI       2532 GGAAAAACTGGTGAAATCCGAATAAAGTCTGNAGTTTAGTTAATAGTANT 2581

  hg38_dna            1181 GTGCCAATGTTAATTTCTTAACTTTGGT-ACTTTACAAGGGTTATGTAAG 1229
                             i                 ii    ii- v v   v v           
  L1MD3_3end#LI       2582 GTACCAATGTTAATTTCTTAGTTTTGACAAATGTACCATGGTTATGTAAG 2631

  hg38_dna            1230 ATGTTAACATGAGAGGAAGCTGGGTGAAGGGTATACAAAAA--CACTGCA 1277
                                     v  i                      iii  -- v   i 
  L1MD3_3end#LI       2632 ATGTTAACATTAGGGGAAGCTGGGTGAAGGGTATACGGGAACTCTCTGTA 2681

  hg38_dna            1278 CTATCTTTGCAA--TTCTTGTAAATTTAAAATTATTTCAGAATAAAA 1322
                                       --  ii       i          i  i       
  L1MD3_3end#LI       2682 CTATCTTTGCAACTTTTCTGTAAATCTAAAATTATTCCAAAATAAAA 2728

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 18.58
Transitions / transversions = 1.86 (136/73)
Gap_init rate = 0.03 (42 / 1250), avg. gap size = 2.74 (115 / 42)

+ 3438   21.4  5.5  3.6  hg38_dna   1319  2460 (10457) + L1ME3     LINE/L1           3914   5076 (1070)   3 *

ANNOTATION EVIDENCE:
 3438  21.35 5.47 3.58  hg38_dna   1319  2460    9187 + L1M5_orf2 LINE/L1           1805   2967    327    
3438 21.35 5.47 3.58 hg38_dna 1319 2460 (9187) L1M5_orf2#LINE/L1 1805 2967 (327) m_b1s551i2

  hg38_dna            1319 AAAATGAATTTGA--AAATTCAATACTCATTTGCGAAAGCAATTCTCAGT 1366
                               v v      --        i  i    iii  v iv  i      i
  L1M5_orf2#LIN       1805 AAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACTCTCAGC 1854

  hg38_dna            1367 GAACTAGAAACAGAAGAAAATTTCCTCAATCTGGTAAAGAACATCTACAA 1416
                           i      i  i     ii  i        i   i     ii       i 
  L1M5_orf2#LIN       1855 AAACTAGGAATAGAAGGGAACTTCCTCAACCTGATAAAGGGCATCTACGA 1904

  hg38_dna            1417 AAAAAGTACAGTAAACATCACCCTTAATAGTGAAATATTGAGGTATTCTC 1466
                               vv     i?       iv      i      ? i   i?-ii i  
  L1M5_orf2#LIN       1905 AAAACCTACAGCNAACATCATACTTAATGGTGAAANACTGAAN-GCTTTC 1953

  hg38_dna            1467 CCCTTAAGATGAGGAA-AAGGCAAGGATATCCTTTGTTAATACTTCTGTT 1515
                              i      vi    -   i       i   vi ? i vi      i  
  L1M5_orf2#LIN       1954 CCCCTAAGATCGGGAACAAGACAAGGATGTCCGCTNTCACCACTTCTATT 2003

  hg38_dna            1516 AAATATTGTTCTAGAGGTCCCAGCCAGTGCAATAAGGCAAGAAAAGGCGA 1565
                           v  i     v  i       i                        i vi 
  L1M5_orf2#LIN       2004 CAACATTGTACTGGAGGTCCTAGCCAGTGCAATAAGGCAAGAAAAAGAAA 2053

  hg38_dna            1566 AAAAGAGAATAGA-ATTGTAAAGGCATATTTAAA-CCATTTTTTTTC-CA 1612
                           v   ii v   i -    v     v v vv    - ii i?  v   -  
  L1M5_orf2#LIN       2054 TAAAAGGCATAAAGATTGGAAAGGAAGAAATAAAACTGTCNTTATTCGCA 2103

  hg38_dna            1613 GATGGCATGACAGC--ACATTAAAAACAAAAACAAAAACAAAAACAAATC 1660
                               i     iv i--  i vi    ivv?  vi  vvi v   ?   --
  L1M5_orf2#LIN       2104 GATGACATGATTGTNTACGTAGAAAATCCNAAAGAATCTACAAANAAA-- 2151

  hg38_dna            1661 TGCATACTGCCAAAACTA-TAAGTGAATTTAGCAAGCGCACAAAATACAA 1709
                           ------  i i i     -                 vv i ?ii      
  L1M5_orf2#LIN       2152 ------CTACTAGAACTAATAAGTGAATTTAGCAAGGTCGCNGGATACAA 2195

  hg38_dna            1710 GATCAATATATAAAAATAAATTTTGTTTCCATACACTAGGCAA--GATGT 1757
                            i        i      v    v i    i   i     -   --i iiv
  L1M5_orf2#LIN       2196 GGTCAATATACAAAAATCAATTGTATTTCTATATACTAG-CAACGAACAA 2244

  hg38_dna            1758 TTGGAAAATAAAACTGGGGGAAAAAAAAAACTCCACCACTTACAACAGCA 1807
                                    i   i v?--------      vvi    i      i    
  L1M5_orf2#LIN       2245 TTGGAAAATGAAATTTN--------AAAAACAATACCATTTACAATAGCA 2286

  hg38_dna            1808 TCAAAAAAACATTAAATGTCTAGAAATAAATTGAACAA----TGTGTAAG 1853
                                   -   ?    iii   i       iv     ----    i   
  L1M5_orf2#LIN       2287 TCAAAAAA-CATNAAATACTTAGGAATAAATCTAACAAAANATGTGCAAG 2335

  hg38_dna            1854 TCCTCTATACTGAATA-TACAAAACAATGTTGAAAGTAACTGTAGAAGAA 1902
                           v   ?  i      v -         v  i   i  v  i iv      v
  L1M5_orf2#LIN       2336 ACCTNTACACTGAAAACTACAAAACATTGCTGAGAGAAATTAAAGAAGAC 2385

  hg38_dna            1903 CT---------------TATGCAATG---AAGG---GAAAGACTCAATTC 1931
                             ---------------   i v   --- v  --- i          vi
  L1M5_orf2#LIN       2386 CTAAATAAATGGAGAGATATACCATGTTCATGGATTGGAAGACTCAATAT 2435

  hg38_dna            1932 TGTTAAAATGTTCACTTTCCCAAAGTTGCTCTGTAGAGTCAATGCAATCC 1981
                              ?  i    iv i i    v  i   v   i    v            
  L1M5_orf2#LIN       2436 TGTNAAGATGTCAATTCTCCCCAAATTGATCTATAGATTCAATGCAATCC 2485

  hg38_dna            1982 CAATCAAAATTCTGGTAGGCTTTTTTTTTTTTTTTTAATGGACATTGACA 2031
                                     i ii i   i      -----------i i  v       
  L1M5_orf2#LIN       2486 CAATCAAAATCCCAGCAGGTTTTTTT-----------GTAGAAATTGACA 2524

  hg38_dna            2032 AGCACATTTGAAAATTTATATGGAAATGTAAAGCACTTA-AATAGTCAAA 2080
                              vv   iv                  i    v  i? -     i    
  L1M5_orf2#LIN       2525 AGCTGATTCTAAAATTTATATGGAAATGCAAAGGACCNAGAATAGCCAAA 2574

  hg38_dna            2081 ACATTTGTTTAA----AAGAACAAAACTGGAGGGTTTACAATACC--ATG 2124
                              v i-  v  ----         ii      ii     v    --  ?
  L1M5_orf2#LIN       2575 ACAATC-TTGAAAAAGAAGAACAAAGTTGGAGGACTTACACTACCNGATN 2623

  hg38_dna            2125 TCAAGACTTACCATAAA-CTACAGTAATTAAAAAAGTATGGTACTGATGC 2173
                                     ii     -          i  i v   i     i  ii i
  L1M5_orf2#LIN       2624 TCAAGACTTATTATAAAGCTACAGTAATCAAGACAGTGTGGTATTGGCGT 2673

  hg38_dna            2174 AAGAATGGATAATTAGTCCAAGTGGAA-AGAAC--AGAGTCCAGAAACAG 2220
                              i  i  i  v   vi   -     -    i--            i  
  L1M5_orf2#LIN       2674 AAGGATAGACAAATAGATCAA-TGGAACAGAATAGAGAGTCCAGAAATAG 2722

  hg38_dna            2221 ACC--CAAATATATGACCATTCATTTATTAACAAA-GTCCCCACGCAATT 2267
                              --  v       i?  ? iiv  v  i     -  v  v ?      
  L1M5_orf2#LIN       2723 ACCCACACATATATGGNCANTTGATTTTTGACAAAGGTGCCAANGCAATT 2772

  hg38_dna            2268 CAATGGGAAAAGAAAGGTGTTGTTTTTTTCAATAAAT-GTG-TAGAGTAG 2315
                             i    i    i ------ iv i       i    -   - i  ii i
  L1M5_orf2#LIN       2773 CAGTGGGGAAAGGA------TAGTCTTTTCAACAAATGGTGCTGGAACAA 2816

  hg38_dna            2316 ATGGATGTCCATAT---ACAAAATAAATCTTGATCCCCCCCTCACACCAT 2362
                           v     i       --- v     i  ?  i  i   iv           
  L1M5_orf2#LIN       2817 TTGGATATCCATATGGAAAAAAATGAANCTCGACCCCTACCTCACACCAT 2866

  hg38_dna            2363 ACACAAAAATCAACTGGTGAT-AATCACAGATC------CAACAGCTAAA 2405
                                     i  i v?v   -i    i   i ------i  v  ?    
  L1M5_orf2#LIN       2867 ACACAAAAATTAATTCNAGATGGATCATAGACCTAAATGTAAAAGNTAAA 2916

  hg38_dna            2406 ACTATAAAGTTTCTGGAGGAAAACAAAGGCAAATGTCTTCAAAATCTTGA 2455
                                   ii    i  i       v   vi   i     ivi i    i
  L1M5_orf2#LIN       2917 ACTATAAAACTTCTAGAAGAAAACATAGGAGAATATCTTCGTGACCTTGG 2966

  hg38_dna            2456 GAGTG 2460
                           ---- 
  L1M5_orf2#LIN       2967 ----G 2967

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 25.47
Transitions / transversions = 2.06 (159/77)
Gap_init rate = 0.06 (68 / 1141), avg. gap size = 1.54 (105 / 68)

+ 2451    8.8  0.0  0.0  hg38_dna   2461  2766 (10151) + AluY      SINE/Alu             1    306    (5)   4

