+ 326 13.7 0.0 0.0 UnnamedSequence 1 51 (50513) + RMER13B LTR/ERVK 38 88 (820) 1
ANNOTATION EVIDENCE:
326 13.73 0.00 0.00 UnnamedSequence 1 51 43842 + RMER13B LTR/ERVK 38 88 820
326 13.73 0.00 0.00 UnnamedSequence 1 51 (43842) RMER13B#LTR/ERVK 38 88 (820) m_b1s501i0
UnnamedSequen 1 CTAAGGCTAGAAACCCTGGTGACCCTAAAGAGACGGAAGGCGTTTTGACC 50
? i ? i i v i v i
RMER13B#LTR/E 38 CTAAGGCTNGAAACCCCGGNGACCCTGAAGGGACGGTAGGCGTTTCGCCT 87
UnnamedSequen 51 C 51
RMER13B#LTR/E 88 C 88
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 11.53
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.00 (0 / 50), avg. gap size = 0.0 (0 / 0)
+ 386 25.8 17.4 0.0 UnnamedSequence 475 606 (49958) + RMER21B LTR/ERV1 413 567 (275) 2
ANNOTATION EVIDENCE:
386 25.76 17.42 0.00 UnnamedSequence 475 606 43287 + RMER21B LTR/ERV1 413 567 275
386 25.76 17.42 0.00 UnnamedSequence 475 606 (43287) RMER21B#LTR/ERV1 413 567 (275) m_b1s501i1
UnnamedSequen 475 CTCCGAAGA--CCCTATAAACGCCTGCCCCTCAACCTAA---CCCACTGT 519
i v -- v v ivvi vi ii i--- ii
RMER21B#LTR/E 413 CCCCCAAGAAACCCTATATAAGCCCTGTCCTCTGCTCAGTTCCCTGCTGT 462
UnnamedSequen 520 AGTCTCTCTTCCAGT-TCAGAAGCAGCCACCTTAAAGT--GTCTC---GC 563
vv? i i i v-v i iiivii -- i ---
RMER21B#LTR/E 463 CTNCTCCCTCCCGGGAGCAGAGGCAGCCACTCCTGGGTTCGTCCCTCCGC 512
UnnamedSequen 564 ------------CCAATAAATCTCCTGTGTGAGGTTTGTTGCATAGTGTG 601
------------ i iii
RMER21B#LTR/E 513 GNNNCGNNNNCTCCAATAAATCTCTTGTGTGAGGTTTGTTGCGCGGTGTG 562
UnnamedSequen 602 ACTTT 606
RMER21B#LTR/E 563 ACTTT 567
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 29.51
Transitions / transversions = 2.09 (23/11)
Gap_init rate = 0.05 (6 / 131), avg. gap size = 3.83 (23 / 6)
+ 405 21.4 4.0 2.9 UnnamedSequence 1300 1360 (49204) + RMER15 LTR/ERVL 474 531 (44) 3
ANNOTATION EVIDENCE:
405 21.42 3.96 2.94 UnnamedSequence 1300 1360 42584 + RMER15 LTR/ERVL 474 531 44
405 21.42 3.96 2.94 UnnamedSequence 1300 1360 (42584) RMER15#LTR/ERVL 474 531 (44) m_b1s501i2
UnnamedSequen 1300 GGACATTGGTGCCATTGTTATGTCTTTGGTCTGTCATAGGCTCCTTTTCT 1349
v vi ivv --- i i i i v
RMER15#LTR/ER 474 GGACTTTGGTGGTATCCGTA---CTTTGGTCTGTCGTGGGTTCCCTATCT 520
UnnamedSequen 1350 GGGTTGCATAG 1360
v vi
RMER15#LTR/ER 521 GGGGTGAGTAG 531
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.59
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.05 (3 / 60), avg. gap size = 1.00 (3 / 3)
+ 61 0.0 0.0 0.0 UnnamedSequence 1361 1412 (49152) + (GT)n Simple_repeat 1 52 (0) 4
ANNOTATION EVIDENCE:
61 0.00 0.00 0.00 UnnamedSequence 1361 1412 49152 + (GT)n Simple_repeat 1 52 0
61 0.00 0.00 0.00 UnnamedSequence 1361 1412 (49152) (GT)n#Simple_repeat 1 52 (0) c_b1s251i0
UnnamedSequen 1361 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 1410
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50
UnnamedSequen 1411 GT 1412
(GT)n#Simple_ 51 GT 52
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 405 21.4 4.0 2.9 UnnamedSequence 1413 1451 (49113) + RMER15 LTR/ERVL 532 574 (1) 3
ANNOTATION EVIDENCE:
405 21.42 3.96 2.94 UnnamedSequence 1413 1451 42493 + RMER15 LTR/ERVL 532 574 1
405 21.42 3.96 2.94 UnnamedSequence 1413 1451 (42493) RMER15#LTR/ERVL 532 574 (1) m_b1s501i2
UnnamedSequen 1413 T---TGTTTTGCATTACCCCAGGAAAAG-TCTGTCACACAACA 1451
i--- v i i iv - i
RMER15#LTR/ER 532 CGTGTGTGTCGCGTCTCCCCAGGAAAAGTTTTGTCACACAACA 574
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.59
Transitions / transversions = 2.50 (5/2)
Gap_init rate = 0.05 (2 / 38), avg. gap size = 2.00 (4 / 2)
+ 257 2.6 0.0 0.0 UnnamedSequence 1488 1525 (49039) C Lx8b LINE/L1 (0) 7477 7440 5 *
ANNOTATION EVIDENCE:
257 2.63 0.00 0.00 UnnamedSequence 1488 1525 42419 C Lx8b_3end LINE/L1 1854 1891 0
257 2.63 0.00 0.00 UnnamedSequence 1488 1525 (42419) C Lx8b_3end#LINE/L1 (0) 1891 1854 m_b1s551i0
UnnamedSequen 1488 TTTTATTAGTTTTTTGAGAATTTCATACAATGTATTTT 1525
? i
C Lx8b_3end#LIN 1891 TTTTNTTAGTTCTTTGAGAATTTCATACAATGTATTTT 1854
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 2.78
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 37), avg. gap size = 0.0 (0 / 0)
+ 5519 18.9 9.8 2.8 UnnamedSequence 1525 2947 (47617) C Lx9 LINE/L1 (0) 7644 6124 6
ANNOTATION EVIDENCE:
5519 18.86 9.84 2.76 UnnamedSequence 1525 2947 40997 C Lx9_3end LINE/L1 538 2058 0
5519 18.86 9.84 2.76 UnnamedSequence 1525 2947 (40997) C Lx9_3end#LINE/L1 (0) 2058 538 m_b1s551i1
UnnamedSequen 1525 TTTTTATTTTT-GAGAGTATAATACAATTACAATATTTTCTCTTCACCTT 1573
- v i vi i i i iv
C Lx9_3end#LINE 2058 TTTTTATTTTTTGAGATTATAATATAATTACATCATTTCCCCCTTCCCTT 2009
UnnamedSequen 1574 TC-TCCCTCCAAACCCTACCATATGCCCCTTCCCCCTCTCCTTCTAACTC 1622
- v i i iiv i v i
C Lx9_3end#LINE 2008 TCCTCCCTCCAAACCCTCCCATATACCCCTCCTTGCTCTCTTTCAAATTC 1959
UnnamedSequen 1623 ATGGCATCTTTTGTCATAAATTGTTAT----------------------- 1649
v v v i -----------------------
C Lx9_3end#LINE 1958 ATGGCCTCTTTTTTCATTAATTGTTGTTACATATATACATATACGTATAT 1909
UnnamedSequen 1650 ---TGTATGCAT------TCCTAAATACA--------ACCAGCTCAGTCC 1682
--- i ------ -------- v
C Lx9_3end#LINE 1908 ATATATATGCATATATATTCCTAAATACATAAATACAACCTGCTCAGTCC 1859
UnnamedSequen 1683 ATCTAATGTTATTTGTATGTAT--GTTTTCAGGGCTGACCATTTGGCATT 1730
i v i -- i
C Lx9_3end#LINE 1858 GTATAATGTTACTTGTATGTATATGTTTTCAGGGCTGACCATTTGGTATT 1809
UnnamedSequen 1731 GGACAACCAATTGTTGTGCTCTTCCTTATAAAAAAAAAAAAAAGCCCACC 1780
i v i i----------iii v i i-
C Lx9_3end#LINE 1808 GGATAACCAATTGGTGTGCTCTTCCCTG----------GGGAAGACTAT- 1770
UnnamedSequen 1781 TTATCCCAATCCTGGCTTTACT------CTTGTAGTTCTTTCTGGAAAGT 1824
v iv iii v v ------ i v v ii
C Lx9_3end#LINE 1769 TTCTCCCGCTCTCAGCATTCCTTAGTTGCCTGTAGTTCTTTGTGTAGGGT 1720
UnnamedSequen 1825 TGAAGCTTCGTGGGCTTTTCCTTGTTCACATTGTCAAATCTGCTG-TGTC 1873
i i i ii i ? v vi ii -
C Lx9_3end#LINE 1719 TGAGGCCTCGTGGGCTTTCCCCCGTCCACNTTGGCATGTCTATTGGTGTC 1670
UnnamedSequen 1874 ATTCTTGTTCAGC-AATATTTTGGGATAGTCATGTTGGGAAGACTTTCTG 1922
i i -v i v --i i vi v
C Lx9_3end#LINE 1669 GTCCTTGTTCAGCTCATGTTTAGG--CAGCCATGTTGGTGAGACTTTATG 1622
UnnamedSequen 1923 GTTGTAGCTTCTGGCATT---AGGAGACAAAATTGCACAGCAAATTTCCT 1969
v i --- v iv i i
C Lx9_3end#LINE 1621 GGTGTAGCTTCTGACATTNCTAGGAGACACAATCTCACAGCAAACTCCCT 1572
UnnamedSequen 1970 GATCCTCTGGCTCATACTGTCTTTCCACCCC-TCTTCTCAAATGCCCCCA 2018
? v vi i - ivv ii v
C Lx9_3end#LINE 1571 GNTCCTCTGGCTCTTACAATCTTTCCGCCCCCTCTTCCGCAATGTTCCCT 1522
UnnamedSequen 2019 GAGCCTTAGGTTTGAGAGT-GTTTTGTAGATGGATTCGCTGGGTCTGGAC 2067
vi i - ? v i i v i
C Lx9_3end#LINE 1521 GAGCCTTAGGTGCGGGAGTTGTNTTGTAGATGTATCCGTTGGGACTGGGC 1472
UnnamedSequen 2068 TTCACAACTCTGCAGTTTG-TTGGTTCTGTTTTTTTGTAGTTCTCTCCAT 2116
i v - i v v i i vv i
C Lx9_3end#LINE 1471 TCCACAACTCTGCATTTTGATCGGTTGTGGTTTTCTGTAATGGTCTCCGT 1422
UnnamedSequen 2117 C-------------GGTTTCCTTGATAAAG-------ACTACACT-ATCT 2145
-------------i i i ------- -
C Lx9_3end#LINE 1421 CTGTTGCAAAGAGAAGTTTCCTTGATGAGGGGTGAGGACTACACTTATCT 1372
UnnamedSequen 2146 GTGGGTATAAGAACAAATGTTTACATATTAGT-GTTAGGTTTTATCCTAG 2194
i i v - -- - vv v i
C Lx9_3end#LINE 1371 GTGGGTATAAGGACAAATATTTAGA-AT--GTAGTTAGGGATTATGCTGG 1325
UnnamedSequen 2195 TTTAGCAAATTCATGCTTATAGGTTCTCCTCAAATAACCAGGAA---ACT 2241
i v vii v i v v v v v---
C Lx9_3end#LINE 1324 TTTAGTAAAGTGGCGGTTGTAGGTTCTCCTCCAAGATCCATGACTTCACT 1275
UnnamedSequen 2242 GGAACACAGTAGTTCGCTAG-TTTCCAGTACCAGGAATGGTCTACCTCTT 2290
i vv vvi v - v i i v
C Lx9_3end#LINE 1274 AGCCCTGGGTAGTTGGCTAGGTTTCCAGTACCAGGCATGATTTCCCTCTT 1225
UnnamedSequen 2291 GTCAGGCAGGTCTTAAGTTCAATTAGAGAGCTTTTTAGTCACCACCAAGG 2340