ANNOTATION EVIDENCE:
 2451   8.82 0.00 0.00  hg38_dna   2461  2766   10151 + AluY      SINE/Alu             1    306      5    
2451 8.82 0.00 0.00 hg38_dna 2461 2766 (10151) AluY#SINE/Alu 1 306 (5) c_b1s352i0

  hg38_dna            2461 GGCTGGGCGCGGTGGCTCACACCTGTAATCCCAGCACTTTGGGAGGCCAA 2510
                              i                i                           i 
  AluY#SINE/Alu          1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50

  hg38_dna            2511 GGCGGGTGGATCACGAGGTCAGGAGATCAAGACCATCCTGGCCAACGCGG 2560
                                 i                     i             i   i   
  AluY#SINE/Alu         51 GGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCTGGCTAACACGG 100

  hg38_dna            2561 TGAAACCCCGTCTGTACTAAAAATACAAAAAATTATCCAGGCATAGTGGT 2610
                                        v                     v  i   i i    i
  AluY#SINE/Alu        101 TGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTGGTGGC 150

  hg38_dna            2611 GGGTGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCAT 2660
                              i                                            i 
  AluY#SINE/Alu        151 GGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGT 200

  hg38_dna            2661 GAACCTGGGAGGCGGAGTTTGCAGTGAGCCGAGGTCGTGCCACTGCACTC 2710
                                i           i               i   i            
  AluY#SINE/Alu        201 GAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCGCGCCACTGCACTC 250

  hg38_dna            2711 CAGCCTGGGTGATAAAGTGAGACTCCATCTCAAAAAAAAAAAAAAAAGAG 2760
                                    i  i i  i        i                    i i
  AluY#SINE/Alu        251 CAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAA 300

  hg38_dna            2761 AATAAA 2766
                             v   
  AluY#SINE/Alu        301 AAAAAA 306

Matrix = 14p39g.matrix
Kimura (with divCpGMod) = 4.58
Transitions / transversions = 8.00 (24/3)
Gap_init rate = 0.00 (0 / 305), avg. gap size = 0.0 (0 / 0)

+ 3438   23.0  6.5  1.9  hg38_dna   2767  2981  (9936) + L1ME3     LINE/L1           5077   5424  (738)   3

ANNOTATION EVIDENCE:
  263  27.85 5.95 5.95  hg38_dna   2767  2960    8687 + L1M3_orf2 LINE/L1           3082   3287      1    
263 27.85 5.95 5.95 hg38_dna 2767 2960 (8687) L1M3_orf2#LINE/L1 3082 3287 (1) m_b1s551i3

  hg38_dna            2767 TA-GGCAAACTTCAG---GGTAGAAAATTCCTGCAAAC-ATATACCCAAG 2811
                           v -     v  v i ---  v       vii       -     i ii v
  L1M3_orf2#LIN       3082 AAAGGCAACCTACGGAATGGGAGAAAATATTTGCAAACCATATATCTGAT 3131

  hg38_dna            2812 AAAGATTCCCTATCCAGATTATATTAGGAACT---AAAAATCATTAACAA 2858
                             i iv ivv      i v     v       --- v  v   v  i   
  L1M3_orf2#LIN       3132 AAGGGGTTAATATCCAAAATATATAAGGAACTCNTACAACTCAATAGCAA 3181

  hg38_dna            2859 AAAGG----TAACCTAATTTTTAAAAAATGGGCAAAATATTTCAATAGGC 2904
                              ii----     ii   ?---             iv ii v     i 
  L1M3_orf2#LIN       3182 AAAAACAAATAACCCGATTN---AAAAATGGGCAAAGGACCTGAATAGAC 3228

  hg38_dna            2905 AGGT---GATAAAGGAAATCTAAATAGCTGATTAAGATATTTTAAGATGT 2951
                            vv ---v v i i  v  vi    i  ii iviiv    vvv      i
  L1M3_orf2#LIN       3229 ATTTCTCCAAAGAAGACATACAAATGGCCAACAGGTATATGAAAAGATGC 3278

  hg38_dna            2952 TCAACATTA 2960
                                  i 
  L1M3_orf2#LIN       3279 TCAACATCA 3287

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 34.21
Transitions / transversions = 1.11 (30/27)
Gap_init rate = 0.05 (9 / 193), avg. gap size = 2.00 (18 / 9)

 3438  21.35 5.47 3.58  hg38_dna   2767  2774    8873 + L1M5_orf2 LINE/L1           2968   2975    319    
3438 21.35 5.47 3.58 hg38_dna 2767 2774 (8873) L1M5_orf2#LINE/L1 2968 2975 (319) m_b1s551i2

  hg38_dna            2767 TAGGCAAA 2774
                                   
  L1M5_orf2#LIN       2968 TAGGCAAA 2975

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 25.47
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 7), avg. gap size = 0.0 (0 / 0)

  381  25.24 7.25 1.47  hg38_dna   2768  2960    8687 + L1M5_orf2 LINE/L1           3091   3294      0    
381 25.24 7.25 1.47 hg38_dna 2768 2960 (8687) L1M5_orf2#LINE/L1 3091 3294 (0) m_b1s551i4

  hg38_dna            2768 AGGCAAACTTCAG---GGTAGAAAATTCCTGCAA-ACATATACCCAAGAA 2813
                                 i iv   ---  v       vii     -       i ii v  
  L1M5_orf2#LIN       3091 AGGCAAGCCACAGANTGGGAGAAAATATTTGCAANACATATATCTGACAA 3140

  hg38_dna            2814 AGATTCCCTATCCAGATTATATTAGGAA---CTAAAAATCATTAACAAAA 2860
                             ivii v        v     v i   ---   v  ?   v   ?    
  L1M5_orf2#LIN       3141 AGGACTCGTATCCAGAATATATAAAGAACTCCTACAANTCAATAANAAAA 3190

  hg38_dna            2861 AG----GTAACCTAATTTTTAAAAAATGGGCAAAATATTTCAATAGGCAG 2906
                             ----ii    i  --- v?              v i  v  i  i  v
  L1M5_orf2#LIN       3191 AGACAAACAACCCAA---TANAAAAATGGGCAAAAGACTTGAACAGACAC 3237

  hg38_dna            2907 GTGATAAAGGAA---ATCTAAATAGCTGATTAAGATATTTTAAGATGTTC 2953
                           v v i   i   ---  ?i    i  ii  v iv i  vvv      i  
  L1M5_orf2#LIN       3238 TTCACAAAAGAAGATATNCAAATGGCCAATAAGCACATGAAAAGATGCTC 3287

  hg38_dna            2954 AACATTA 2960
                              ? i 
  L1M5_orf2#LIN       3288 AACNTCA 3294

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 32.43
Transitions / transversions = 1.29 (27/21)
Gap_init rate = 0.04 (8 / 192), avg. gap size = 2.12 (17 / 8)

  420  22.28 6.25 1.80  hg38_dna   2822  2981    8666 + L1ME3_3end LINE/L1              5    171    738    
420 22.28 6.25 1.80 hg38_dna 2822 2981 (8666) L1ME3_3end#LINE/L1 5 171 (738) m_b1s551i5

  hg38_dna            2822 TATCCAGATTATATTAGGAACT---AAAAATCATTAACAAAAAGGTAA-- 2866
                                   v     v i     --- v      v   v      ii  --
  L1ME3_3end#LI          5 TATCCAGAATATATAAAGAACTCCTACAAATCAATAAGAAAAAGACAAAC 54

  hg38_dna            2867 --CCTAATTTTTAAAAAATGGGCAAAATATTTCAATAGGCAGGTGATAAA 2914
                           --  i    ---               v i  v  i     vv v i   
  L1ME3_3end#LI         55 AACCCAATT---AAAAAATGGGCAAAAGACTTGAACAGGCACTTCACAAA 101

  hg38_dna            2915 ---GGAAATCTAAATAGCTGATTAAGATATTTTAAGATGTTCAACATTAT 2961
                           ---   v   i    i  ii  v iv    vvv   i  i       i  
  L1ME3_3end#LI        102 AGAGGATATCCAAATGGCCAATAAGCATATGAAAAGGTGCTCAACATCAT 151

  hg38_dna            2962 TAGTGTTTATGGAAATGCAA 2981
                               vv i v          
  L1ME3_3end#LI        152 TAGTCATCAGGGAAATGCAA 171

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 26.57
Transitions / transversions = 0.84 (16/19)
Gap_init rate = 0.04 (7 / 159), avg. gap size = 1.86 (13 / 7)

+  494   24.7  5.8  3.1  hg38_dna   2986  3173  (9744) + L1ME3     LINE/L1           5610   5802  (360)   3

ANNOTATION EVIDENCE:
  494  24.71 5.85 3.11  hg38_dna   2986  3173    8474 + L1ME3_3end LINE/L1            357    549    360    
494 24.71 5.85 3.11 hg38_dna 2986 3173 (8474) L1ME3_3end#LINE/L1 357 549 (360) m_b1s551i6

  hg38_dna            2986 CCTACC--AAAAACCATCAATTCAACTCCTTGGTATATAGCTGAGAGA-- 3031
                                 -- vi v   v      v      v        v ii     --
  L1ME3_3end#LI        357 CCTACCCTATGACCCAGCAATTCCACTCCTAGGTATATACCCAAGAGAAA 406

  hg38_dna            3032 ------TATATGTCTACCAACGGAAGT-TGGAAGAACATTCCTCACAATT 3074
                           ------i       i     vi  vi - iv     ii   v vi  ii 
  L1ME3_3end#LI        407 TGAGTGCATATGTCCACCAAAAGACATGTACAAGAATGTTCATAGCAGCT 456

  hg38_dna            3075 CAATTCTTAATGGCCCAACAATGAAAACAACTCAAATGTTAATCGACAAG 3124
                           iv    v    i   ?  v v  i       i       iv   i   i?
  L1ME3_3end#LI        457 TTATTCATAATAGCCNAAAACTGGAAACAACCCAAATGTCCATCAACAGN 506

  hg38_dna            3125 AAAATGAATAAGTAAATTGCTCATATTATATATCCACATAATGTAATAC 3173
                            i    i    i       ------ vi     i  i i    v     
  L1ME3_3end#LI        507 AGAATGGATAAATAAATTG------TGGTATATTCATACAATGGAATAC 549

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 31.12
Transitions / transversions = 1.50 (27/18)
Gap_init rate = 0.05 (10 / 187), avg. gap size = 1.70 (17 / 10)

+  531   17.0  0.0  1.1  hg38_dna   3182  3276  (9641) C MER58A    DNA/hAT-Charlie    (1)    223    130   5

ANNOTATION EVIDENCE:
  531  17.02 0.00 1.06  hg38_dna   3182  3276    8371 C MER58B    DNA/hAT-Charlie    247    340      1    
531 17.02 0.00 1.06 hg38_dna 3182 3276 (8371) C MER58B#DNA/hAT-Charlie (1) 340 247 m_b1s502i0

  hg38_dna            3182 AGGTGTCAATAAATTTTTTTCTGTAAATGGCCACGTGGTAAATAGTTTAG 3231
                              v   iii   i     -       v     vi i       v     
C MER58B#DNA/hA        340 AGGGGTCGGCAAACTTTTT-CTGTAAAGGGCCAGATAGTAAATATTTTAG 292

  hg38_dna            3232 GCTTTGTGGGCCATATGGCCTCTATAACAACTACTCAACTCTGCC 3276
                                 i        i  i    i vi                  
C MER58B#DNA/hA        291 GCTTTGCGGGCCATACGGTCTCTGTCGCAACTACTCAACTCTGCC 247

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 14.64
Transitions / transversions = 2.20 (11/5)
Gap_init rate = 0.01 (1 / 94), avg. gap size = 1.00 (1 / 1)

+  790   22.1  0.0  0.7  hg38_dna   3303  3452  (9465) C AluJb     SINE/Alu          (16)    296    148   6

ANNOTATION EVIDENCE:
  790  22.15 0.00 0.67  hg38_dna   3303  3452    8195 C AluJb     SINE/Alu           148    296     16    
790 22.15 0.00 0.67 hg38_dna 3303 3452 (8195) C AluJb#SINE/Alu (16) 296 148 m_b1s357i0

  hg38_dna            3303 TTTTTTTTTTTTTTAAGATGGGGTCATCTCACTGTCACCCAGGCTGCAGT 3352
                                         i   ii     -  v v     i         v   
C AluJb#SINE/Al        296 TTTTTTTTTTTTTTGAGACAGGGTC-TCGCTCTGTCGCCCAGGCTGGAGT 248

  hg38_dna            3353 GCAGTGGCATGATCGTAGTTCACTGTAAGCTCGAACTCCTGAGCTCAAGA 3402
                                   ii    iii i      i iv     v    i i       v
C AluJb#SINE/Al        247 GCAGTGGCGCGATCACGGCTCACTGCAGCCTCGACCTCCCGGGCTCAAGC 198

  hg38_dna            3403 GATTCTCCTGCCTCAGCCTCTTGACTGGCTGGAATTATAGACAGGAGCCA 3452
                              i    i           ii  v i     i i  i  i iv v    
C AluJb#SINE/Al        197 GATCCTCCCGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGCGCGCGCCA 148

Matrix = 18p39g.matrix
Kimura (with divCpGMod) = 19.96
Transitions / transversions = 2.67 (24/9)
Gap_init rate = 0.01 (1 / 149), avg. gap size = 1.00 (1 / 1)

+  407   20.6  0.0  0.0  hg38_dna   3464  3536  (9381) C MER58A    DNA/hAT-Charlie  (151)     73      1   5

ANNOTATION EVIDENCE:
  407  20.55 0.00 0.00  hg38_dna   3464  3536    8111 C MER58A    DNA/hAT-Charlie      1     73    151    
407 20.55 0.00 0.00 hg38_dna 3464 3536 (8111) C MER58A#DNA/hAT-Charlie (151) 73 1 m_b1s502i1

  hg38_dna            3464 CCAATAAAATTTTATAAACAGAAACATGCAGTGGGTTGGAATTGGCCCAC 3513
                                    i     vv   i     v  i i   ii   v       i 
C MER58A#DNA/hA         73 CCAATAAAACTTTATTTACAAAAACAGGCGGCGGGCCGGATTTGGCCCGC 24

  hg38_dna            3514 AGGCCATAGTTTGCCAACCCTTG 3536
                           i    i         i    i  
C MER58A#DNA/hA         23 GGGCCGTAGTTTGCCGACCCCTG 1

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 13.04
Transitions / transversions = 2.75 (11/4)
Gap_init rate = 0.00 (0 / 72), avg. gap size = 0.0 (0 / 0)

+  667   22.0 12.6  2.6  hg38_dna   3603  3849  (9068) + L1ME3     LINE/L1           5892   6162    (0)   3

ANNOTATION EVIDENCE:
  667  22.03 12.55 2.58  hg38_dna   3603  3849    7798 + L1ME3_3end LINE/L1            639    909      0    
667 22.03 12.55 2.58 hg38_dna 3603 3849 (7798) L1ME3_3end#LINE/L1 639 909 (0) m_b1s551i7

  hg38_dna            3603 ACAAAAGAATAAA--CTGTATGACTCCGTTTATATGAAGTTTAAAAACAT 3650
                                   i  v --        i   i             i  i    v
  L1ME3_3end#LI        639 ACAAAAGAGTACATACTGTATGATTCCATTTATATGAAGTTCAAGAACAG 688

  hg38_dna            3651 TTGAAAATAATACATGGTCATAGAAATCGGGACAGTAGTTGACTGGGGGA 3700
                           vii   v    vi     v      i  i i i   i   iv  vv   i
  L1ME3_3end#LI        689 GCAAAACTAATCTATGGTGATAGAAGTCAGAATAGTGGTTACCTTTGGGG 738

  hg38_dna            3701 AGCGAGTGGCTCCATTGA-TAGGAAGGGGCAGAAGGAA------------ 3737
                             - i  ------     - i          vi   i ------------
  L1ME3_3end#LI        739 AG-GGGT------ATTGACTGGGAAGGGGCACGAGGGAGCCTTCTGGGGT 781

  hg38_dna            3738 --TGAAAATGTTTTATATGTTTATCTGGGTAGTAATCACAAAGGTATACA 3785
                           --  i       i     v  v        i  ii i   vi   i  i 
  L1ME3_3end#LI        782 GCTGGAAATGTTCTATATCTTGATCTGGGTGGTGGTTACACGGGTGTATA 831

  hg38_dna            3786 CATATGT-AAATTTCACCAAGCTACACACTT----TTT------TTTGTT 3824
                                  -   v    i i    ii      ----   ------   ii 
  L1ME3_3end#LI        832 CATATGTAAAAATTCATCGAGCTGTACACTTAAGATTTGTGCACTTTACT 881

  hg38_dna            3825 GTACATAAATTATA---GAACTAAAAAA 3849
                              ii   i     ---v  i       
  L1ME3_3end#LI        882 GTATGTAAGTTATACCTCAATTAAAAAA 909

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 25.39
Transitions / transversions = 2.53 (38/15)
Gap_init rate = 0.06 (15 / 246), avg. gap size = 2.53 (38 / 15)

+  278   28.6  7.6  0.0  hg38_dna   3836  4045  (8872) + L1MEd     LINE/L1           1065   1290 (5831)   7 *

ANNOTATION EVIDENCE:
  278  28.57 7.62 0.00  hg38_dna   3836  4045    7602 + L1MEd_5end LINE/L1           1030   1255    969    
278 28.57 7.62 0.00 hg38_dna 3836 4045 (7602) L1MEd_5end#LINE/L1 1030 1255 (969) m_b1s551i8

  hg38_dna            3836 ATAGAACTAAAAAACATATGTAGAATTCAACATGGATAAA-AAATATATT 3884
                                v  i  i  vv  ivi     v  i  ii  v i -   v v  v
  L1MEd_5end#LI       1030 ATAGATCTGAAGAAATTACCCAGAATGCAGCACAGAGAGATAAAGAGATG 1079

  hg38_dna            3885 AAATACATTAAATCTACCTTAAAAGATGTGGGTGATAGAGTGAGGAAGTC 3934
                           i  v i  v   vvv vv    i   ii   iv      i    i i   
  L1MEd_5end#LI       1080 GAAAATATGAAAGAGAGGTTAAGAGACATGGAGGATAGAATGAGAAGGTC 1129

  hg38_dna            3935 TAACAGAAGTCTAATCATAGCTCCTAAAGAATAGGACA---AAAATGTGT 3981
                                v v       ?iv  i   vi   i v  i i --- i    v v
  L1MEd_5end#LI       1130 TAACATACGTCTAATNGGAGTTCCAGAAGGAGAGAATAGAGAGAATGGGG 1179

  hg38_dna            3982 GAA----AATA----AAGAGATAAAAGAC-AAAACTTTCCTGAATTAATG 4022
                             i----    ----         vi vi- i  i     v     i   
  L1MEd_5end#LI       1180 GAGAGGCAATATTCGAAGAGATAATGGCTGAGAATTTTCCAGAATTGATG 1229

  hg38_dna            4023 AA--ACATAAA-CCTTAGAGACAGGA 4045
                             --    ?  -   i   vv     
  L1MEd_5end#LI       1230 AAAGACATNAATCCTCAGATTCAGGA 1255

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 36.94
Transitions / transversions = 1.07 (31/29)
Gap_init rate = 0.03 (7 / 209), avg. gap size = 2.29 (16 / 7)

+   43   18.6  3.7  1.8  hg38_dna   4056  4162  (8755) + (AT)n     Simple_repeat        1    109    (0)   8

ANNOTATION EVIDENCE:
   43  18.58 3.74 1.83  hg38_dna   4056  4162    7485 + (AT)n     Simple_repeat        1    109      0    
43 18.58 3.74 1.83 hg38_dna 4056 4162 (7485) (AT)n#Simple_repeat 1 109 (0) m_b1s252i0

  hg38_dna            4056 ATATATATATATACATTTATATAAATATATTTA-ATTTTTATATAAACTC 4104
                                        i  v      v      v  -  v v      v - v
  (AT)n#Simple_          1 ATATATATATATATATATATATATATATATATATATATATATATATA-TA 49

  hg38_dna            4105 TACAGAGAGAT-TATATATA-ATCTATATATAAAGTGTATGTGTATATAT 4152
                             i v v v  -        -  v        v - i   i i       
  (AT)n#Simple_         50 TATATATATATATATATATATATATATATATATA-TATATATATATATAT 98

  hg38_dna            4153 -TATATATATA 4162
                           -          
  (AT)n#Simple_         99 ATATATATATA 109

Matrix = Unknown
Transitions / transversions = 0.42 (5/12)
Gap_init rate = 0.06 (6 / 106), avg. gap size = 1.00 (6 / 6)

+  238   21.9 11.2  4.3  hg38_dna   4236  4431  (8486) + L1MEd     LINE/L1           2736   2944 (3202)   7