iii i i v -i i i
C Lx9_3end#LINE 1224 GTTGAGCGGGTCTTAAGTCCAATTAGAGAGCTGTT-GGTTACCGCCAAGG 1176
UnnamedSequen 2341 CATGTATGCCAGTACCACACTCTTCAGGTTATAATGCCAGGATGGTCATG 2390
i ii v ii i vi vi v v v
C Lx9_3end#LINE 1175 TATGCGTGCCACTACTGCACCCTTAGGGTTATCGTGCCATGCTGGTCATT 1126
UnnamedSequen 2391 GGTGTGGCTCAGGGGCATCATGTCTAGAGAGGAACATTGGTTAATTTCCT 2440
v i vi i iv i iv vii iv i
C Lx9_3end#LINE 1125 GTTGTGGTTCATAGGCGTCATAGCTGGGTAGGACTGTTGGTTGCTTCCCT 1076
UnnamedSequen 2441 CCTTCAGAA--TTG--TGGTACATTCTAGTGTCAT---------TCCTCA 2477
ii -- -- ii v i ii ---------
C Lx9_3end#LINE 1075 CCTTTGGAAGCTTGCATGGCGCCTTCTGGTACCATGAAAGCTAGTCCTCA 1026
UnnamedSequen 2478 GA-AGGGGACAGCTCAGA-GAGTTCCAGTTTAGGGAGTCTCTGGACCCTG 2525
i- i i -vi i-v ? i i ?-i i
C Lx9_3end#LINE 1025 GGGAGGAGGC-TTTCAGGTCAGNTCCAGCTCAGGGN-CCTCTGGGCCCTG 978
UnnamedSequen 2526 TCTCTGATATGCATGGTGTCTTCAGCAATAGGGAATTAACACCTACACAT 2575
v vi v v vi i viv
C Lx9_3end#LINE 977 TGTCTGAAGTGCATGGTGTCTTCAGCAATAGGGACTTACCTTCCACCTCT 928
UnnamedSequen 2576 GGAGGGGGGGGCAACCAAGGGCAACAGCAATATGCTATA-TGTTTTGGGA 2624
----- vv i -
C Lx9_3end#LINE 927 GG-----GGGGCAACCAAGGGCAACAGCAATAGCCTGTANTGTTTTGGGA 883
UnnamedSequen 2625 GTCTTTTTGGATAGCTCTGGCCAACAACTCAAAAGATGGCTTCTCATGTC 2674
i - i i i i v i
C Lx9_3end#LINE 882 GTCTCTT-GGACAACCCTGACCAACAACTCAAAAGAGGGCTTCTCATGCC 834
UnnamedSequen 2675 TGGTATTGTTTTATTTTGTTTTTTTCCCCAGATGGTCTTTGGCTAATGGA 2724
i vvv - --------- ? vv
C Lx9_3end#LINE 833 TGGTGTTGGGGT-TTTTGTT---------AGATGGTCTNTGGCTCTTGGA 794
UnnamedSequen 2725 ATGACCACTGTCAGCCCATATGAGATAAGATCATT--AAAACTATATG-- 2770
iv v i v i v vv -- ??? --
C Lx9_3end#LINE 793 GGGAGCATTGTCAGCCCAGATGGGAAAATTTCATTTAAANNNTATATGTG 744
UnnamedSequen 2771 --TTTATATACAGAATTATGTG-AATTATGGGATT-TTCTA--------- 2807
-- i ? i - ?v v - i ---------
C Lx9_3end#LINE 743 TATTTATACACAGANTTACGTGTANATATGGTATTATTTTATNNANAGAT 694
UnnamedSequen 2808 ------ATGTGAGTA------GTTAATAT------TATGTCTCCTTGTGA 2839
------ v ? ------ ?v? ------ vi i
C Lx9_3end#LINE 693 ATATATATGTGTGNATATNTTGNGNATATTTNAAGTATGATTCCTTATGA 644
UnnamedSequen 2840 CTTTTTTCAGACATCCTCATTGTAAGTTTA-----ACCTCCTTTTTTTAT 2884
- i i v v -----v i i i
C Lx9_3end#LINE 643 C-TTTTTCAGACATCCTTACTGTTATTTTACCTCTCCCTCCTTCTTCTGT 595
UnnamedSequen 2885 ATTTACCTCATTCCCCTACTTCCTGGAGAATCCCTTTTCCATTTCCCCTA 2934
v ? i- i i-- i -- i -i
C Lx9_3end#LINE 594 ATTTACCTCCTTCNCCC-CTCCCC--AGGA--CCTTTCCCATTTCCCC-G 551
UnnamedSequen 2935 TAAGATCACTTGT 2947
vi
C Lx9_3end#LINE 550 TCGGATCACTTGT 538
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 20.58
Transitions / transversions = 1.44 (154/107)
Gap_init rate = 0.05 (77 / 1422), avg. gap size = 2.36 (182 / 77)
+ 1139 26.6 11.2 6.4 UnnamedSequence 2947 3561 (47003) C Lx8b LINE/L1 (22) 7455 6813 7 *
ANNOTATION EVIDENCE:
1139 26.58 11.22 6.38 UnnamedSequence 2947 3561 40383 C Lx8b_3end LINE/L1 1227 1869 22
1139 26.58 11.22 6.38 UnnamedSequence 2947 3561 (40383) C Lx8b_3end#LINE/L1 (22) 1869 1227 m_b1s551i2
UnnamedSequen 2947 TCTTACAATGTATTTTGATCATATTCATCCTTCTCCTGAGCCTACCCCAC 2996
v -- ---------- v
C Lx8b_3end#LIN 1869 TCATACAATGTATTTTGATCATATTCA--CTTCTCC----------CCAA 1832
UnnamedSequen 2997 CTCCCTATCCACATAACTATTCTCTGTGTGTCTATTTCCCTCTCTGCCAT 3046
--- - v v i i i i---------i vi ii --
C Lx8b_3end#LIN 1831 CTCC---TCC-CAGATCCATCCCCC---------CTTCCCTACCCACC-- 1797
UnnamedSequen 3047 CATCTCTCTCCATCTCTCTTTGCCTTTTTCTCCCCCACTCCATC-TCTT- 3094
v i v --i ii ? vi?? ??? v? ii i??? - -
C Lx8b_3end#LIN 1796 CAACTTTGT--GTCCTTNTTTTTNNTTTTNNNCGNCGTTTNNNCGTCTTT 1749
UnnamedSequen 3095 ---CCCA----GTCCAGTTCCTGTTGGCCAACTAATCCTAAGTATGGATC 3137
--- ---- i iv i v ?v v i iii i viv
C Lx8b_3end#LIN 1748 AAACCCATCAAGTCCAATTTGTGCTGCCCANATATTCTTGGATGTGTGGC 1699
UnnamedSequen 3138 CTGTCTA--AGAGTGTGCCTAATATAC---AGGTATC-AGACCATTAAAG 3181
- i --i i viii iv ---i i i - v v
C Lx8b_3end#LIN 1698 CT-TCCACTGGAGCGTGGTCGACCTACCAGGGGCACCTACACCCTTAAAG 1650
UnnamedSequen 3182 AAAAGTAGATTTCCCTATTTCAGTGGCAATAAAATGCCAATAGCTCTTCA 3231
v iiv i v ii ii v v v i
C Lx8b_3end#LIN 1649 AAAACTGACTCTCCCTCTCCCAGCAGCTATCAATTGCCAATAGCTCCTCA 1600
UnnamedSequen 3232 --------------------------CCCCTTCTGAATGATAGAATTTTG 3255
--------------------------i i vv v i i
C Lx8b_3end#LIN 1599 GCTAGGGGTGGGACTTCGTGCCCACCTCCCCTCTCCATGCTGGGATTTTG 1550
UnnamedSequen 3256 T-TGGCTGGATCTTGGGCAGGTCTTGTGCA-GTTGTTACAAC-CACTGCA 3302
- v v v - i i - i ii
C Lx8b_3end#LIN 1549 TCTGGCTTGAGCTTGCGCAGGTCTTGTGCATGCTGTCACAACNCGCTGTG 1500
UnnamedSequen 3303 AATTCAGCATGCACAGAGGCCCTATTGTATTTGGGAACTGCTTTTTTTTT 3352
i -i ii vv ii i ii i vii v ii
C Lx8b_3end#LIN 1499 AGTTCA-TATGTGCAGCTGCCCTGCTGTGTCCGGAAAACACTGTTTCCTT 1451
UnnamedSequen 3353 TTTTTTTTTTTTTATCATCTACTACCTCTGGCTCTTTCAGACTTTCTGCT 3402
v v----------i i ii v iv i
C Lx8b_3end#LIN 1450 GTA----------GTCATCCACCGCCTCTGGCTCTTACAATCTTTCTGCC 1411
UnnamedSequen 3403 CCCT-CTTCTATGTAGACCCCTAGGCGTTCATAGGAGGA----------- 3440
i - ? i iivv i ii v viv i-----------
C Lx8b_3end#LIN 1410 CTCTTCTNCCACAATGATCCCTGAGCCTTGGGAGGAGGGGGTGTGATATA 1361
UnnamedSequen 3441 -ACATCTCATTTAGATCTGAGTAGTCTG--AAACCTTTTATTCTCTGCAC 3487
- ii i iv i v --? ii i
C Lx8b_3end#LIN 1360 GATGTCCCATTTAGGGCTGAGCATTCTGCANAGTCTCTTATTCTCTGCAC 1311
UnnamedSequen 3488 ACTGACC-----TA-----CTATGTTGATCACCAAATACAGCAAGAAGAA 3527
?i ----- i----- i i i vv v i
C Lx8b_3end#LIN 1310 NTTGACCAGTTGTGGGTCTCTGTGTTAATCGCCATCTACTGCAAAAAGAA 1261
UnnamedSequen 3528 GCTTCTCTGATGAGAGGTGAGTGGTATATTGACC 3561
i v v i ii i i i
C Lx8b_3end#LIN 1260 GCTTCTCTGATGAGGGTTGAGAGATGCACTAATC 1227
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 33.32
Transitions / transversions = 2.00 (102/51)
Gap_init rate = 0.09 (58 / 614), avg. gap size = 1.90 (110 / 58)
+ 326 23.2 2.4 2.4 UnnamedSequence 3565 3648 (46916) C L1_Mur3 LINE/L1 (3617) 2263 2180 8
ANNOTATION EVIDENCE:
326 23.17 2.38 2.38 UnnamedSequence 3565 3648 40296 C L1_Mur3_orf2 LINE/L1 978 1061 3617
326 23.17 2.38 2.38 UnnamedSequence 3565 3648 (40296) C L1_Mur3_orf2#LINE/L1 (3617) 1061 978 m_b1s551i3
UnnamedSequen 3565 TTTCACCTTTTTGCCCCAACATGGTGTCTGTTGTTGATGGCTTG--GTGT 3612
i ? i i ii vi i i iv -- --
C L1_Mur3_orf2# 1061 TTCCANCCTTTTACCCTGAGGTGATGTCTATCCTTGATG--TTGAGGTGT 1014
UnnamedSequen 3613 GCTGCTTGGAGGCAGCAAAAAGATGGATCTTCTTCT 3648
i v v i i i v i
C L1_Mur3_orf2# 1013 GTTTCTTGGATGCAGCAGAAGGATGGATCCTGTTTT 978
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.46
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.04 (3 / 83), avg. gap size = 1.33 (4 / 3)
+ 56 2.0 0.0 0.0 UnnamedSequence 3688 3739 (46825) + (AT)n Simple_repeat 1 52 (0) 9
ANNOTATION EVIDENCE:
56 1.96 0.00 0.00 UnnamedSequence 3688 3739 46825 + (AT)n Simple_repeat 1 52 0
56 1.96 0.00 0.00 UnnamedSequence 3688 3739 (46825) (AT)n#Simple_repeat 1 52 (0) c_b1s251i1
UnnamedSequen 3688 ATATATATATATATATATATATATATATGTATATATATATATATATATAT 3737
i
(AT)n#Simple_ 1 ATATATATATATATATATATATATATATATATATATATATATATATATAT 50
UnnamedSequen 3738 AT 3739
(AT)n#Simple_ 51 AT 52
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 51), avg. gap size = 0.0 (0 / 0)
+ 1652 24.7 5.8 6.8 UnnamedSequence 3752 4360 (46204) C Lx10 LINE/L1 (201) 7406 6804 10
ANNOTATION EVIDENCE:
1652 24.67 5.75 6.80 UnnamedSequence 3752 4360 39635 C Lx10_3end LINE/L1 470 1072 201
1652 24.67 5.75 6.80 UnnamedSequence 3752 4360 (39635) C Lx10_3end#LINE/L1 (201) 1072 470 m_b1s551i4
UnnamedSequen 3752 TATGTATATACTTT-ATGGCTGACCACTT--GATTGATTAATCACTTAGG 3798
i iv - v --v iv i v ?