ANNOTATION EVIDENCE:
  238  21.86 11.22 4.31  hg38_dna   4236  4431    7216 + L1M5_orf2 LINE/L1            627    835   2459    
238 21.86 11.22 4.31 hg38_dna 4236 4431 (7216) L1M5_orf2#LINE/L1 627 835 (2459) m_b1s551i9

  hg38_dna            4236 CCATAAAGCAATTCTCGA---ATTTCAAAGAATTGTTGGCCTTGACAC-G 4281
                                  i   v    i ---    ?    i    vviv v --   v- 
  L1M5_orf2#LIN        627 CCATAAAACAAGTCTCAATAAATTTNAAAGGATTGAAATCAT--ACAGAG 674

  hg38_dna            4282 TATG----CTAACTACAGTG----CAAATTAGAAATCAGTAACAAAAGGA 4323
                               ----  i  i   i  ----i             i        i  
  L1M5_orf2#LIN        675 TATGTTCTCTGACCACAATGGAATTAAATTAGAAATCAATAACAAAAAGA 724

  hg38_dna            4324 TAACTCACAAAACCTTCCACA---TTGG-AACTAGACTAC---TTTCTAC 4366
                             ?  - v    i -i   v ---    -  i  i  v  ---i     v
  L1M5_orf2#LIN        725 TANCT-AGAAAATC-CCCAAATATTTGGAAATTAAACAACACACTTCTAA 772

  hg38_dna            4367 AAATCTCTTAGGGGAAGAAAAAATATCACAATGAAAAAATCTT---AAAT 4413
                            v v i v i  vv  ii  i  -       ? i   ----  ---    
  L1M5_orf2#LIN        773 ATAACCCATGGGTCAAAGAAGAA-ATCACAANGGAAA----TTAGAAAAT 817

  hg38_dna            4414 TCTTAGAACTGAACAATA 4431
                           vi  v        ii ? 
  L1M5_orf2#LIN        818 ATTTTGAACTGAATGANA 835

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 27.08
Transitions / transversions = 1.41 (24/17)
Gap_init rate = 0.09 (17 / 195), avg. gap size = 1.82 (31 / 17)

+  238   25.5  0.7 23.1  hg38_dna   4834  4981  (7936) + MER3      DNA/hAT-Charlie      9    129   (80)   9

ANNOTATION EVIDENCE:
  238  25.49 0.68 23.14  hg38_dna   4834  4981    6666 + MER3      DNA/hAT-Charlie      9    129     80    
238 25.49 0.68 23.14 hg38_dna 4834 4981 (6666) MER3#DNA/hAT-Charlie 9 129 (80) m_b1s502i2

  hg38_dna            4834 TCCAATATAAATTTCTGCAATGATGGAAATATTCTGT-TCTATAATGTAT 4882
                                  v  v       i           i    i -   iiiv   vi
  MER3#DNA/hAT-          9 TCCAATAGAACTTTCTGCGATGATGGAAATGTTCTATATCTGCGCTGTCC 58

  hg38_dna            4883 AATGTAAAATATATAACATAATAAAATATAATAAAATATTAAAGTCATAT 4932
                              iiii------  i -------------------i i  -- i  i  
  MER3#DNA/hAT-         59 AATACGG------TAGC-------------------CACTA--GCCACAT 81

  hg38_dna            4933 GAGGCTATTGAGCACTAAAAATGTGGCCTGAAAGAACTGAGGAACAGAA 4981
                            v              vi         iv viv -          v   
  MER3#DNA/hAT-         82 GTGGCTATTGAGCACTTGAAATGTGGCTAGTGCG-ACTGAGGAACTGAA 129

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 26.23
Transitions / transversions = 1.90 (19/10)
Gap_init rate = 0.20 (29 / 147), avg. gap size = 1.00 (29 / 29)

+  540   29.0 17.4  2.8  hg38_dna   5453  5904  (7013) C L1ME3B    LINE/L1           (61)   6181   5649  10

ANNOTATION EVIDENCE:
  540  29.01 17.44 2.84  hg38_dna   5453  5904    5979 C L1ME3B_3end LINE/L1            396    928     61    
540 29.01 17.44 2.84 hg38_dna 5453 5904 (5979) C L1ME3B_3end#LINE/L1 (61) 928 396 m_b1s551i10

  hg38_dna            5453 TGTATCATTTAACAAAGAGTTACAAAGCAAACACCCATGTAACCATTGCA 5502
                               ivi      i  v?i   i     i       i        iii v
C L1ME3B_3end#L        928 TGTACAGTTTAACGAATNATTATAAAGCGAACACCCGTGTAACCACCACC 879

  hg38_dna            5503 CAGGTCAGGCGATAAAGCATTTCCAGCATCTCTGA------------GCC 5540
                                  i vi   i i    v      i i v  ------------   
C L1ME3B_3end#L        878 CAGGTCAAGAAATAGAACATTGCCAGCACCCCAGAAGCCCCCCGCGTGCC 829

  hg38_dna            5541 CCT----------GACCCTCTCCT-----CCCCACTAGGAGATGACCATT 5575
                              ----------i    i   i -----    v ivi   i i    i 
C L1ME3B_3end#L        828 CCTTCCCGATCACAACCCCCTCTTCCCTCCCCCCCCCAGAGGTAACCACT 779

  hg38_dna            5576 AGCTTGACTTT--------------------TTTTCTTTACTACTTTTAA 5605
                            v i       --------------------         -  v     v
C L1ME3B_3end#L        778 ATCCTGACTTTTATGGTAATCATTTCCTTGCTTTTCTTTA-TAGTTTTAC 730

  hg38_dna            5606 TGCCTATACATGCATCCCTAAACA--ACAGCTTTGCTCCACCAGGTTCTG 5653
                           ii    ?ii               -- i  i  v i iii  v v  i  
C L1ME3B_3end#L        729 CACCTANGTATGCATCCCTAAACAATATAGTTTAGTTTTGCCTGTTTTTG 680

  hg38_dna            5654 AATTTTACATAGAAGATATCACACA----GCATTCTCCGGCAACTTTTTT 5699
                             i    i   i v iv    i  ?---- i     iiv ii--- i  v
C L1ME3B_3end#L        679 AACTTTATATAAATGGAATCATACNGTATGTATTCTTTTGTG---TCTTG 633

  hg38_dna            5700 TTTTTTTGGTTCAACAC--------TGAAAGGCATTTGTGTTGAAACACA 5741
                           i  i   v i      i--------   i vv   iii     vvi iii
C L1ME3B_3end#L        632 CTTCTTTCGCTCAACATTATGTTTGTGAGATTCATCCATGTTGTTGCGTG 583

  hg38_dna            5742 AA-----AATAC-TTCATTGGC--CACTGTACAGTGTGCCCTTTTTATGA 5783
                           v ----- i v -      vv --ii     i   i -i  v  v     
C L1ME3B_3end#L        582 TAGCTGTAGTTCGTTCATTTTCATTGCTGTATAGTAT-TCCATTGTATGA 534

  hg38_dna            5784 GTGGTGTATAATTTATCT-----TTCTCCTTCAGGTAGGCATGAAGGCGG 5828
                           i ivvvi i       i -----    v  viv i i i   vvi  iv 
C L1ME3B_3end#L        533 ATATACCACAATTTATTTATCCATTCTACTGTTGATGGACATTTGGGTTG 484

  hg38_dna            5829 CATCCAGTTTTCTGCCATTACA------------GTCAACCTTCTTGTAC 5866
                           iv         ?v  i     i------------i v   v         
C L1ME3B_3end#L        483 TTTCCAGTTTTNGGCTATTACGAACAATGCTGCTATGAACATTCTTGTAC 434

  hg38_dna            5867 ACGTCTGCTTGTGGACATGTATTAAAATTTATCTAGGG 5904
                            i  ? v  v   v      iivvivi   v       
C L1ME3B_3end#L        433 ATGTNTCCTGGTGCACATGTGCACGCGTTTCTCTAGGG 396

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 36.47
Transitions / transversions = 1.73 (85/49)
Gap_init rate = 0.04 (17 / 451), avg. gap size = 5.35 (91 / 17)

+  362   27.5 13.9  3.5  hg38_dna   5905  6141  (6776) C MER112    DNA/hAT-Charlie    (0)    261      1  11

ANNOTATION EVIDENCE:
  362  27.53 13.92 3.45  hg38_dna   5905  6141    6460 C MER112    DNA/hAT-Charlie      1    261      0    
362 27.53 13.92 3.45 hg38_dna 5905 6141 (6460) C MER112#DNA/hAT-Charlie (0) 261 1 c_b1s401i0

  hg38_dna            5905 CAGTGGCTTTCAAACTTTTTTGTCCATGACTCATACTAAGGAATGACGTT 5954
                                                 v  ii   i  i v    i   -  i  
C MER112#DNA/hA        261 CAGTGGCTTTCAAACTTTTTTGACCGCGACCCACAGTAAGAAAT-ACATT 213

  hg38_dna            5955 TTACATCATG---------ACACACATTTGTGTATGTATGAAACTGAGGA 5995
                                  ii ---------       iviiiii iii  iv      ---
C MER112#DNA/hA        212 TTACATCGCGACCCAGTACACACACACACACACACACATATAACTGA--- 166

  hg38_dna            5996 GGGGGAGAGAGATTCATAAAGCGA-AC--ACCCCTATGACCTGAGAGACA 6042
                           ---iivi i  v    ii  i i -  --    i  iv  v  v  vi  
C MER112#DNA/hA        165 ---AACAAAAGTTTCACGAAACAATACTTACCCTTACTACGTGCGATGCA 119

  hg38_dna            6043 --CTGATG--TTCTATTCTCCGTCTGT---------GTTTTACAAATTCT 6079
                           --     i--         vivi  i ---------v     v    v  
C MER112#DNA/hA        118 CTCTGATATTTTCTATTCTATTCCTATTTCATTTTATTTTTAAAAATGCT 69

  hg38_dna            6080 GATC---ATCCATTTAAATGACTTTACGACCCACTAAAATGGACTTCAA- 6125
                            i  --- i   i v  v   i  i          --     iiiv i -
C MER112#DNA/hA         68 GGTCGCGACCCACTAAATTGATTTCACGACCCACT--AATGGGTCGCGAC 21

  hg38_dna            6126 ----ATTCTGAAAAACATTG 6141
                           ---- v i         i  
C MER112#DNA/hA         20 CCGCAGTTTGAAAAACACTG 1

Matrix = 18p39g.matrix
Kimura (with divCpGMod) = 31.21
Transitions / transversions = 2.32 (44/19)
Gap_init rate = 0.08 (18 / 236), avg. gap size = 2.33 (42 / 18)