C Lx10_3end#LIN 1072 TGTGTATATGGTTTCAGGGCTGACCACTTTGCATTGGATAACCAATNAGG 1023
UnnamedSequen 3799 AGGCTCATCCCTGGAGAAAAATGATTAATTTTC--TCTCAACCATTATAA 3846
i - i --- ii i -- v vi ----
C Lx10_3end#LIN 1022 GGGCTCATCCCTGG-GAGA---GGCTAATTCTCCTTCTCATCAGTT---- 981
UnnamedSequen 3847 AAAGTCTGTCGCCATTCGTCTAGGAATGGGCTCTTATGAGATT---CCTC 3893
--- i v iiv i ii vi iii i --- i
C Lx10_3end#LIN 980 ---GCCTGTAGTTCTTTGTCTAGGGGTGGGACCCCGTGAAATTTTTCCCC 934
UnnamedSequen 3894 CATCTAAG-----GTGTCAACTGATATGGCTACTGTTCAGTCATATTGTA 3938
v i v -----i v i v i i ? --i v -
C Lx10_3end#LIN 933 CTTCCACGTTAGCATGTCTATTGATATTGCCATTGTTCNG--GTCTTGT- 887
UnnamedSequen 3939 GAGACTATAGGGGTACAATGTCCCTGTCATATATAGAAGAAACTATCCTG 3988
----i i------ -------- i v v i i i iiii
C Lx10_3end#LIN 886 ----TTATG------CA--------GCCATTTCTAGGAGAGACTGTTTCA 855
UnnamedSequen 3989 AAACAGACATCTTTCCTAGTTCTCTGTCTCATTACA------------CT 4026
v i ---- i vi v - ------------
C Lx10_3end#LIN 854 CAGCAGAC----TTCCTGGTATTCTGGCTC-TTACAATCTTTCGCCCCCT 810
UnnamedSequen 4027 CTTTCACAGTGTCCCCTGAGCCTTGGGAGTAAAGGGTGAACTCTAGAAGT 4076
i i ii i v i iv i iii v vi? v v
C Lx10_3end#LIN 809 CTTCCGCGATGTTCCCTGAGCCATAGATGCAGGAGCTGTGNTGTAGATGT 760
UnnamedSequen 4077 ATCAACTGGAGATGGGCACCCCTTGGTCAGTTCTTCTCTGCAGTTTGACC 4126
vii i v -i vi i v vv v v v
C Lx10_3end#LIN 759 ATCCGTTGGGGCTGGGC-TCCCACGATCCGTTGATCTCTGCATTGTGTCC 711
UnnamedSequen 4127 AGTTGTGGCTTCCTGTAATGGTC---TCGATCTGTTGCAAA-AGAAGCCT 4172
i i i --- - i i i - i
C Lx10_3end#LIN 710 AGTTGTGGTTTTCTGTGATGGTCCTCTC-ATTTGCTGTAAAGAGAAGCTT 662
UnnamedSequen 4173 CTT----GAGTTGGAGAGAGCTACACTTATCTGTAGATTTAAGGATAAGT 4218
---- v- v iv i i v v
C Lx10_3end#LIN 661 CTTTGATGAGG-GGTGGTAGCTACACTTATCTGTGGGTATAAGGATAAGA 613
UnnamedSequen 4219 ATTTAGAATGTAGTTTAGAAATACTACTGGTTTAGAGAAGGGACAGTAG- 4267
v ? ?- i vv i i vi v i i -
C Lx10_3end#LIN 612 TTNTAGAATGTAGTN-AGGAATTATGCTGGTCTAGCAAAGTGGCGGTAGT 564
UnnamedSequen 4268 -AATTCTCTTCTAAGATCCTTGGCCTCACCAGCCATTAGTAGTAGTCTAG 4316
-i i i v i i vivi v v v
C Lx10_3end#LIN 563 AGATTCTTTTCTAAGGTCCATGACCTCACTAGCCCCGGGAAGTTGGCTAG 514
UnnamedSequen 4317 GTTTACAGTGCCTGACATGAATTCCCTCCTATTAAGTGGGCCTT 4360
v i v i v i i
C Lx10_3end#LIN 513 GTTTCCAGTACCAGGCATGATTTCCCTCCTGTTGAGTGGGCCTT 470
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.12
Transitions / transversions = 1.59 (86/54)
Gap_init rate = 0.09 (52 / 608), avg. gap size = 1.46 (76 / 52)
+ 980 20.8 0.0 0.4 UnnamedSequence 4368 4630 (45934) C L1_Rod LINE/L1 (4442) 1405 1147 11 *
ANNOTATION EVIDENCE:
980 20.79 0.00 0.00 UnnamedSequence 4368 4569 39426 C L1_Rod_orf2 LINE/L1 2 203 4442
980 20.79 0.00 0.00 UnnamedSequence 4368 4569 (39426) C L1_Rod_orf2#LINE/L1 (4442) 203 2 m_b1s551i5
UnnamedSequen 4368 GATACTCTATTTTATCCTCACATTGCGATGTTCAGTGTTCTGCTTGATTC 4417
v i i ivi ivi i vi v
C L1_Rod_orf2#L 203 GATCCTCTACTTTATCTTCGAGTCCTGATATTCTATCTTCTGCTTGATTC 154
UnnamedSequen 4418 ACTCTACTGGTAAGACTTTCCCTTTAGTTTTCTATGTAGGTTATTGGACT 4467
i v i i v vv i ii
C L1_Rod_orf2#L 153 ATTCTACTTGTAAGGCTTTCCTTTGAGTTTTCTAGTTGGGTTATTGGGTT 104
UnnamedSequen 4468 TTTTATTTCTATTTTTATTTCAGCTTGAGTCCTCTTCAGTATTTCTGTTC 4517
i v i i i i i i ii
C L1_Rod_orf2#L 103 TTTCAATTCCATCTTCATTTCAGCTTGAGTCCTCTTCAATGTTTCTATCT 54
UnnamedSequen 4518 CTTTATTGAATTTCATTTTTAAATCGTGGATTGTATTTAATATTTCCATC 4567
i i i v v iivi ?
C L1_Rod_orf2#L 53 CTTTATTGAATTCCGTTTTCAAATCCTGGATTGTCTTCGTCATTTCCNTC 4
UnnamedSequen 4568 AG 4569
C L1_Rod_orf2#L 3 AG 2
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 23.14
Transitions / transversions = 2.23 (29/13)
Gap_init rate = 0.00 (0 / 201), avg. gap size = 0.0 (0 / 0)
937 20.96 0.00 1.90 UnnamedSequence 4417 4630 39365 C L1_Rod_5end LINE/L1 711 920 0
937 20.96 0.00 1.90 UnnamedSequence 4417 4630 (39365) C L1_Rod_5end#LINE/L1 (0) 920 711 m_b1s551i6
UnnamedSequen 4417 CACTCTACTGGTAAGACTTTCCCTTTAGTTTTCTATGTAGGTTATTGGAC 4466
i v i i v vv i ii
C L1_Rod_5end#L 920 CATTCTACTTGTAAGGCTTTCCTTTGAGTTTTCTAGTTGGGTTATTGGGT 871
UnnamedSequen 4467 TTTTTATTTCTATTTTTATTTCAGCTTGAGTCCTCTTCAGTATTTCTGTT 4516
i v i i i i i i i i
C L1_Rod_5end#L 870 TTTTCAATTCCATCTTCATTTCAGCTTGAGTTCTCTTCAATGTTTCTATC 821
UnnamedSequen 4517 CCTTTATTGAATTTCATTTTTAAATCGTGGATTGTATTTAATATTTCCAT 4566
i i i i v v iivi ??
C L1_Rod_5end#L 820 TCTTTATTGAATTCCGTTTTCAAATCCTGGATTGTCTTCGTCATTTCNNT 771
UnnamedSequen 4567 CAGTCTTATGTTTGTGTTTTCTTAGGTATTTATTAATAAACTGTTTATTC 4616
i i ----i i v v ivii
C L1_Rod_5end#L 770 CAGCCTTATGTTTGTGTTTTCTTGGG----CATCACTCAGGCATTTATTC 725
UnnamedSequen 4617 TCTCTAAGATCATT 4630
ii v v
C L1_Rod_5end#L 724 TCCTTAAGCTCTTT 711
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 24.29
Transitions / transversions = 2.38 (31/13)
Gap_init rate = 0.02 (4 / 213), avg. gap size = 1.00 (4 / 4)
+25365 5.1 1.3 0.5 UnnamedSequence 4620 8840 (41724) + L1MdMus_I LINE/L1 161 4400 (2170) 12
ANNOTATION EVIDENCE:
477 22.90 6.80 1.95 UnnamedSequence 4620 4766 39229 + L1MdMus_I_5end LINE/L1 329 482 841
477 22.90 6.80 1.95 UnnamedSequence 4620 4766 (39229) L1MdMus_I_5end#LINE/L1 329 482 (841) m_b1s551i7
UnnamedSequen 4620 CTAAGATC-ATTAAGATTTTGGTCACCTCCGCCATCTTCCGTCTGAACGC 4668
ii - v i ivv i v i i iv v
L1MdMus_I_5en 329 CTGGGATCCATTCAGGTCGGGGCCAGCCCCGCCATCTTCTGCGTGAACCC 378
UnnamedSequen 4669 AGCAGAGGCCGCTAAGGGCTCCAGAGTACTCTCCACGCCACAGGACCTCA 4718
i v v iiv ? v i i v
L1MdMus_I_5en 379 GGCCGAGGGCGTCTAGGGCNCCAGAGGACTCTCCACGCCGCAGGACCCCT 428
UnnamedSequen 4719 GG---ATC----ACCTTGAGATCACCTCGAGATCACTGGTGAGTG--AAA 4759
i --- i ---- i?v - v -- i i -- i
L1MdMus_I_5en 429 AGCACACCCAGGACCTCNTGATCACCT-GAGAGCAC--GTGGGCGACAGA 475
UnnamedSequen 4760 CGCAACA 4766
v
L1MdMus_I_5en 476 AGCAACA 482
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 23.53
Transitions / transversions = 1.36 (19/14)
Gap_init rate = 0.05 (7 / 146), avg. gap size = 1.86 (13 / 7)
8604 6.86 2.74 1.27 UnnamedSequence 4639 5805 38190 + L1MdMus_I_5end LINE/L1 140 1323 0
8604 6.86 2.74 1.27 UnnamedSequence 4639 5805 (38190) L1MdMus_I_5end#LINE/L1 140 1323 (0) m_b1s551i8
UnnamedSequen 4639 GGTCACCTCCGCCATCTTCCGTCTGAACGCAGCAGAGGCCGCTAAGGGCT 4688
i i v i v i i
L1MdMus_I_5en 140 GGCCACCCCCGCCATCTTCCTTCTGAGCCCAGCGGAGGCCGCCAAGGGCT 189
UnnamedSequen 4689 CCAGAGTACTCTCCACGCCACAGGACCTCAGGATCACCTTGAGATCACCT 4738
i i i -----------
L1MdMus_I_5en 190 CCAGAGTGCTCTCCACGCCGCAGGACCTCGGGATCACCT----------- 228
UnnamedSequen 4739 CGAGATCACTGGTGAGTGAAACGCAACATCAGCTCCAAAGAATCGAGGAG 4788
i v i v
L1MdMus_I_5en 229 CGGGATCACGGGTGAGTGGAACGCAACATCAGCTCCAAAGAATCGCGGAG 278
UnnamedSequen 4789 GGTCTTGTGCCAGCAGGAACAGGGACTGAGGAACCCCGCCGGACCAGAGG 4838
vi v
L1MdMus_I_5en 279 GGTCTTGTGCCAGCAGGAACAGGGACAAAGGAACCCCGCCCGACCAGAGG 328
UnnamedSequen 4839 CTGGGATCCGTTCAGGTCAGGGCCAGCCCCACCATCTACTGCATGAACCC 4888
i i i v i
L1MdMus_I_5en 329 CTGGGATCCATTCAGGTCGGGGCCAGCCCCGCCATCTTCTGCGTGAACCC 378
UnnamedSequen 4889 AGCGGAGGGCGTTGAGGTCCCCAGAGGACTCGCCACGCCACAGGACCCCT 4938
i v iv v ? v i
L1MdMus_I_5en 379 GGCCGAGGGCGTCTAGGGCNCCAGAGGACTCTCCACGCCGCAGGACCCCT 428
UnnamedSequen 4939 AGCACACCCAGGACCTCGGGATCACTGGAGAGCACATGGGTGATAGAAGC 4988
?v iv i i i
L1MdMus_I_5en 429 AGCACACCCAGGACCTCNTGATCACCTGAGAGCACGTGGGCGACAGAAGC 478
UnnamedSequen 4989 AACAGAGCTTCTTGGACAGGGTCCCATCAGGCCTTCATCCTTAGCCAGGA 5038
? ? i i
L1MdMus_I_5en 479 AACAGAGCTTCTTGGNCAGGGTCCCNTCGGGCCTTCATCCTCAGCCAGGA 528
UnnamedSequen 5039 GGCAGACCTGAGACCCAGACCCCTGGGCACCTTCCTGGCCAGAGGAGAGT 5088
v v
L1MdMus_I_5en 529 GGCAGAGCTGAGACCCAGACCCCTGGGCACCTTCCTTGCCAGAGGAGAGT 578
UnnamedSequen 5089 TGGCCTACAGAGAGGGCTCTGACACCAGGACTCAGGAGGTGGATCAGAAC 5138
i i v i
L1MdMus_I_5en 579 CGGCCTACAGGGAGGGCTCTGACCCCAGGACTCAGGAGGTGGATCAGAGC 628
UnnamedSequen 5139 TCCAGATTTCTGGACACCTGCCCTGCAAGAGGAGAGCTTGCCTGCAGAGA 5188
i
L1MdMus_I_5en 629 TCCAGACTTCTGGACACCTGCCCTGCAAGAGGAGAGCTTGCCTGCAGAGA 678
UnnamedSequen 5189 GTGCTCTGACCACTGGGACTCAGGTGAGAGTTGGACTCCCAGGAGTGCTG 5238
L1MdMus_I_5en 679 GTGCTCTGACCACTGGGACTCAGGTGAGAGTTGGACTCCCAGGAGTGCTG 728
UnnamedSequen 5239 ACAAAGGCTAACAGAATTACAGGAGGATCAAGCTCCAGACAGAGACAGCT 5288
i i v
L1MdMus_I_5en 729 ACAGAGGCTAACAGAATCACAGGAGGATCAAGCTCCAGCCAGAGACAGCT 778
UnnamedSequen 5289 AGAACATTAACACCAGAGATTATCAGGTAG-AAAAGACAAACATAAGAAT 5337
v ?i i i -i i i
L1MdMus_I_5en 779 TGAACATTAACACCAGAGATTNCCAGATGGCGAAAGGCAAACGTAAGAAT 828
UnnamedSequen 5338 CTTACTAACAGAAAGCAAGAACAATGGGCATCATCAGAACCCAGTACGCC 5387
v v
L1MdMus_I_5en 829 CTTACTAACAGAAACCAAGAACACTGGGCATCATCAGAACCCAGTACGCC 878
UnnamedSequen 5388 CAACACAGTGTGTCCTGGATACCCCAACACAACTGAAAAGCAAGACTCAG 5437
v i v v i ? i
L1MdMus_I_5en 879 CACCACAGCGAGTCCTGGATACCCCAACACACCCGAAAAGCAAGACNCGG 928
UnnamedSequen 5438 ATTTGAAATCATATCTCATCATGGTGATAAAAGCTTTTAAGAAGGACATT 5487
i v i i v i
L1MdMus_I_5en 929 ATTTAAAATCATATCTCATGATGGTGGTAGAAGATTTTAAGAAGGGCATT 978
UnnamedSequen 5488 AATAACTCACTTAAAGAAATACAGGAGAACACTGCTAAACAGGTAGAAGC 5537
L1MdMus_I_5en 979 AATAACTCACTTAAAGAAATACAGGAGAACACTGCTAAACAGGTAGAAGC 1028
UnnamedSequen 5538 CCTTAAAGAGGAAGCATAAAAATCCCTCAAGGAATTACAGGAGAAAACTG 5587
i v
L1MdMus_I_5en 1029 CCTTAAAGAGGAAGCACAAAAATCCCTCAAGGAATTACAGGAGAACACTG 1078
UnnamedSequen 5588 CTAAGCAGGTAGAAGTCCTTAA---------------------------- 5609
i ----------------------------
L1MdMus_I_5en 1079 CTAAACAGGTAGAAGTCCTTAAAGAACTACAGGCAAACACTGCTAAACAG 1128
UnnamedSequen 5610 --AGAGGAAACACAAAAACCCCTTAAAGAA-TACAGGAAAACACAACCAA 5656
-- i i -
L1MdMus_I_5en 1129 GTAGAAGAAACACAAAAATCCCTTAAAGAATTACAGGAAAACACAACCAA 1178
UnnamedSequen 5657 ACAGGTGATGGGATTGAACAAAACCATCCAAGATCTAAAAATGGAAGTAG 5706
i i
L1MdMus_I_5en 1179 ACAGGCGATGGAATTGAACAAAACCATCCAAGATCTAAAAATGGAAGTAG 1228
UnnamedSequen 5707 AAACAATGAAGAAAACCCAATGGGAGGCAACTCTGGGGATAGAAACCCTA 5756
v i i
L1MdMus_I_5en 1229 AAACAATGAAGAAAACCCAAAGGGAGACAACTCTGGAGATAGAAACCCTA 1278
UnnamedSequen 5757 GGAAAGAAATCAGGAACCATAGATGTAAGTAAGCATCAGCAACAGAATA 5805
---- i
L1MdMus_I_5en 1279 GGAAAGAAATCAGGAACCATAGAT----GTGAGCATCAGCAACAGAATA 1323
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 5.71
Transitions / transversions = 1.93 (52/27)
Gap_init rate = 0.02 (19 / 1166), avg. gap size = 2.47 (47 / 19)
25365 4.47 0.79 0.25 UnnamedSequence 5660 8840 35270 + L1MdMus_I_orf2 LINE/L1 1 3198 1483
25365 4.47 0.79 0.25 UnnamedSequence 5660 8840 (35270) L1MdMus_I_orf2#LINE/L1 1 3198 (1483) m_b1s551i9
UnnamedSequen 5660 GGTGATGGGATTGAACAAAACCATCCAAGATCTAAAAATGGAAGTAGAAA 5709
i i
L1MdMus_I_orf 1 GGCGATGGAATTGAACAAAACCATCCAAGATCTAAAAATGGAAGTAGAAA 50
UnnamedSequen 5710 CAATGAAGAAAACCCAATGGGAGGCAACTCTGGGGATAGAAACCCTAGGA 5759
v i i
L1MdMus_I_orf 51 CAATGAAGAAAACCCAAAGGGAGACAACTCTGGAGATAGAAACCCTAGGA 100
UnnamedSequen 5760 AAGAAATCAGGAACCATAGATGTAAGTAAGCATCAGCAACAGAATACAAG 5809
i ----
L1MdMus_I_orf 101 AAGAAATCAGGAACCATAGATGTGAG----CATCAGCAACAGAATACAAG 146
UnnamedSequen 5810 AGATTGAAGAGAGAATCTCAGGTGCAGAAGATTCCATAGAGAGCATGGGC 5859
v i i i
L1MdMus_I_orf 147 AGATGGAAGAGAGAATCTCAGGTGCAGAAGATTCCATAGGGAACATGGAC 196
UnnamedSequen 5860 ACAAAAATCAAAGAAAATGCAAAATGCAAAAAGATCCTAACTCAAAACAT 5909
v
L1MdMus_I_orf 197 ACAACAATCAAAGAAAATGCAAAATGCAAAAAGATCCTAACTCAAAACAT 246
UnnamedSequen 5910 CCAGGAAATCCAGAACACAATGAGAAGATCAAACCTACGGATAATAGGAG 5959
i i
L1MdMus_I_orf 247 CCAGGAAATCCAGGACACAATGAGAAGACCAAACCTACGGATAATAGGAG 296
UnnamedSequen 5960 TAGATGAGAATGAAGATTTTCAATTTAAAGGGCCAGGAAATATCTTCAAC 6009