+  540   29.0 17.4  2.8  hg38_dna   6142  6181  (6736) C L1ME3B    LINE/L1          (594)   5648   5620  10

ANNOTATION EVIDENCE:
  540  29.01 17.44 2.84  hg38_dna   6142  6181    5702 C L1ME3B_3end LINE/L1            367    395    594    
540 29.01 17.44 2.84 hg38_dna 6142 6181 (5702) C L1ME3B_3end#LINE/L1 (594) 395 367 m_b1s551i10

  hg38_dna            6142 TTCTTAAGGATGAATACCCAGGCGTGCAACTGCTGGATCA 6181
                           ---------  --     i   v   v  i      i   
C L1ME3B_3end#L        395 ---------AT--ATACCTAGGAGTGGAATTGCTGGGTCA 367

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 36.47
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.28 (11 / 39), avg. gap size = 1.00 (11 / 11)

+   11   14.2  0.0  8.8  hg38_dna   7043  7079  (5838) + (GGACCC)n Simple_repeat        1     34    (0)  12

ANNOTATION EVIDENCE:
   11  14.21 0.00 8.82  hg38_dna   7043  7079    4804 + (GGACCC)n Simple_repeat        1     34      0    
11 14.21 0.00 8.82 hg38_dna 7043 7079 (4804) (GGACCC)n#Simple_repeat 1 34 (0) m_b1s252i1

  hg38_dna            7043 GGTCCCGCACCCGGCCCCGCGGAGCCCGGACCCGCAC 7079
                             v    v      -v  -    -          v  
  (GGACCC)n#Sim          1 GGACCCGGACCCGG-ACC-CGGA-CCCGGACCCGGAC 34

Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.08 (3 / 36), avg. gap size = 1.00 (3 / 3)

+  397   24.4 12.6  0.0  hg38_dna   7892  8010  (4907) C MIR       SINE/MIR          (19)    243    110  13

ANNOTATION EVIDENCE:
  397  24.37 12.61 0.00  hg38_dna   7892  8010    3873 C MIR       SINE/MIR           110    243     19    
397 24.37 12.61 0.00 hg38_dna 7892 8010 (3873) C MIR#SINE/MIR (19) 243 110 m_b1s601i0

  hg38_dna            7892 TGAGCACTGACCGTGAGCCAGGCACTGTCCTAAGCACTTTGCAGGTA--A 7939
                                i  v  ii  v            i      i    i  v   -- 
C MIR#SINE/MIR         243 TGAGCGCTTACTATGTGCCAGGCACTGTTCTAAGCGCTTTACATGTATTA 194

  hg38_dna            7940 ATACGTGTAATCCTCACAGCAACACTGGGAG--AAATA-----------C 7976
                            iv i v           i    v  iv   -- ii  ----------- 
C MIR#SINE/MIR         193 ACTCATTTAATCCTCACAACAACCCTATGAGGTAGGTACTATTATTATCC 144

  hg38_dna            7977 CCGTCTCACAGCTGAAGAAACGAAGACGCAGAAA 8010
                             i i i    v   i     vi  i i    i 
C MIR#SINE/MIR         143 CCATTTTACAGATGAGGAAACTGAGGCACAGAGA 110

Matrix = 25p39g.matrix
Kimura (with divCpGMod) = 28.12
Transitions / transversions = 2.22 (20/9)
Gap_init rate = 0.03 (3 / 118), avg. gap size = 5.00 (15 / 3)

+  634   28.1 17.7  1.3  hg38_dna   8011  8602  (4315) C HAL1b     LINE/L1          (212)   2209   1522  14

ANNOTATION EVIDENCE:
  634  28.07 17.74 1.31  hg38_dna   8011  8602    3281 C HAL1b     LINE/L1           1522   2209    212    
634 28.07 17.74 1.31 hg38_dna 8011 8602 (3281) C HAL1b#LINE/L1 (212) 2209 1522 m_b1s551i11

  hg38_dna            8011 GGGTAGACAGAAGTAATTTTCTAATTACGGTATCACACTACGTCTGCT-- 8058
                             i    i    i       v   vv i  v    i    iiiv    --
C HAL1b#LINE/L1       2209 GGATAGATAGAAATAATTTTATAAAAATGGGATCATACTATACATGCTAT 2160

  hg38_dna            8059 -TCATATAA----TTTCAAATTTTTCATGTTACTGGAATTTAA-----GA 8098
                           - i v  ? ---- v i      --v  v     v        -----  
C HAL1b#LINE/L1       2159 TTTAAATNAAAAGTATTAAATTT--AATTTTACTTGAATTTAACAGAAGA 2112

  hg38_dna            8099 AAAATAAACTGAAGGGAATCTCTA----TTGCT----------------- 8127
                               v         v   v  vv ----     -----------------
C HAL1b#LINE/L1       2111 AAAAGAAACTGAAGTGAAACTGAAGGAATTGCTGAACTTCAGATAAATGT 2062

  hg38_dna            8128 TTCTTCCCTAAAAGACGTG---CTTTTTAAAAGG--CCTATAAGCATTAC 8172
                                 v i v    vi i---?  ii      i--   v    -i   v
C HAL1b#LINE/L1       2061 TTCTTCACCACAAGAGATATTANTTCCTAAAAGATCCCTCTAAG-GTTAA 2013

  hg38_dna            8173 GTAAAAAGATTAAGAGAGGTGTAAGGAGCTC------------------- 8203
                            v          v  i iiii v i   v i-------------------
C HAL1b#LINE/L1       2012 GAAAAAAGATTATGAAAAACATTAAGAGGTTGGAGTCATTATNTTTTTAA 1963

  hg38_dna            8204 ACTACATGTT-CGGGTTTAGAAAGT---------CTCATAGCTCTGAAAG 8243
                                     - iiv      v   ---------   viv   v      
C HAL1b#LINE/L1       1962 ACTACATGTTTCAATTTTAGACAGTATCGATTGACTCCCTGCTATGAAAG 1913

  hg38_dna            8244 ATGAGGTTAATTAGCA-TCATACACCTCCACCTACCTTTAGGGGGTAACC 8292
                                 v-        -  v     i   v  i    i v-----ivvi 
C HAL1b#LINE/L1       1912 ATGAGGA-AATTAGCACTCTTACACTTCCTCCCACCTCTC-----CTCTC 1869

  hg38_dna            8293 CTGCCTCTCAATTTCCATTAGTTCTGTTACTTTCGGCTTCCTAGCAATGA 8342
                            ii    i i    iii   ?  v i   i   iiv?  vii iviv v 
C HAL1b#LINE/L1       1868 CCACCTCCCGATTTTTGTTANTTATATTATTTTTACNTTGTCAAGGTTTA 1819

  hg38_dna            8343 GAACATTTGCAAT-TGCTCTGCAACTTTATTTTTC-CAGATGTT--GTCT 8388
                           v       i  v -  i    i   iv  v  ii -   v    --    
C HAL1b#LINE/L1       1818 TAACATTTACATTCTGTTCTGTAACCATAATTCCCACAGTTGTTTAGTCT 1769

  hg38_dna            8389 TAATTCTATCTTTAAATGAATTTGATATTCACT----GT----------- 8423
                             i      v        i   iii ii    i----  -----------
C HAL1b#LINE/L1       1768 TAGTTCTATATTTAAATGGATTCAGTGCTCACCACCAGTCCTTTTACCAC 1719

  hg38_dna            8424 AACTTATCTATCCCTGAATT-TTTATTTTTATTTAGTTCTTGATGGACTT 8472
                           ii   v  i  i     i  -        v   i vi     i v i  v
C HAL1b#LINE/L1       1718 GGCTTCTCCATTCCTGAGTTCTTTATTTTGATTCATCTCTTGGTTGGCTG 1669

  hg38_dna            8473 C-CTTCATTTTCAAGTCATATTCCTAAGGAGGGTTTATA----------- 8510
                           v-i     iv      vi v  iii   i    i i  i-----------
C HAL1b#LINE/L1       1668 GATTTCATCGTCAAGTAGTTTTTTCAAGAAGGGCTCATGGGTGCTATATT 1619

  hg38_dna            8511 ----GAGTGCTGCCATGTTTGAGAAGATCTGGTGTTTTTCTCTATACATA 8556
                           ----    v  vi            vi    vivv  vi  i     v i
C HAL1b#LINE/L1       1618 CCCTGAGTTCTTTCATGTTTGAGAATGTCTGCCTGTTGCCTTTATACTTG 1569

  hg38_dna            8557 AATAAAAAGTGAGTTGGGTA-AATATTTTCAATTCACACCTTCCTTC 8602
                             ii v  v vi i      -  ?   i iiiv      i   i   
C HAL1b#LINE/L1       1568 AACGACAACTTGGCTGGGTATAANATTCTTGGGTCACACTTTCTTTC 1522

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 35.43
Transitions / transversions = 1.41 (96/68)
Gap_init rate = 0.05 (31 / 591), avg. gap size = 3.68 (114 / 31)

+ 5808    5.3  0.0  0.4  hg38_dna   8636  9354  (3563) C L1PA7     LINE/L1            (2)   6152   5437  15