i v
L1MdMus_I_orf 297 TAGATGAGAATGAAGATTTTCAACTTAAAGGGCCAGCAAATATCTTCAAC 346
UnnamedSequen 6010 AATATTATAGAAGAAAACTTCCCATACCTAAAGCAAGAGATGCCCATGAA 6059
v v
L1MdMus_I_orf 347 AAAATTATAGAAGAAAACTTCCCATACCTAAAGAAAGAGATGCCCATGAA 396
UnnamedSequen 6060 CATACAAAAATCCTACAGAACTCCAAATAGACTGGACCAGAAAAGAAATT 6109
i v
L1MdMus_I_orf 397 CATACAAGAAGCCTACAGAACTCCAAATAGACTGGACCAGAAAAGAAATT 446
UnnamedSequen 6110 TCTCCCGACACATAATAATCAGAACAAAAAATGCACTAAATAAAGACAGA 6159
i v
L1MdMus_I_orf 447 CCTCCCGACACATAATAATCAGAACAACAAATGCACTAAATAAAGACAGA 496
UnnamedSequen 6160 GTATTAAAAGCAGAAAGGGAAAAAGGTCAAGTAACATGTAAAGGTAGGCC 6209
i v i i
L1MdMus_I_orf 497 ATATTAAAAGCAGTAAGGGAAAAAGGTCAAGTAACATATAAAGGCAGGCC 546
UnnamedSequen 6210 TATTAGAATTACTCCAGACTTCTCACCAGA---------AGCCAGAAGAT 6250
---------
L1MdMus_I_orf 547 TATTAGAATTACTCCAGACTTCTCACCAGAGACTATGAAAGCCAGAAGAT 596
UnnamedSequen 6251 CCTGGACAAATGTTATACAGACAGTAAGAGAAGACAAATGCCAGCCCAGG 6300
i v v
L1MdMus_I_orf 597 CCTGGACAGATGTTATACAGACACTAAGAGAACACAAATGCCAGCCCAGG 646
UnnamedSequen 6301 CTGCTATACCCAACAAAACTCTCAATTACCATAGATGGAGAAACCAAAGT 6350
i i
L1MdMus_I_orf 647 CTACTATACCCAGCAAAACTCTCAATTACCATAGATGGAGAAACCAAAGT 696
UnnamedSequen 6351 ATTCAATGACAAAACCAAATTCACACAATATCTTTCCACGAATCCAGCCC 6400
v
L1MdMus_I_orf 697 ATTCCATGACAAAACCAAATTCACACAATATCTTTCCACGAATCCAGCCC 746
UnnamedSequen 6401 TTCAAAGGATAATAAAGGGAAAACACCAACACAAAAATGGAAACTACAGC 6450
i v
L1MdMus_I_orf 747 TTCAAAGGATAATAAAGGGAAAACACCAACACAAAGATGGAAACTACACC 796
UnnamedSequen 6451 CTAGAAAAAGCAAGAAAGTAATCCTTCAACAAAACTAAAAGAAGACAGCC 6500
L1MdMus_I_orf 797 CTAGAAAAAGCAAGAAAGTAATCCTTCAACAAAACTAAAAGAAGACAGCC 846
UnnamedSequen 6501 ACAAGAACAGAATCCCAAGAATAACAACAAAAATGACAGGAAGTAGCAAT 6550
? vvv i i
L1MdMus_I_orf 847 ACAAGAACAGANTCCCAACTTTAACAACAAAAATGACAGGAAGCAACAAT 896
UnnamedSequen 6551 TACTTTTCTTTGATTTCTCTTAACATCAATGGAATCAATTCCCCCAATAA 6600
v -
L1MdMus_I_orf 897 TACTTTTCTTTGATTTCTCTTAACATCAATGGACTCAATTCCCC-AATAA 945
UnnamedSequen 6601 AAAGACATAGACTAATAGACTGGCTACACAAACAGGACCCAACATTTTGT 6650
i i
L1MdMus_I_orf 946 AAAGACATAGACTAACAGACTGGCTACACAAACAGGACCCAACATTTTGC 995
UnnamedSequen 6651 TGCTTACAGAAAACCCACCTCAGGGACAAAGACAGACACTACTTCAGAGT 6700
i i
L1MdMus_I_orf 996 TGCTTACAGGAAACCCACCTCAGGGACAAAGACAGACACTACCTCAGAGT 1045
UnnamedSequen 6701 AGAAGGCTGGAAAACAATATTCCAAGCAAACGGTCCAAAGAAACAAGCTG 6750
i v i i
L1MdMus_I_orf 1046 AAAAGGCTGGAAAACAATTTTCCAAGCAAATGGTCCGAAGAAACAAGCTG 1095
UnnamedSequen 6751 AAGTAGCCATTCTAATATCGAATAAAATTGACTTCCAACCCAAAGTTATC 6800
i
L1MdMus_I_orf 1096 GAGTAGCCATTCTAATATCGAATAAAATTGACTTCCAACCCAAAGTTATC 1145
UnnamedSequen 6801 AAAAAAGACAAGGAGGGGCACTTCATACTCATCAAAGGTAAAATCTACCA 6850
L1MdMus_I_orf 1146 AAAAAAGACAAGGAGGGGCACTTCATACTCATCAAAGGTAAAATCTACCA 1195
UnnamedSequen 6851 ATATAAACTCTCAATTCTAAAGATCTCTGCTCCAAATGCAAGGGCACCCA 6900
v i v v v
L1MdMus_I_orf 1196 AGATGAACTCTCAATTCTAAATATCTATGCTCCAAATGCAAGGGCAGCCA 1245
UnnamedSequen 6901 AATTTATTAAAG--------------TTCAAAGCACACATTGCACCTCAC 6936
v i --------------i
L1MdMus_I_orf 1246 CATTCATTAAAGAAACTTTAGTAAAGCTCAAAGCACACATTGCACCTCAC 1295
UnnamedSequen 6937 ACAATAATAGTGGGAGGCTTCAACACCCCACTCTCATCAATGGACAGATC 6986
i i
L1MdMus_I_orf 1296 ACAATAATAGTGGGAGACTTCAACACCCCACTCTCACCAATGGACAGATC 1345
UnnamedSequen 6987 TTGGAAACAGAAACTAAACAGAGACACATGGACACTAACAGAAGTTATGA 7036
i
L1MdMus_I_orf 1346 CTGGAAACAGAAACTAAACAGAGACACATGGACACTAACAGAAGTTATGA 1395
UnnamedSequen 7037 AACACATAGATTTAACAGATATCTACAGAACATTTCATCCTAAAACAAAA 7086
v i i
L1MdMus_I_orf 1396 AACAAATGGATTTAACAGATATCTACAGAACATTTTATCCTAAAACAAAA 1445
UnnamedSequen 7087 GGATATACCTTCTTCTCAGCACCTCATGGTACCTCCTCCAAAATTGACCA 7136
L1MdMus_I_orf 1446 GGATATACCTTCTTCTCAGCACCTCATGGTACCTCCTCCAAAATTGACCA 1495
UnnamedSequen 7137 TATCATTGGTCACAAAACAG-CCTCAACAGATACAAAAATATTGAAATTA 7185
v i -
L1MdMus_I_orf 1496 TATAATCGGTCACAAAACAGGCCTCAACAGATACAAAAATATTGAAATTA 1545
UnnamedSequen 7186 TCCCATGCATCCTATCAGATCACCACAGACTAAGGCTGATCTTCAATAAC 7235
i
L1MdMus_I_orf 1546 TCCCATGCATCCTATCAGATCACCACGGACTAAGGCTGATCTTCAATAAC 1595
UnnamedSequen 7236 AGCATAAATAATAGAAAGCCAACATTCACATGGAAACTGACCAATACTCT 7285
i v i
L1MdMus_I_orf 1596 AGCATAAATAATAGAAAGCCAACATTCACGTGGAAACTGAACAACACTCT 1645
UnnamedSequen 7286 ACTAAATGATACCTTGGTCAAGGAAGAAATAAAGAAAGAAATTAAAGGCA 7335
v i v
L1MdMus_I_orf 1646 ACTCAATGATACCTTGGTCAAGGAAGAAATAAAGAAAGAAATTAAAGACT 1695
UnnamedSequen 7336 TTTTAGAGTTTAATGAAAATGAAGCCACAACATACCCAAACTTACGGGAC 7385
i
L1MdMus_I_orf 1696 TTTTAGAGTTTAATGAAAATGAAGCCACAACATACCCAAACTTATGGGAC 1745
UnnamedSequen 7386 ACAATGAAAGCAGTCCTAAGAGGAAAATTCATAGCCCTGAGTGCCTCCAA 7435
i
L1MdMus_I_orf 1746 ACAATGAAAGCAGTCCTAAGAGGAAAACTCATAGCCCTGAGTGCCTCCAA 1795
UnnamedSequen 7436 AAAGAAACTAGAGAGAGCATACACTAGCAGTGTGACCGCACACCTAGAAG 7485
v v
L1MdMus_I_orf 1796 AAAGAAACTAGAGAGAGCATACACTAGCAGTCTGACAGCACACCTAGAAG 1845
UnnamedSequen 7486 CTCTAGAACGAAAGGAAGCAAATTCACCCAATAGGAGTAGAAGGCAGGAA 7535
v v
L1MdMus_I_orf 1846 CTCTAGAACGAAAGGAAGCAAATTCACCCAAGAGGAGTAGACGGCAGGAA 1895
UnnamedSequen 7536 ATTATAAAACTTAGGGCTGAAATCAACCAAGTGGAAACAAAAAGAACTAT 7585
v v
L1MdMus_I_orf 1896 ATAATCAAACTTAGGGCTGAAATCAACCAAGTGGAAACAAAAAGAACTAT 1945
UnnamedSequen 7586 TCAAAGAGTCAACCAAAGGAGGAGCTGGTTCTTTGAGAAAATCGACAAGA 7635
i vv i
L1MdMus_I_orf 1946 TCAAAGAATCAACCAAACCAGGAGCTGGTTCTTTGAGAAAATCAACAAGA 1995
UnnamedSequen 7636 TAGATAAACCCTTAGTCAGACTAACTAGAGGGCACAGGGACAGCATCCTA 7685
i i
L1MdMus_I_orf 1996 TAGATAAACCCTTAGCCAGACTAACTAGAGGGCACAGGGACAGTATCCTA 2045
UnnamedSequen 7686 ATTAACAAAATCAGAAATGAAAAAGGAGATATAACAACAGAACCTGAGGA 7735
i v
L1MdMus_I_orf 2046 ATTAACAAAATCAGAAATGAAAAAGGAGACATAACAACAGATCCTGAGGA 2095
UnnamedSequen 7736 AATCCAAAACATCATCAGATCCTACTACAAAAGGCTATACTCAACAAAAC 7785
L1MdMus_I_orf 2096 AATCCAAAACATCATCAGATCCTACTACAAAAGGCTATACTCAACAAAAC 2145
UnnamedSequen 7786 TGGAAAACCTGGATGAAATGAACAACTTCCTAGATAGATACCAGGTACCA 7835
i i
L1MdMus_I_orf 2146 TGGAAAACCTGGATGAAATGGACAACTTCCTAGACAGATACCAGGTACCA 2195
UnnamedSequen 7836 AAGTTAAATCAAGATCAGGTTAATGATCTAAACAGTCCTATATCCCCTAA 7885
i i i v i v
L1MdMus_I_orf 2196 AAGTTAAATCAGGATCAGATTAACGATCTTAACAGTCCCATTTCCCCTAA 2245
UnnamedSequen 7886 AGAAATAGAAGCAGTCATTAATAGTCTCCTAACAAAAAAAAAAGCCCAGG 7935
i v --
L1MdMus_I_orf 2246 AGAAATAGAAGCAGTCATTAATAGTCTCCCAACCAAAAAAA--GCCCAGG 2293
UnnamedSequen 7936 ACCAGATGGGTTTAGT-CAGAGTTCTATCAGACCTTCAAAGAAGATCTAA 7984
- i
L1MdMus_I_orf 2294 ACCAGATGGGTTTAGTGCAGAGTTCTATCAGACCTTCAAAGAAGACCTAA 2343
UnnamedSequen 7985 TCCCAGTTCTTCACAAACTATTCCACAAAAGAGAAACAGAAGGTACTCTA 8034
i ii i v v
L1MdMus_I_orf 2344 TTCCAACTCTCCTCAAACTATTCCACAAAATAGAAACAGAAGGTACTCTA 2393
UnnamedSequen 8035 CCCAATTCATTCTGTGAAGCCACAATTACTCTGATATCTAAACCACACAA 8084
i i
L1MdMus_I_orf 2394 CCCAATTCATTCTATGAAGCCACAATTACTCTGATACCTAAACCACACAA 2443
UnnamedSequen 8085 AGATCCAACAAAGAAAGAGAACTTCAGACGAATTTCCCTTATGAATATTG 8134
v i
L1MdMus_I_orf 2444 AGATCCAACAAAGAAAGAGAACTTCAGACCAATTTCCCTTATGAATATCG 2493
UnnamedSequen 8135 ATGCAAAAATACTCAATAGAATCCTCGCAAACTGAATCCAAGAACACATC 8184
i i
L1MdMus_I_orf 2494 ATGCAAAAATACTCAATAAAATCCTCGCAAACCGAATCCAAGAACACATC 2543
UnnamedSequen 8185 AAAACAATTATGCATCCTGACCAAGTAGGCTTCATCCCAGGGTTGCAGGG 8234
i i v v v
L1MdMus_I_orf 2544 AAAACGATCATCCATCATGACCAAGTAGGCTTCATCCCAGGGATGCAGGG 2593
UnnamedSequen 8235 ATGGTTTATTATATGGAAATCCATCAATGCAATCCACTATATAAACAAAC 8284
v i i i
L1MdMus_I_orf 2594 ATGGTTTAATATACGGAAATCCATCAACGTAATCCACTATATAAACAAAC 2643
UnnamedSequen 8285 TCAAAGTCAAAAATCACATGATCATCTCGTTAGATGCTGAGAAAGCATTT 8334
v
L1MdMus_I_orf 2644 TCAAAGACAAAAATCACATGATCATCTCGTTAGATGCTGAGAAAGCATTT 2693
UnnamedSequen 8335 GACTAAATCCAACACCCCTTCATGACAAAAGTCTTGGAAAGATCAGGAAT 8384
v i v
L1MdMus_I_orf 2694 GACAAAATCCAACACCCCTTCATGATAAAAGTCATGGAAAGATCAGGAAT 2743
UnnamedSequen 8385 TCAAGGCCCATACCTAAACATGATAAAAGCAATCTACAGCAAACCAGTAG 8434
i v
L1MdMus_I_orf 2744 TCAAGGCCCATACCTAAACATAATAAAAGCAATATACAGCAAACCAGTAG 2793
UnnamedSequen 8435 CCAACATCAAAGTAAATGGATAAAAGCTGGAAGCAATCGCACTAAAATCA 8484
v i v
L1MdMus_I_orf 2794 CCAACATCAAAGTAAATGGAGAGAAGCTGGAAGCAATCCCACTAAAATCA 2843
UnnamedSequen 8485 GGGACTAGATAAGGCTGCCCACTTTCTCCCTACCTACTCAATATAGTACT 8534
i i
L1MdMus_I_orf 2844 GGGACTAGACAAGGCTGCCCACTTTCTCCCTACCTATTCAATATAGTACT 2893
UnnamedSequen 8535 TGAAGTCCTAGCCAGAGCAAATCGACAACAAAAGGAGCTCAAGTGGATAC 8584
v v v
L1MdMus_I_orf 2894 TGAAGTCCTAGCCAGAGCAATTCGACAACAAAAGGAGATCAAGGGGATAC 2943
UnnamedSequen 8585 AAATTGGAAAGGAAGAAGTAAAAATATCACTATTTTCAGATGATATGATA 8634
v v
L1MdMus_I_orf 2944 AAATTGGAAAGGAAGAAGTCAAAATATCACTATTTGCAGATGATATGATA 2993
UnnamedSequen 8635 GTATATATAAGTGACCCTAAAAATTCCACCAGAGAACTCCTAAACCTGAA 8684
v
L1MdMus_I_orf 2994 GTATATATAAGTGACCCTAAAAATTCCACCAGAGAACTCCTAAACCTGAT 3043
UnnamedSequen 8685 AAACAGCTTCAGTGCAGTAGCTGGATATAAAATTAACTCAAACAAATCAG 8734
L1MdMus_I_orf 3044 AAACAGCTTCAGTGCAGTAGCTGGATATAAAATTAACTCAAACAAATCAG 3093
UnnamedSequen 8735 TGGCCTTTCTCTACAGAAAGGATAAACAGGATGAGAAAGATATTATGGAA 8784
v v v
L1MdMus_I_orf 3094 TGGCCTTTCTCTACACAAAGGATAAACAGGATGAGAAAGAAATTAGGGAA 3143
UnnamedSequen 8785 ACAACACCCTTCTCAATAGTCTCAAAAAAATATAAAATACCTTGGTGTGA 8834
v v - v
L1MdMus_I_orf 3144 ACAACACCCTTCACAATAGTCAC-AAATAATATAAAATACCTTGGTGTGA 3192
UnnamedSequen 8835 CTCTAA 8840
L1MdMus_I_orf 3193 CTCTAA 3198
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 4.29
Transitions / transversions = 1.18 (77/65)
Gap_init rate = 0.00 (12 / 3180), avg. gap size = 2.75 (33 / 12)
+ 825 7.8 0.9 0.0 UnnamedSequence 8841 8956 (41608) + L1MdMus_I LINE/L1 6448 6564 (6) 13
ANNOTATION EVIDENCE:
825 7.76 0.86 0.00 UnnamedSequence 8841 8956 36800 + L1MdMus_I_3end LINE/L1 862 978 6
825 7.76 0.86 0.00 UnnamedSequence 8841 8956 (36800) L1MdMus_I_3end#LINE/L1 862 978 (6) c_b1s451i0
UnnamedSequen 8841 GGAACACCAGGGGCAAGAAGTGGGAGTGAGTGGGTAGAGGAGCACGGCAG 8890
i v i v i
L1MdMus_I_3en 862 GGAACGCCAGGGCCAAGAAGTGGGAGTGAGTGGGTAGGGGAGCAGGGCGG 911
UnnamedSequen 8891 GAG-AGGGTATAGGGGACTTTTGGGATAGCATTTGAAATTTAAGTGAAGA 8939
i - v i
L1MdMus_I_3en 912 GGGGAGGGTATAGGGGACTTTTGGGATAGCATTTGAAATGTAAATGAAGA 961
UnnamedSequen 8940 AAGTATCTAATAAAAAA 8956
i
L1MdMus_I_3en 962 AAATATCTAATAAAAAA 978
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 6.50
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.01 (1 / 115), avg. gap size = 1.00 (1 / 1)
+ 6000 7.4 2.5 1.1 UnnamedSequence 8967 9741 (40823) + L1MdV_III LINE/L1 5863 6647 (2) 14
ANNOTATION EVIDENCE:
6000 7.44 2.45 1.15 UnnamedSequence 8967 9741 36015 + L1MdV_III_3end LINE/L1 277 1061 2
6000 7.44 2.45 1.15 UnnamedSequence 8967 9741 (36015) L1MdV_III_3end#LINE/L1 277 1061 (2) c_b1s451i1
UnnamedSequen 8967 AAAGAACACACATAGGATATACTCACTGATAAATGGATATTAGCCCAAAC 9016
i v ii i v
L1MdV_III_3en 277 AAAGAACACACATGGTATGCACTCACTGATAAGTGGATATTAGCCCAAAA 326
UnnamedSequen 9017 GCTCCAAATACCCAAGATACAATTTACAGACCACATGAAGCTCAAGAAGA 9066
v i
L1MdV_III_3en 327 GCTCCAAATAACCAAGATACAATTCACAGACCACATGAAGCTCAAGAAGA 376
UnnamedSequen 9067 AGGAAGACCAAAGTGTGGGTGCTTCTGTCCTTCTTAG---GAGAACAAAA 9113
v ---
L1MdV_III_3en 377 AGGAAGACCAAAGTGTGGGTGCTTCGGTCCTTCTTAGAAGGAGAACAAAA 426
UnnamedSequen 9114 TATTCATAGGAGCAAATATGGAAACAAAGTGTAGAGCAGAGACTGAAGTA 9163
i i i i v
L1MdV_III_3en 427 TACTCACAGGAGCAAATATGGAGATAAAGTGTAGAGCAGAGACTGAAGGA 476
UnnamedSequen 9164 AATGTCATCCAGAGACTGGGTGATTCACCCCACCTGGGGATTCACCCCAT 9213
v i ---------i i
L1MdV_III_3en 477 AAGGCCATCCAGAGACTG---------TCCCACCTGGGGATTCATCCCAT 517
UnnamedSequen 9214 ATACAGTTACCAAACCCAGACACTATTGTGGATGCCAAGAAGTGCATGCT 9263
L1MdV_III_3en 518 ATACAGTTACCAAACCCAGACACTATTGTGGATGCCAAGAAGTGCATGCT 567
UnnamedSequen 9264 GAAAGGAGACTGATATGGCTAA-----GAGAGGCCCTGCCAGGGCCTTAC 9308
v iv----- i
L1MdV_III_3en 568 GAAAGGAGCCTGATATGGCTGTCTCCTGAGAGGCCCTGCCAGAGCCTTAC 617
UnnamedSequen 9309 AAATACAGAGGCAGATGCTTGCATCCAACCATTGGACTGAGTGTGGGGTC 9358
i i v i i
L1MdV_III_3en 618 AAATACAGAGGCGGATGCTCGCAGCCAACCATTGGACTGAGCGCGGGGTC 667
UnnamedSequen 9359 CCCAATAGAGAAGTTAGAGAAATGACTGAAGGAATTGAAGGGGTTTGCAA 9408
i v i
L1MdV_III_3en 668 CCCAATAGAGGAGTTAGAGAAAGGACTGAAGGAGTTGAAGGGGTTTGCAA 717
UnnamedSequen 9409 CCCCATAGGAAGAACAACAATATCAACCAACCAGACCCCCCAGAGCTCCC 9458
L1MdV_III_3en 718 CCCCATAGGAAGAACAACAATATCAACCAACCAGACCCCCCAGAGCTCCC 767
UnnamedSequen 9459 AGGGACTAAGCCATCAACCATGGAGTACACAGGGCTCCAGCTTCATATGT 9508
v v v v
L1MdV_III_3en 768 AGGGACTAAGCCATCAACAAAGGAGTACACATGGCTCCAGCTGCATATGT 817
UnnamedSequen 9509 AGCAGAGGATGGCCTTGTCAGGCATCAATGAGAGGAAA-------GGTCC 9551
v i i -------
L1MdV_III_3en 818 AGCAGAGGATGGCCTTGTCATGCATCAATGGGAGGAGAGGTCCTTGGTCC 867
UnnamedSequen 9552 TATGAAGGCTTGATAAAGGCCCCAGTGTAGGGGAATCGAGGGCAAGGAGG 9601
i i v ii
L1MdV_III_3en 868 TATGAAGGCTCGATAGATGCCCCAGTGTAGGGGAATCGAGGGCGGGGAGG 917
UnnamedSequen 9602 TGGGA----GTGGTTGGATGGAGGAACACCCTCATAGAAGCAGGAGGAGG 9647
---- v i i
L1MdV_III_3en 918 TGGGAGTGGGTGGGTGGGTGGAGGAACACCCTCATAGAAGCAGGGGGAGG 967
UnnamedSequen 9648 GAGGATAGGATAGGGGCTTTTCAGGAAGGGAAGAAATTGGGAAAGAGGAT 9697
i v i i i ii ii i
L1MdV_III_3en 968 GAGGATGGGATAGGGGGTTTCCGGGAGGGGGGGAAACCGGGAAAGGGGAT 1017
UnnamedSequen 9698 AACATTTGAAATGTAAATAAAGAAAAGATCCAATAAAAACAAAA 9741
v v
L1MdV_III_3en 1018 AACATTTGAAATGTAAATAAAGAAAATATCCAATAAAAAAAAAA 1061
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 6.83
Transitions / transversions = 1.85 (37/20)
Gap_init rate = 0.02 (13 / 774), avg. gap size = 2.15 (28 / 13)
+ 1257 20.8 13.9 1.5 UnnamedSequence 9770 10121 (40443) C L1_Rod LINE/L1 (6483) 1125 731 11
ANNOTATION EVIDENCE:
1257 20.77 13.92 1.52 UnnamedSequence 9770 10121 34763 C L1_Rod_5end LINE/L1 295 689 231
1257 20.77 13.92 1.52 UnnamedSequence 9770 10121 (34763) C L1_Rod_5end#LINE/L1 (231) 689 295 m_b1s551i10
UnnamedSequen 9770 TTTTGTTGAGTCTTCTTTAAA---------TTCTTTGATGAAGTTTATAA 9810
iv v --------- i
C L1_Rod_5end#L 689 TTTCTTTGTGTCTTCTTTAAACTCCTTGAATTCTTTGATGAAGTTTATGA 640
UnnamedSequen 9811 ------------------------GAGTTTTATCTAGGTAATTCTCAATG 9836
------------------------ i v i v
C L1_Rod_5end#L 639 TTGTTCTTTTAAATTCTGTGTCCTGGGGTTCATCTAGGTAATTCTCATTG 590
UnnamedSequen 9837 GCAAGCATTCTTATAGGACTGGT-GAATTTGGTGGGAGAGATATTGCCTT 9885
i i ii - iv v i - i ?