ANNOTATION EVIDENCE:
 5808   5.31 0.00 0.42  hg38_dna   8636  9354    3247 C L1PA7_3end LINE/L1            184    899      2    
5808 5.31 0.00 0.42 hg38_dna 8636 9354 (3247) C L1PA7_3end#LINE/L1 (2) 899 184 c_b1s451i0

  hg38_dna            8636 TTTATTTTTTTATTATACTTTAAGTTTTGGGATACATGTGCAGAACGGGC 8685
                              v    v                 i                    v  
C L1PA7_3end#LI        899 TTTTTTTTATTATTATACTTTAAGTTCTGGGATACATGTGCAGAACGTGC 850

  hg38_dna            8686 AGGTTTGTTACATAGGTATACACATGCCATGGTGGTTTGCTGCACTCATC 8735
                                                  i                     i    
C L1PA7_3end#LI        849 AGGTTTGTTACATAGGTATACACGTGCCATGGTGGTTTGCTGCACCCATC 800

  hg38_dna            8736 AACCCGTCATCTACATTAGGCATTTCTCCTAATGCTATCCCTACCCCACT 8785
                                               i                     v   --- 
C L1PA7_3end#LI        799 AACCCGTCATCTACATTAGGTATTTCTCCTAATGCTATCCCTCCCC---T 753

  hg38_dna            8786 AGCCCCCCACTCCCCAACAGGCCCCAGTGTGTGATGTTCCCCTCCCTGAG 8835
                                     i    i         i                      v 
C L1PA7_3end#LI        752 AGCCCCCCACCCCCCGACAGGCCCCGGTGTGTGATGTTCCCCTCCCTGTG 703

  hg38_dna            8836 TCCATGTGTTCTCATTGTTCAACTCCCACTTATGAATGAGAACATGCGGT 8885
                                                              i              
C L1PA7_3end#LI        702 TCCATGTGTTCTCATTGTTCAACTCCCACTTATGAGTGAGAACATGCGGT 653

  hg38_dna            8886 GTTTAGTTTTCTGTTCCTGTGTTAGTTTGCTGAGAATGATGGTTTCCAGC 8935
                               i                                             
C L1PA7_3end#LI        652 GTTTGGTTTTCTGTTCCTGTGTTAGTTTGCTGAGAATGATGGTTTCCAGC 603

  hg38_dna            8936 TTCATCCATGTCCCTACAAAGGACATGAACTCATCCTTTTTTATGGCTGC 8985
                                          i                                  
C L1PA7_3end#LI        602 TTCATCCATGTCCCTGCAAAGGACATGAACTCATCCTTTTTTATGGCTGC 553

  hg38_dna            8986 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCA 9035
                                                               v             
C L1PA7_3end#LI        552 ATAGTATTCCATGGTGTATATGTGCCACATTTTCTTTATCCAGTCTATCA 503

  hg38_dna            9036 CCAATGGCCATTTGGGTTGATTCCAAGTCTTTGCTATTGTGAATAGTGCT 9085
                           iii    v           i                       i     i
C L1PA7_3end#LI        502 TTGATGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAACAGTGCC 453

  hg38_dna            9086 TCAATAAACATACGTGTGCATGTGTCTTTACAGTAGAATGATTTATAATT 9135
                           v                             i                  i
C L1PA7_3end#LI        452 GCAATAAACATACGTGTGCATGTGTCTTTATAGTAGAATGATTTATAATC 403

  hg38_dna            9136 CTTTGGGTATATACCCAGTAATGAGATTGCTGGGTCAAATGGTATTTCTG 9185
                                                  i                          
C L1PA7_3end#LI        402 CTTTGGGTATATACCCAGTAATGGGATTGCTGGGTCAAATGGTATTTCTG 353

  hg38_dna            9186 GTTCTAGATCCTTGAGGAATTGCCACACTGTCTTCCACGATGGTTGAACC 9235
                                               i                 i          i
C L1PA7_3end#LI        352 GTTCTAGATCCTTGAGGAATCGCCACACTGTCTTCCACAATGGTTGAACT 303

  hg38_dna            9236 AATTTACACTCCCACCAACAGCGTAAAAGCGTTCCTATTTCTCCACATCC 9285
                                                i                            
C L1PA7_3end#LI        302 AATTTACACTCCCACCAACAGTGTAAAAGCGTTCCTATTTCTCCACATCC 253

  hg38_dna            9286 TCTCCAGCATCTGTTGTTTCCTGACTTTTTAATGATTATCATTCTAACTG 9335
                                                               iii           
C L1PA7_3end#LI        252 TCTCCAGCATCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTG 203

  hg38_dna            9336 GCATGAGATGTTACCTGAT 9354
                             i       v  i  v  
C L1PA7_3end#LI        202 GCGTGAGATGGTATCTCAT 184

Matrix = 18p39g.matrix
Kimura (with divCpGMod) = 4.57
Transitions / transversions = 2.80 (28/10)
Gap_init rate = 0.00 (3 / 718), avg. gap size = 1.00 (3 / 3)

+ 8270    4.2  0.8  0.3  hg38_dna   9355 10498  (2419) + L1PA7     LINE/L1           4274   5422  (750)  15

ANNOTATION EVIDENCE:
 8270   4.18 0.71 0.35  hg38_dna   9355 10479    2122 + L1P3_orf2 LINE/L1           2165   3293      1    
8270 4.18 0.71 0.35 hg38_dna 9355 10479 (2122) L1P3_orf2#LINE/L1 2165 3293 (1) m_b1s551i12

  hg38_dna            9355 AAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCAC 9404
                                                                             
  L1P3_orf2#LIN       2165 AAGCAACTTCAGCAAAGTCTCAGGATACAAAATCAATGTGCAAAAATCAC 2214

  hg38_dna            9405 AAGCATTCCTATACCCCAATAGTAGACAAATAAGAGAGCCAACACATGAG 9454
                                         v      i        i -         vv      
  L1P3_orf2#LIN       2215 AAGCATTCCTATACACCAATAATAGACAAACA-GAGAGCCAAATCATGAG 2263

  hg38_dna            9455 TGAACTCTGATTCACAATGGCGACAAAGAGAATAAAATACCTAGGAATAC 9504
                                  iv         v  v                            
  L1P3_orf2#LIN       2264 TGAACTCCCATTCACAATTGCTACAAAGAGAATAAAATACCTAGGAATAC 2313

  hg38_dna            9505 AACTTACAAGAGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTG 9554
                                     i                                       
  L1P3_orf2#LIN       2314 AACTTACAAGGGATGTGAAGGACCTCTTCAAGGAGAACTACAAACCACTG 2363

  hg38_dna            9555 CTTAAGGAAATCAGAGAGGACACAAACAAATGGAAAAACATTCCATGCTC 9604
                             i        v                                      
  L1P3_orf2#LIN       2364 CTCAAGGAAATAAGAGAGGACACAAACAAATGGAAAAACATTCCATGCTC 2413

  hg38_dna            9605 ATGGATTGGAAGAATCAATTATCATGAAAATTGCCATACTGCCCAAAGTA 9654
                                 v            -   i       v                  
  L1P3_orf2#LIN       2414 ATGGATAGGAAGAATCAAT-ATCGTGAAAATGGCCATACTGCCCAAAGTA 2462

  hg38_dna            9655 ATTTATAGATTCAATGCTATCCCCATCAAGCTACCATTGACTTTCTTCAC 9704
                                                                             
  L1P3_orf2#LIN       2463 ATTTATAGATTCAATGCTATCCCCATCAAGCTACCATTGACTTTCTTCAC 2512

  hg38_dna            9705 AGAATTAGAAGAAACTACTTTAAATTTCATATGGAACCAAAAAAGAGCCC 9754
                                     i                                       
  L1P3_orf2#LIN       2513 AGAATTAGAAAAAACTACTTTAAATTTCATATGGAACCAAAAAAGAGCCC 2562

  hg38_dna            9755 GTATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATTACA 9804
                                                                         i  i
  L1P3_orf2#LIN       2563 GTATAGCCAAGACAATCCTAAGCAAAAAGAACAAAGCTGGAGGCATCACG 2612

  hg38_dna            9805 CTACCTGACTTCAAACTACACTACAAGGCTACAGTAACCAAAACTGCATG 9854
                                             i                         v     
  L1P3_orf2#LIN       2613 CTACCTGACTTCAAACTATACTACAAGGCTACAGTAACCAAAACAGCATG 2662

  hg38_dna            9855 GTACTGGTACCAAAACAGATATATGGACCAATGGAACAGAACAGAGTCCT 9904
                                                   i                     v   
  L1P3_orf2#LIN       2663 GTACTGGTACCAAAACAGATATATAGACCAATGGAACAGAACAGAGGCCT 2712

  hg38_dna            9905 CAGAAATAACACCACACATCTACAACCATCTGATCTGTGACAAACCTGAC 9954
                                     i                         v             
  L1P3_orf2#LIN       2713 CAGAAATAACGCCACACATCTACAACCATCTGATCTTTGACAAACCTGAC 2762

  hg38_dna            9955 AAAAACAAGCAATAGGTAAAAGATTCCCTAGTTAATAAATGGTGTTGGGA 10004
                                        i  v   i         v                  -
  L1P3_orf2#LIN       2763 AAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGTTGGG- 2811

  hg38_dna           10005 AAAACTGGTTAGCCATATGCAGAAAACTGAAACTGGACCGCTTCGTTACA 10054
                                   i                              v    v     
  L1P3_orf2#LIN       2812 AAAACTGGCTAGCCATATGCAGAAAACTGAAACTGGACCCCTTCCTTACA 2861

  hg38_dna           10055 CCTTATACAAAAATTAACTCAAGATGGACTAAAGACTTAAAACATCAGAC 10104
                                                       i         -    i v    
  L1P3_orf2#LIN       2862 CCTTATACAAAAATTAACTCAAGATGGATTAAAGACTT-AAACGTAAGAC 2910

  hg38_dna           10105 CTAAAACCATAAAAAGCCTAGAAGAAAACCTAGGCAATACCATTCAGGAC 10154
                                          v                                  
  L1P3_orf2#LIN       2911 CTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCAATACCATTCAGGAC 2960

  hg38_dna           10155 ATAGGCATGGGCAGAG--TTCATAACTAAAACACCAAAAGCAATGGCAAC 10202
                                        i  --     i                          
  L1P3_orf2#LIN       2961 ATAGGCATGGGCAAAGACTTCATGACTAAAACACCAAAAGCAATGGCAAC 3010

  hg38_dna           10203 AAAAGCCAAAATTGACAATTGGGATCTAATTAAACTAAAGAGCTTCTGCA 10252
                                             v                               
  L1P3_orf2#LIN       3011 AAAAGCCAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCA 3060

  hg38_dna           10253 CACCAAAAGAAACTATCATCAGACTGAACAGGCAACCTACAGAATGGGAG 10302
                             v                    v                          
  L1P3_orf2#LIN       3061 CAGCAAAAGAAACTATCATCAGAGTGAACAGGCAACCTACAGAATGGGAG 3110

  hg38_dna           10303 AAAATTTTTGCAAT-TATCCATCTGACAAAGGGCTAATATCCAGAATCTA 10351
                                         -                                   
  L1P3_orf2#LIN       3111 AAAATTTTTGCAATCTATCCATCTGACAAAGGGCTAATATCCAGAATCTA 3160

  hg38_dna           10352 CAAAGCACTTAAACAAATTTATAAGAAAA----AAACAACTCCATCAAAA 10397
                              i v               i       ----       i         
  L1P3_orf2#LIN       3161 CAAGGAACTTAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAA 3210

  hg38_dna           10398 AGTGGGCAAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGTG 10447
                                  i                                        i 
  L1P3_orf2#LIN       3211 AGTGGGCGAAGGATATGAACAGACACTTCTCAAAAGAAGACATTTATGCG 3260

  hg38_dna           10448 GCCAACAAACATATG-AAAAAAGCTCATCATTA 10479
                                          -               i 
  L1P3_orf2#LIN       3261 GCCAACAAACATATGAAAAAAAGCTCATCATCA 3293