C L1_Rod_5end#L 589 GCGAACATTTCTATAGGACTGGTAGGTTTTGGAGAGA-AGATACTGNCTT 541
UnnamedSequen 9886 TATCTTTCATACTGTTTGTATT--------------TGGGTCTATGGTCC 9921
v i -------------- iv i v i
C L1_Rod_5end#L 540 GATCTTTCATATTGTTTGTATTTTTGCGATGAGATCTGGGCATGTGGACT 491
UnnamedSequen 9922 TTTTTAAATTAGTTTTGTGTCTGATATGTACAAAGTAGATTGACACAAAA 9971
i -vi i v i i i ivi i
C L1_Rod_5end#L 490 TCTTT-TGTTAGTTCTGTGTCTGATATGGACAGAGCAGGTTGGGGCAGAA 442
UnnamedSequen 9972 CACAGAATATGCTGGCATGGTTGAGCCTA-ATGTTCATTATAGTTTAGGT 10020
v v i i v i- i - v vivv i i i
C L1_Rod_5end#L 441 GAGAGGATGTGCGGGCG-GGTTGGGCCTAGAGGTTGGAAATGGCTTGGGT 393
UnnamedSequen 10021 GGAATGAAGTCAAGTGGAAAAAAAGGGCTGGGCTGGTATGCAGGATATGC 10070
i v i ii i i i i
C L1_Rod_5end#L 392 GGAATGAAGTCAGGTGGACAGAGGGGACTGGGCTGGTGTACAGGATGTGC 343
UnnamedSequen 10071 ATCCTGATCAATGTCTGGAGTTTTGGAGATTGATCTGAGGTTTGGGGAAA 10120
? i v v i - v i i v -- i v v i
C L1_Rod_5end#L 342 NTCCTGGTCCAAGCCTGGAG-TGTGGGGGTAGATCT--GGCTGGGTGGAA 296
UnnamedSequen 10121 A 10121
C L1_Rod_5end#L 295 A 295
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 24.31
Transitions / transversions = 1.77 (46/26)
Gap_init rate = 0.03 (11 / 351), avg. gap size = 5.00 (55 / 11)
+ 647 31.8 3.2 0.9 UnnamedSequence 10997 11215 (39349) + ID_B1 SINE/B4 1 224 (0) 15
ANNOTATION EVIDENCE:
647 31.79 3.20 0.89 UnnamedSequence 10997 11215 38250 + ID_B1 SINE/B4 1 224 0
647 31.79 3.20 0.89 UnnamedSequence 10997 11215 (38250) ID_B1#SINE/B4 1 224 (0) c_b1s355i0
UnnamedSequen 10997 GAGTCTTGGAATGCTATTTGGTTGGTAGAATGCTTGCCAAACAGACATGA 11046
i v v i ivii ii i v i vi i
ID_B1#SINE/B4 1 GGGGCTGGGGATGTAGCTCAGTTGGTAGAGTGCTTGCCTAGCATGCACGA 50
UnnamedSequen 11047 AGCCTCGGGTTTCATCTCCAGCACTGAATATAA-TAAGTAT-GTGGCTAC 11094
ii iv i i v v -iii ii - -i
ID_B1#SINE/B4 51 AGCCCTGGGTTCGATCCCCAGCACCGCATAAAACCGGGCGTGGTGGC-GC 99
UnnamedSequen 11095 ATATCTACAACATCAGCA----GGAGTGGGAAGCAGGAAGACTCGGGGGT 11140
iii ii ivi ---- vv i i - i ii
ID_B1#SINE/B4 100 ACGCCTGTAATCCCAGCACTCGGGAGGTGGAGGCAGGAGGA-TCAGAAGT 148
UnnamedSequen 11141 T-GAGGTCATCTTTCCCCATATAGTCAGTTCTAGGTCAGTCTGGGGTGTA 11189
-i i ivv i i iv v i i v ii
ID_B1#SINE/B4 149 TCAAGGTCATCCTCGGCTACATAGCGAGTTCGAGGCCAGCCTGGGCTACA 198
UnnamedSequen 11190 TTAAATGTCGTCTGAATAAGAAAAAA 11215
v i ivii v v i
ID_B1#SINE/B4 199 TGAGACCCTGTCTCAAAAAAAAAAAA 224
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 36.50
Transitions / transversions = 2.45 (49/20)
Gap_init rate = 0.03 (6 / 218), avg. gap size = 1.50 (9 / 6)
+ 811 27.3 0.5 2.2 UnnamedSequence 11242 11428 (39136) + B3A SINE/B2 1 184 (14) 16
ANNOTATION EVIDENCE:
811 27.33 0.53 2.17 UnnamedSequence 11242 11428 33674 + B3A SINE/B2 1 184 14
811 27.33 0.53 2.17 UnnamedSequence 11242 11428 (33674) B3A#SINE/B2 1 184 (14) m_b1s501i3
UnnamedSequen 11242 GGGGCTGGAAAGATTGTTCAGTGATTAAGAGTACATCCTGCTCTTCTGGA 11291
i v i i i ii v v vii
B3A#SINE/B2 1 GGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCGCTTGCTGCTCTTGCAGA 50
UnnamedSequen 11292 GGGCCTGAGTTTAATACCCAACCCCCGTATCAGATGGCTCACGATTGTCT 11341
i i iii v i v iii i ii i ii i
B3A#SINE/B2 51 GGACCCGAGTTCGGTTCCCAGCACCCACGTCGGGCGGCTCACAACCGCCT 100
UnnamedSequen 11342 GTGACTCTAGGTCCAGGTGATATGACAGTCTCTCCTTGTCCCTGAGGGCA 11391
i i v v vi ivi i v i i i v
B3A#SINE/B2 101 GTAACTCCAGCTCCAGGGGATCCGACGCCCTCTTCTGGCCTCCGCGGGCA 150
UnnamedSequen 11392 CCTGCACACACATG-GCACACGTTCCACATTCCACAAT 11428
i ? i - i--- -iv
B3A#SINE/B2 151 CCCGCACNCACACGCGCACACA---CACA-CACACAAT 184
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 25.10
Transitions / transversions = 2.85 (37/13)
Gap_init rate = 0.03 (5 / 186), avg. gap size = 1.00 (5 / 5)
+ 236 30.0 0.0 0.0 UnnamedSequence 11475 11554 (39010) + L1MD1 LINE/L1 6135 6214 (28) 17
ANNOTATION EVIDENCE:
236 30.00 0.00 0.00 UnnamedSequence 11475 11554 33548 + L1MD1_3end LINE/L1 882 961 28
236 30.00 0.00 0.00 UnnamedSequence 11475 11554 (33548) L1MD1_3end#LINE/L1 882 961 (28) m_b1s551i11
UnnamedSequen 11475 TATCATTGTGAAAAACTTCCTAAAGCCTATCCAGAGTAAATCTATATTAT 11524
i v ii vvv vv iv i ii vvv i
L1MD1_3end#LI 882 TACCATTGGGGGAAACTGGGTAAAGGGTACACGGGATCTCTCTGTATTAT 931
UnnamedSequen 11525 TTCTTAGAATTACATGTAAATCAATAATTA 11554
v i i i v i
L1MD1_3end#LI 932 TTCTTACAACTGCATGTGAATCTACAATTA 961
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.80
Transitions / transversions = 1.00 (12/12)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 747 25.1 1.1 3.3 UnnamedSequence 11642 11826 (38738) + MLTR11B LTR/ERVK 302 482 (0) 18
ANNOTATION EVIDENCE:
747 25.15 1.08 3.31 UnnamedSequence 11642 11826 33276 + MLTR11B LTR/ERVK 302 482 0
747 25.15 1.08 3.31 UnnamedSequence 11642 11826 (33276) MLTR11B#LTR/ERVK 302 482 (0) m_b1s501i4
UnnamedSequen 11642 CTAACTCTTCCTCCCTGTGCTGTGTGAAATAAACATGTTGCTCTTCTGGA 11691
--- iiiv i i vvv i i
MLTR11B#LTR/E 302 CTAACTC---CTCCCTGTGCTGTACATAATAAACACGCTGAGGTTCCGGG 348
UnnamedSequen 11692 CTTTCGCATAGTTGGTGCTACCCCAGCACAGCAAGCATGGCCCACCGGAT 11741
i vii i ii i v v i ii v i
MLTR11B#LTR/E 349 TTGCTGCGTAGTTGGTGCCGCTCCATCAGAGCGAGCACAGCCCACCCGAC 398
UnnamedSequen 11742 TCTGGCTTTTCTGTGCATGTGTCTGTGTGACTG-CCTTTCTTTAATCTGT 11790
i ii -- v - i v iv
MLTR11B#LTR/E 399 CCCAGCTTTTCTGT--ATGTGTCTGTGTGTCTGTCCTTTCTTCATTCCCT 446
UnnamedSequen 11791 CATTGTCCTAGTCA-GTTTCCAGGGACAATTTATATA 11826
iii - i - iv vii ii
MLTR11B#LTR/E 447 CGCCG-CCCAGTCAGGTTTCCAGGACCAAGCCATGCA 482
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 26.13
Transitions / transversions = 2.46 (32/13)
Gap_init rate = 0.04 (8 / 184), avg. gap size = 1.00 (8 / 8)
+ 954 29.9 5.0 1.9 UnnamedSequence 11864 12224 (38340) C L1MD1 LINE/L1 (84) 6158 5787 19
ANNOTATION EVIDENCE:
954 29.92 4.99 1.88 UnnamedSequence 11864 12224 32878 C L1MD1_3end LINE/L1 534 905 84
954 29.92 4.99 1.88 UnnamedSequence 11864 12224 (32878) C L1MD1_3end#LINE/L1 (84) 905 534 m_b1s551i12
UnnamedSequen 11864 TTTAGTCAGTTTTCAACAATGGTGGCCTCTTAAAAAACAATTTTATAAC- 11912
vi i vv ii v iv v vv i i-
C L1MD1_3end#LI 905 TTTACCCAGTTTCCCCCAATGGTAACATCTTGCAAAACTATAGTACAATA 856
UnnamedSequen 11913 TTATAGCCAGGGTATTAGTGTTGTCACAATCATAAGACCACAGAACATT- 11961
i i i i iiii vi i -- i- -
C L1MD1_3end#LI 855 TCACAACCAGGATATTGACATTGATACAGTCA--AGAT-ACAGAACATTT 809
UnnamedSequen 11962 -CACTACTAGAAAGGTCCCCCTGAGTTATTCTTTTATAGTCATATGCACT 12010
- ii i v i i i -iv iii i i iv
C L1MD1_3end#LI 808 CCATCACCACAAGGATCCCTC-ATGTTGCCCTTTTATAGCCACACCCACT 760
UnnamedSequen 12011 GTCCTCCTGTC----------TTTTAAGCCCCTAGGAACCACTATTAAG- 12049
vi i i ---------- ii v i i v v vv -
C L1MD1_3end#LI 759 TCCCTCCCGCCCCCACCCCCCTCCTTAACCCCTGGCAACCACTAATCTGT 710
UnnamedSequen 12050 -CTGCATTTCTATAACTTCACCATTTCAATACTATCACTTAAAGGGACTC 12098
- v i iii v v i i iv v v
C L1MD1_3end#LI 709 TCTCCATTTCTATAATTTTGTCATTTCAAGAATGTTATATAAATGGAATC 660
UnnamedSequen 12099 GTATAGTATATAATCTTTCTGGACTGAC---TTCCATTCATGACAACTCT 12145
i i i i iv i i --- i i vv i i
C L1MD1_3end#LI 659 ATACAGTATGTAACCTTTTGGGATTGGCTTTTTTCACTCAGCATAATTCT 610
UnnamedSequen 12146 CCAGAGACTCACCTAGGATGTTGACTGAGTCAGTGTTTCTGTCTTTTTCA 12195
ii i i i v vv vi i iv vv i i
C L1MD1_3end#LI 609 CTGGAGATTCATCCAGGTTGTTGCGTGTATCAATAGTTCGTTCCTTTTTA 560
UnnamedSequen 12196 TTGCTGCATAAAAATATCACGTGGTATGG 12224
vi --- i iv i
C L1MD1_3end#LI 559 TTGCTGAGT---AGTATTCCATGGTATGG 534