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 3.80
Transitions / transversions = 1.14 (25/22)
Gap_init rate = 0.01 (8 / 1124), avg. gap size = 1.50 (12 / 8)

 1170   4.27 3.05 0.00  hg38_dna  10335 10498    2103 + L1PA8_3end LINE/L1              1    169    750    
1170 4.27 3.05 0.00 hg38_dna 10335 10498 (2103) L1PA8_3end#LINE/L1 1 169 (750) m_b1s551i13

  hg38_dna           10335 CTAATATCCAGAATCTACAAAGCACTTAAACAAATTTATAAGAAAAAAAC 10384
                                               i v               i           
  L1PA8_3end#LI          1 CTAATATCCAGAATCTACAAGGAACTTAAACAAATTTACAAGAAAAAAAC 50

  hg38_dna           10385 AA----CTCCATCAAAAAGTGGGCAAAGGATATGAACAGACACTTCTCAA 10430
                             ---- i                i                         
  L1PA8_3end#LI         51 AAACAACCCCATCAAAAAGTGGGCGAAGGATATGAACAGACACTTCTCAA 100

  hg38_dna           10431 AAGAAGACATTTATGTGGCCAACAAACATATG-AAAAAAGCTCATCATTA 10479
                                          i                -               i 
  L1PA8_3end#LI        101 AAGAAGACATTTATGCGGCCAACAAACATATGAAAAAAAGCTCATCATCA 150

  hg38_dna           10480 CTGGTCATTAGAGAAATGC 10498
                                              
  L1PA8_3end#LI        151 CTGGTCATTAGAGAAATGC 169

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 3.26
Transitions / transversions = 6.00 (6/1)
Gap_init rate = 0.01 (2 / 163), avg. gap size = 2.50 (5 / 2)

+  490   25.3  4.0  5.0  hg38_dna  10507 10706  (2211) C HAL1b     LINE/L1          (947)   1474   1277  14

ANNOTATION EVIDENCE:
  490  25.28 4.00 5.05  hg38_dna  10507 10706    1895 C HAL1b     LINE/L1           1277   1474    947    
490 25.28 4.00 5.05 hg38_dna 10507 10706 (1895) C HAL1b#LINE/L1 (947) 1474 1277 m_b1s551i14

  hg38_dna           10507 TTTCTGTGGAAAGATCTTAATCCCATGTAATTTT---CCCCTTGGAGGTG 10553
                             v       i ii   v iv  viiv i     ---       v     
C HAL1b#LINE/L1       1474 TTGCTGTGGAGAAGTCTGAGGCCAGCCTGATTTTTTCCCCCTTGTAGGTG 1425

  hg38_dna           10554 GCTTGATTTTTCTGCTTGGATACCTGAAGAATTCTTTAACATTAATATAC 10603
                           i    v         i     i               v---  ----  i
C HAL1b#LINE/L1       1424 ACTTGCTTTTTCTGCCTGGATGCCTGAAGAATTCTTTC---TT----TAT 1382

  hg38_dna           10604 CCTTTA-GT---ATT-CTTATCTGGGCTATGCCTCTGTGTCAGTTATTCT 10648
                               v -  ---  v-    v ii  v    i   v     ii ii    
C HAL1b#LINE/L1       1381 CCTTGAAGTTCAATAACTTAACCAGGATATGTCTCGGTGTCGATCGTTCT 1332

  hg38_dna           10649 AGATCAATTTTTCCCCCCAGCATACAGTATGATCTTCCAATTTATAGATT 10698
                           iv          ---  ii v i  i  i  vi   i i  i ii     
C HAL1b#LINE/L1       1331 GTATCAATTTTT---CCTGGAACACGGTGTGCCCTTTCGATCTGCAGATT 1285

  hg38_dna           10699 ATGTTCTT 10706
                           vv      
C HAL1b#LINE/L1       1284 CAGTTCTT 1277

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 28.48
Transitions / transversions = 1.67 (30/18)
Gap_init rate = 0.07 (14 / 199), avg. gap size = 1.29 (18 / 14)

+  871   28.3 11.0  7.1  hg38_dna  10749 11304  (1613) C HAL1b     LINE/L1         (1845)    576      1  14

ANNOTATION EVIDENCE:
  871  28.27 10.97 7.12  hg38_dna  10749 11304    1297 C HAL1b     LINE/L1              1    576   1845    
871 28.27 10.97 7.12 hg38_dna 10749 11304 (1297) C HAL1b#LINE/L1 (1845) 576 1 m_b1s551i15

  hg38_dna           10749 TTTCAGGGCTGAATGTTG-TTTCTATCTACTTGTTCTGTGATCCAAGGTT 10797
                              v       ii i   -        i    -      iii ii   --
C HAL1b#LINE/L1        576 TTTGAGGGCTGGGTATTGCTTTCTATCCACTT-TTCTGTAGCCTGAGG-- 530

  hg38_dna           10798 TTTCGGACAAGGAGAGGTGGGGGAAAAGGGGATGTGTGGAATTCAGCTCA 10847
                           ------i iv  i  --        ii     ------  ii  i   vi
C HAL1b#LINE/L1        529 ------GCGCGGGGA--TGGGGGAAGGGGGGA------GAGCTCGGCTGG 494

  hg38_dna           10848 GACAGAGTATAAAGCTTGCTGGAGGA-----ACTCAACCTTCACATCTGA 10892
                            i v ?  ii ivvi   i       -----i   vi ii  v v     
C HAL1b#LINE/L1        493 GGCTGNGTGCAGCCTTTGTTGGAGGACCTGGGCTCTGCTCTCTCTTCTGA 444

  hg38_dna           10893 GATTCCTTTAA--GTCCTCTGGCAGCTGGACT---TCAAGCTAGCCAAGG 10937
                               i v    --     v iv   --- i  ---  viv      ii  
C HAL1b#LINE/L1        443 GATTTCGTTAAATGTCCTGTACCAG---GGCTCACTCCGCCTAGCCGGGG 397

  hg38_dna           10938 GAACATCCCATGCCTCAGAGTTTCAGTTCATTTGCTCAGTTCAGCACAGT 10987
                            vii      iv  ivv i i   i ?     iv i  i      i i ?
C HAL1b#LINE/L1        396 GCGTATCCCACTCCCGTGGGCTTCGGNTCATTCCCCCAATTCAGCGCGGN 347

  hg38_dna           10988 ATCCCAGAAAGTGGGAAACT----------TTCCTGCCTCTGGCAAGATC 11027
                           ii  ii   ii   v  i i----------            v i  i  
C HAL1b#LINE/L1        346 GCCCTGGAAGATGGCAAGCCCTGGCGGCCCTTCCTGCCTCTGCCGAGGTC 297

  hg38_dna           11028 CAACAGTGGTATGCAAAGG-------------------TTCCTCAACATC 11058
                            vi i      i i ii  -------------------     ii  v i
C HAL1b#LINE/L1        296 CCGCGGTGGTACGTAGGGGCTTCTACTCTCGAGGGTTTTTCCTTGACTTT 247

  hg38_dna           11059 TCACAGGTGTGCC----------------CTGC--CTTTCCACATTGGGG 11090
                             v ?  vv    ---------------- i  --  i    v     i 
C HAL1b#LINE/L1        246 TCCCNGGGCTGCCTACTCACCCCCTCAGTCCGCTTCTCTCCAAATTGGAG 197

  hg38_dna           11091 GACGTTTGTGAGAATTCTTAGGATTTGGTCTGATCATCTT-TTTCCTCAA 11139
                            iii  v           i       v   viv   i   -        i
C HAL1b#LINE/L1        196 GGTATTAGTGAGAATTCTCAGGATTTTGTCGACTCACCTTCTTTCCTCAG 147

  hg38_dna           11140 CATGTCTTGCAGCGGTGGGTGGAGGGCTGGGCAGACATAGG-TTCATCTG 11188
                           i ivv   ---vi  v      -    v   i-----    -vi  i---
C HAL1b#LINE/L1        146 TACCGCTT---CTGGGGGGTGG-GGGCGGGGT-----TAGGAGCCAC--- 109

  hg38_dna           11189 GAGACAAAGCACGCCTCCATAGAATCTTCTGTTCTCTTTGTTTTTGCTAT 11238
                           -- vi ? v i    -----             -     -ii  v  iii
C HAL1b#LINE/L1        108 --GCTANACCGCGCC-----AGAATCTTCTGTT-TCTTT-CCTTGGCCGC 68

  hg38_dna           11239 CAATTCTCAAATTTTACATTATAAGGTTGTA-CTTTTTTCTTCTTTGGTT 11287
                             v  i  i  v    iivi  i        - ii   i   v       
C HAL1b#LINE/L1         67 CACTTTTCGAAGTTTATGGCATGAGGTTGTACCCCTTTCCTTGTTTGGTT 18

  hg38_dna           11288 GCAGCATGTAAGTTTTT 11304
                             v  vv  i i     
C HAL1b#LINE/L1         17 GCTGCTGGTGAATTTTT 1

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 32.03
Transitions / transversions = 2.11 (99/47)
Gap_init rate = 0.09 (52 / 555), avg. gap size = 1.96 (102 / 52)

+ 2046   10.7  0.6  8.1  hg38_dna  11336 11652  (1265) C AluSx     SINE/Alu          (15)    297      3  16

ANNOTATION EVIDENCE:
 2046  10.65 0.63 8.14  hg38_dna  11336 11652    1265 C AluSx     SINE/Alu             3    297     15    
2046 10.65 0.63 8.14 hg38_dna 11336 11652 (1265) C AluSx#SINE/Alu (15) 297 3 c_b1s352i1

  hg38_dna           11336 TTTTGTTTTGTTTTTGAGACAGAGTCTCGCTCTGTCACCCAAGCTGGAGT 11385
                               v    v          i               i    i        
C AluSx#SINE/Al        297 TTTTTTTTTTTTTTTGAGACGGAGTCTCGCTCTGTCGCCCAGGCTGGAGT 248

  hg38_dna           11386 ACAGTGGCATGATCTTGGCTCACCGCAACCT--GCCTCCCGGGTTCAAGC 11433
                           i       ii     i       i       --                 
C AluSx#SINE/Al        247 GCAGTGGCGCGATCTCGGCTCACTGCAACCTCCGCCTCCCGGGTTCAAGC 198

  hg38_dna           11434 AATTCTCCTGTCTCAGCCTCCTGAGTAGCTGGGATTATAGGCGTGCACCA 11483
                           i         i          i               i     i  i   
C AluSx#SINE/Al        197 GATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCGCGCGCCA 148

  hg38_dna           11484 TCACAACCGGCTAATTTTTGTATTTTTAGTAGAGGCTGGTATGGGGGTGC 11533
                           i   iv                            i -------     --
C AluSx#SINE/Al        147 CCACGCCCGGCTAATTTTTGTATTTTTAGTAGAGAC-------GGGGT-- 107

  hg38_dna           11534 TGGGTTGGGGGGAAGTTCGCCATGTTAGCCAGGCTGGTCTCAAACTCCTG 11583
                           ---------------   i       i              i        
C AluSx#SINE/Al        106 ---------------TTCACCATGTTGGCCAGGCTGGTCTCGAACTCCTG 72

  hg38_dna           11584 ACCTCAGGTGATCCGCCTGTCTCAGTCTCCCAAAGTGCTGGGATTACAGA 11633
                                            i i   i i                       i
C AluSx#SINE/Al         71 ACCTCAGGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGG 22

  hg38_dna           11634 CGTGAGCCACCATGCCTGG 11652
                                      ii   i  
C AluSx#SINE/Al         21 CGTGAGCCACCGCGCCCGG 3

Matrix = 14p39g.matrix
Kimura (with divCpGMod) = 5.96
Transitions / transversions = 9.33 (28/3)
Gap_init rate = 0.08 (25 / 316), avg. gap size = 1.04 (26 / 25)

+  568   27.6  9.4  0.4  hg38_dna  11909 12183   (734) C MER102c   DNA/hAT-Charlie    (0)    330     14  17

ANNOTATION EVIDENCE:
  510  26.05 11.32 0.43  hg38_dna  11909 12120     797 C MER102a   DNA/hAT-Charlie     96    330      0    
510 26.05 11.32 0.43 hg38_dna 11909 12120 (797) C MER102a#DNA/hAT-Charlie (0) 330 96 m_b1s502i3

  hg38_dna           11909 CAGGGGTTGCAAACTCAAATCTCTACAAAGTTTAA------AAC------ 11946
                                  i            vi     ii vii i------   ------
C MER102a#DNA/h        330 CAGGGGTCGCAAACTCAAATGCCTACAGGGGCCAGGCAGGTAACGTAAAT 281

  hg38_dna           11947 -AGTGA---GGAACAAT--GGGACTGTGGTAAAGTGAAAAGGACATTCTT 11990
                           -     ---  iv  iv--          i   v  i i  v    v ii
C MER102a#DNA/h        280 GAGTGAAGCGGGCCAGGTGGGGACTGTGGCAAACTGGAGAGCACATGCCC 231

  hg38_dna           11991 TGTGTAA--GGGGCA---GATGCTCAGCTCAGGCCAATGGCTGCCATGTT 12035
                           i  v   --      --- v ?        vi   i  v i        v
C MER102a#DNA/h        230 CGTCTAAAGGGGGCAGCCGCTNCTCAGCTCCAGCCGATTGTTGCCATGTG 181

  hg38_dna           12036 TGAACTCAGG-GCAGGGTTGCCACATCTGCATAATTTTCAAGGGAAGTAT 12084
                           v   iv i  -v   v       v    v vv v        i    ivv
C MER102a#DNA/h        180 GGAATGCGGGCCCAGTGTTGCCAGATCTTCTGATTTTTCAAGAGAAGCCA 131

  hg38_dna           12085 GCTATCTAACATTTTAATATAAAATCTTCTAATTTT 12120
                            vv   i i-     v  i i      i ii     
C MER102a#DNA/h        130 GAAATCCAG-ATTTTTATGTGAAATCTCCCGATTTT 96

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 29.13
Transitions / transversions = 1.12 (29/26)
Gap_init rate = 0.04 (9 / 211), avg. gap size = 2.78 (25 / 9)

  568  32.65 2.85 0.40  hg38_dna  11938 12183     734 C MER102c   DNA/hAT-Charlie     14    265     66    
568 32.65 2.85 0.40 hg38_dna 11938 12183 (734) C MER102c#DNA/hAT-Charlie (66) 265 14 m_b1s502i4

  hg38_dna           11938 GTTTAAAACAGTGAGGAACAATGGG-ACTGTGGTAAAGTGAAAAGGACAT 11986
                             v   i   i ii   iiii    -       ii  v  i i  vi   
C MER102c#DNA/h        265 GTGTAAGACAATAGGGAGTGGTGGGGACTGTGGCGAACTGGAGAGCGCAT 216

  hg38_dna           11987 TCTTTGTGTAA--GGGGCAGATGCT---CAGCTCAGGCCAATGGCTGCCA 12031
                           v iii  v   --       vi   ---      vi   i  v i     
C MER102c#DNA/h        215 GCCCCGTCTAAAGGGGGCAGCCGCTACTCAGCTCCAGCCGATTGTTGCCA 166

  hg38_dna           12032 TGTTTGAACTCAGGGC-AGGGTTGCCACATCTGCATAATTTTCAAGGGAA 12080
                             ivv   iv i  v -  v       v    v vv v        i   
C MER102c#DNA/h        165 TGCGGGAATGCGGGCCCAGTGTTGCCAGATCTTCCGATTTTTCAAGAGAA 116

  hg38_dna           12081 GTATGCTATCTAACATTTTAATATAAAATCTTCTAATTTTGGAAACACTG 12130
                            ivv vv   iii-     v  i i      i ii     vi        
C MER102c#DNA/h        115 GCCAGAAATCCGG-ATTTTTATGTGAAATCTCCCGATTTTTAAAACACTG 67

  hg38_dna           12131 CAGAGGCCACATGAAGTATTTCTCCAGGTCAAACTGGACCCAAGGGTTGC 12180
                           iivi     v vv  ii??v   v i  i ii i v i   iv   ii  
C MER102c#DNA/h         66 TGCGGGCCAAAACAAACNNGTCTGCGGGCCGGATTTGGCCCGCGGGCCGC 17

  hg38_dna           12181 CAG 12183
                              
C MER102c#DNA/h         16 CAG 14

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 34.93
Transitions / transversions = 1.50 (48/32)
Gap_init rate = 0.02 (5 / 245), avg. gap size = 1.60 (8 / 5)

+  397   18.4 10.9  2.2  hg38_dna  12459 12586   (331) + L1M5      LINE/L1           3861   3999 (2147)  18

ANNOTATION EVIDENCE:
  397  18.37 10.94 2.16  hg38_dna  12459 12586     331 + L1M5_orf2 LINE/L1           1752   1890   1404    
397 18.37 10.94 2.16 hg38_dna 12459 12586 (331) L1M5_orf2#LINE/L1 1752 1890 (1404) m_b1s551i16

  hg38_dna           12459 CCACATTAACAAAATAATGGAGGGGGAAAATGTTAT-----TTTCAATTG 12503
                              i       i     ---   i i     vv   ----- i     v 
  L1M5_orf2#LIN       1752 CCATATTAACAGAATAA---AGGAGAAAAATCATATGATCATCTCAATAG 1798

  hg38_dna           12504 ATGCAAAAAGAGCATTTGACAA----CTACACCCCATCCTGAAAAAAAT- 12548
                                i   i            ---- v      vv  v   v     i-
  L1M5_orf2#LIN       1799 ATGCAGAAAAAGCATTTGACAAAATTCAACACCCATTCATGATAAAAACT 1848

  hg38_dna           12549 ----GACAACTAGGAATGGAATGGAACTTCCTTAGCCAGATA 12586
                           ---- vv          i   v          i i  v    
  L1M5_orf2#LIN       1849 CTCAGCAAACTAGGAATAGAAGGGAACTTCCTCAACCTGATA 1890

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 21.20
Transitions / transversions = 0.92 (11/12)
Gap_init rate = 0.06 (7 / 127), avg. gap size = 2.43 (17 / 7)

+ 1020   20.1  2.3  4.2  hg38_dna  12601 12865    (52) C MLT1C2    LTR/ERVL-MaLR     (10)    451    192  19

ANNOTATION EVIDENCE:
 1020  20.10 2.26 4.23  hg38_dna  12601 12865      52 C MLT1C2    LTR/ERVL-MaLR      192    451     10    
1020 20.10 2.26 4.23 hg38_dna 12601 12865 (52) C MLT1C2#LTR/ERVL-MaLR (10) 451 192 m_b1s502i5

  hg38_dna           12601 TCCTATAGCTGCCATAACAAATTACCACAAACTGG-TGGCATAAAACAT- 12648
                                vi      i       ?             -    v       v-
C MLT1C2#LTR/ER        451 TCCTAGGGCTGCCGTAACAAANTACCACAAACTGGGTGGCTTAAAACAAC 402

  hg38_dna           12649 -GAAATTTATTTTCTGA--GTCCGAAAGGCCAGAAGTCTGAAATCAAGAT 12695
                           -          i   v --  i vii            i         i 
C MLT1C2#LTR/ER        401 AGAAATTTATTCTCTCACAGTTCTGGAGGCCAGAAGTCCGAAATCAAGGT 352

  hg38_dna           12696 ATCAGCAAAGGCCGCAGGCGCCATCTAGTGGCTCTAGTGGAGATTCCTTC 12745
                           i  i   i-     i--  v  v   iiv        v     v      
C MLT1C2#LTR/ER        351 GTCGGCAG-GGCCGT--GCTCCCTCTGAAGGCTCTAGGGGAGAATCCTTC 305

  hg38_dna           12746 CTCACAACTTCC-AGCTTTTGGTGACCACTGCCATTCCCTGGCTTCCTCG 12794
                             ii vv     -     i     iiii i v  v   i    v -----
C MLT1C2#LTR/ER        304 CTTGCCTCTTCCTAGCTTCTGGTGGTTGCCGGCAATCCTTGGCGT----- 260

  hg38_dna           12795 GCTTCCTTGGCTTGCGGCCACAGCATGCCAATCTCTGCCTCCATCTTCAC 12844
                           ---           ii   i  v  iv               i       
C MLT1C2#LTR/ER        259 ---TCCTTGGCTTGTAGCCGCATCACTCCAATCTCTGCCTCCGTCTTCAC 213

  hg38_dna           12845 AACGCCTTCTCTGTGCGTGCC 12865
                            vv        iv  i   i 
C MLT1C2#LTR/ER        212 ATGGCCTTCTCCCTGTGTGTC 192

Matrix = 20p39g.matrix
Kimura (with divCpGMod) = 20.83
Transitions / transversions = 1.55 (31/20)
Gap_init rate = 0.06 (16 / 264), avg. gap size = 1.06 (17 / 16)