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 39.56
Transitions / transversions = 1.94 (70/36)
Gap_init rate = 0.04 (14 / 360), avg. gap size = 1.79 (25 / 14)
+ 495 25.9 6.5 6.8 UnnamedSequence 12374 12579 (37985) C L1MD1 LINE/L1 (680) 5562 5362 19
ANNOTATION EVIDENCE:
495 25.95 6.45 6.80 UnnamedSequence 12374 12579 33231 C L1MD1_3end LINE/L1 109 309 680
495 25.95 6.45 6.80 UnnamedSequence 12374 12579 (33231) C L1MD1_3end#LINE/L1 (680) 309 109 m_b1s551i13
UnnamedSequen 12374 CTGTACCATTTTACATTCCCACTAGTAACATA---GTAATATAGTAATAT 12420
i i ii --- i vi -----
C L1MD1_3end#LI 309 CTGTACCATTTTACATTCCCACCAGCAATGTATGAGTGATCCAGT----- 265
UnnamedSequen 12421 TTCACCATGTCTACAT--GC-TTTGCGTGC-ATCACTGTGCTCTTAATGT 12466
v iii iv ii-- - - i-i i -- i v -
C L1MD1_3end#LI 264 TTCTCCGCATCCTCGCCAGCATTTG-GTGTTGTCACTAT--TTTTTAT-T 219
UnnamedSequen 12467 TTAGCCATTGTGTTAGATGTGCAGTGGTATCTTATTATTAATTCATGGGT 12516
v v i i i i i ---------
C L1MD1_3end#LI 218 TTAGCCATTCTGATAGGTGTGTAGTGATATCTCATTGT---------GGT 178
UnnamedSequen 12517 TTTG--TTGAGTCCCCCAAAGATGGA-GATGACTGGTG---ATCTGTTGG 12560
i-- vi ii v -- v-i - v --- v vi
C L1MD1_3end#LI 177 TTTAATTTGCATTTCCCTA--ATGGCTAATGA-TGTTGAACATCTTTTCA 131
UnnamedSequen 12561 TATTCTTTTTTTAAAT---TAA 12579
i v v vvv --- v
C L1MD1_3end#LI 130 TGTGCTTATTTGCCATCTGTAT 109
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.08
Transitions / transversions = 1.56 (28/18)
Gap_init rate = 0.14 (29 / 205), avg. gap size = 1.28 (37 / 29)
+ 5346 9.3 2.7 0.1 UnnamedSequence 12580 13288 (37276) C Lx3_Mus LINE/L1 (8) 7001 6275 20
ANNOTATION EVIDENCE:
5346 9.32 2.68 0.14 UnnamedSequence 12580 13288 32686 C Lx3_Mus_3end LINE/L1 689 1415 8
5346 9.32 2.68 0.14 UnnamedSequence 12580 13288 (32686) C Lx3_Mus_3end#LINE/L1 (8) 1415 689 c_b1s451i2
UnnamedSequen 12580 TTAATT-ACTTTTAACACTCCATATTTTATTTCTC------TCCCATCCA 12622
- i v ii i i ------i
C Lx3_Mus_3end# 1415 TTAATTTATTTTTTACACTCCATATTCCATTCCCCGCCCCTCCCCATCCA 1366
UnnamedSequen 12623 CCCTCTGACTGTTCCTCATCCCATACCTCCTCCCTACCCC---CTGTCTC 12669
i i v i i --- i
C Lx3_Mus_3end# 1365 CCCTCCGACTGCTCCACATCCCACACCTCCTCCCCACCCCACCCCGTCTC 1316
UnnamedSequen 12670 CATGTGGATGTCCCCAACTCCCACCCCACCTGAACTCTAAATTCCCTGGG 12719
i i v i v i
C Lx3_Mus_3end# 1315 CACGTGGATGCCCCCACCCCCCACCCCACCTGACCTCTAAACTCCCTGGG 1266
UnnamedSequen 12720 ATCTCTAATCTCTTGAAGGTTATGTGAATCATCTGTGAATGAACACAGAT 12769
ii i i i v v v i
C Lx3_Mus_3end# 1265 GCCTCCAGTCTCTTGAGGGTTAGGTGCATCATCTCTGAATGAACACAGAC 1216
UnnamedSequen 12770 CCGGCAGTCCTCTACTGTATGCATGTTGGGGGCCTCCTATCAGTTGGTGT 12819
v ii v i
C Lx3_Mus_3end# 1215 CCGGAAGTCCTCTACTGTATGTGTGTTGGGGGCCTCATATCAGCTGGTGT 1166
UnnamedSequen 12820 ATGCTGCCTGTTTGGTGGTTCAGTGCTTGAGAAATCTTGGGGATCCAGAT 12869
i i i i i i
C Lx3_Mus_3end# 1165 ATGCTGTCTGTTTGGTGGTCCAGTGTTTGAGAGATCTCGGGGGTCCAGAT 1116
UnnamedSequen 12870 TAATTGAGACTGCTGGTCCTCCTACAGGGTCGCCCTTCTCCTCAGCTTCT 12919
i
C Lx3_Mus_3end# 1115 TAATTGAGACTGCTGGTCCTCCTACAGGATCGCCCTTCTCCTCAGCTTCT 1066
UnnamedSequen 12920 TTTAGCCTTCCCTAATTCAACAACAGGGGTCAGCTGCTTCTGTCCATTGG 12969
i
C Lx3_Mus_3end# 1065 TTCAGCCTTCCCTAATTCAACAACAGGGGTCAGCTGCTTCTGTCCATTGG 1016
UnnamedSequen 12970 TTGGG--------TCTGCATCTGACTAATTTCATCTGCTTGTTGGGTCTT 13011
-------- -v v
C Lx3_Mus_3end# 1015 TTGGGTGCAAATATCTGCATCTGACT-CTTTCAGCTGCTTGTTGGGTCTT 967
UnnamedSequen 13012 TTGGAGGGCAGTCATGATGGATTCCTTTTTGTGAGTTCTCCATAGCCTCA 13061
i i i i iv
C Lx3_Mus_3end# 966 TCGGAGGGCAGTCATGATAGGTCCCTTTTTGTGAGCGCTCCATAGCCTCA 917
UnnamedSequen 13062 ATAATAGTGTCAGGCCTTGGGATCCCCCCTTGAGATGGATCCCACTTTGG 13111
i i i v
C Lx3_Mus_3end# 916 GTAATAGTGTCAGGCCTTGGGACCTCCCCTTGAGCTGGATCCCACTTTGG 867
UnnamedSequen 13112 GCCTGTCGCTGGTTCTTCTTTTCCTCAGGCTCCTCTCCATTTCCATCCCT 13161
vi
C Lx3_Mus_3end# 866 GCCTGTCGCTGGACCTTCTTTTCCTCAGGCTCCTCTCCATTTCCATCCCT 817
UnnamedSequen 13162 GCAGTGCTTTCAGACAGGAACAATTCTGACTCAGAGTTGTGACTGTGGAA 13211
i i v v iv ? i
C Lx3_Mus_3end# 816 GTAATTCTTTCAGACAGGAACAATTATGGGTCAGAGNTGTGACTGTGGGA 767
UnnamedSequen 13212 TGGCAACCCC-TCCCTCACTTGATGCCCTGTCTTCCTGCTGGAGATGGGC 13260
- i i
C Lx3_Mus_3end# 766 TGGCAACCCCATCCCTCACTTGATGTCCTGTCTTCCTGCTGGAGGTGGGC 717
UnnamedSequen 13261 TCTATAAGTTCTCTCTCCCTACTGTCAG 13288
i i
C Lx3_Mus_3end# 716 TCTATAAGTTCCCTCTCCCTACTGTCGG 689
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 9.06
Transitions / transversions = 2.88 (49/17)
Gap_init rate = 0.01 (6 / 708), avg. gap size = 3.33 (20 / 6)
+ 644 26.8 6.4 3.7 UnnamedSequence 13289 13556 (37008) C L1MD1 LINE/L1 (881) 5361 5081 19
ANNOTATION EVIDENCE:
495 25.95 6.45 6.80 UnnamedSequence 13289 13391 32419 C L1MD1_3end LINE/L1 2 108 881
495 25.95 6.45 6.80 UnnamedSequence 13289 13391 (32419) C L1MD1_3end#LINE/L1 (881) 108 2 m_b1s551i13
UnnamedSequen 13289 TATTCTTAAATGAAATATCCC----TGTGTTTTATCCATGCTATGACTAC 13334
vi vii i i ---- v ii vi v i i iv
C L1MD1_3end#LI 108 TCCTCTTCGGTGAAATGTCTCTTCATGTCTTTTGCCCATTTTCTAATTGG 59
UnnamedSequen 13335 ATTTTGTGTGTTTTTACTGTTGGGCTTTGAGAGGTTTTCATCTTTTGTAG 13384
v v v i i v i i v v v
C L1MD1_3end#LI 58 ATTGTTTGTTTTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCTAG 9
UnnamedSequen 13385 ATTCTAG 13391
v
C L1MD1_3end#LI 8 ATACTAG 2
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 31.08
Transitions / transversions = 1.07 (15/14)
Gap_init rate = 0.01 (1 / 102), avg. gap size = 4.00 (4 / 1)
644 27.28 6.42 1.81 UnnamedSequence 13292 13556 32254 C L1MD_orf2 LINE/L1 2972 3248 46
644 27.28 6.42 1.81 UnnamedSequence 13292 13556 (32254) C L1MD_orf2#LINE/L1 (46) 3248 2972 m_b1s551i14
UnnamedSequen 13292 TCTTAAATGAAATATC----CCTGTGTTTTATCCATGCTATGACTACATT 13337
vii i ---- v v ii vi v i i iv
C L1MD_orf2#LIN 3248 TCTTCGGTGAAATGTCTNTTCATGTCTTTTGCCCATTTTCTAATTGGATT 3199
UnnamedSequen 13338 TTGTGTGTTTTTACTGTTGGGCTTTGAGAGGTTTTCATCTTTTGTAGATT 13387
v v v i i v i i v v v v
C L1MD_orf2#LIN 3198 GTTTGTTTTTTTACTGTTGAGTTTTGAGAGTTCTTTATATATTCTAGATA 3149
UnnamedSequen 13388 CTAGTACTTTGTCAGACATGGGATTTGGAAACTATTTTATCCCACTCTAC 13437
? v i i v i v - v v ii
C L1MD_orf2#LIN 3148 CNAGTCCTTTGTCGGATATGTGGTTTGCAAA-TATTTTCTCCCAGTCTGT 3100
UnnamedSequen 13438 GGTTTGTCCCTTCATCTAGCTGATGAAAAGTCT-------ACCAAG---T 13477
i i ii ivvi i i-- ii ------- v i---
C L1MD_orf2#LIN 3099 AGCTTGTCTTTTCATCCTCTTAAC--AGGGTCTTTCGCAGAGCAAAAGTT 3052
UnnamedSequen 13478 TTTAATTTTGGTGAA-TTTAATTGTATCAACCTCTCTTTTTATGAATCTT 13526
i - ii - ii i i i v
C L1MD_orf2#LIN 3051 TTTAATTTTGATGAAGTCCAATT-TATCAATTTTTCCTTTTATGGATCGT 3003
UnnamedSequen 13527 G--TTTAGTCCTAGATCTTAAACATTTTTTAC 13556
-- i vii ii - iv i i i
C L1MD_orf2#LIN 3002 GCTTTTGGTGTCAAGTC-TAAGAACTCTTTGC 2972
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 34.16
Transitions / transversions = 1.84 (46/25)
Gap_init rate = 0.04 (10 / 264), avg. gap size = 2.20 (22 / 10)
+ 454 19.4 0.0 2.2 UnnamedSequence 13861 13964 (36600) + Lx8 LINE/L1 7238 7332 (141) 21
ANNOTATION EVIDENCE:
287 27.36 0.00 5.68 UnnamedSequence 13861 13953 31857 + Lx8b_3end LINE/L1 1652 1739 152
287 27.36 0.00 5.68 UnnamedSequence 13861 13953 (31857) Lx8b_3end#LINE/L1 1652 1739 (152) m_b1s551i15
UnnamedSequen 13861 TTAAGGGCGTCCAGATACCCACGAGAAACCAAGTAGAACATTCCAGTGGA 13910
i -- i i vi iv iii i vi --- ii
Lx8b_3end#LIN 1652 TTAAGGGTGT--AGGTGCCCCTGGTAGGTCGACCA---CGCTCCAGTGGA 1696
UnnamedSequen 13911 TAGCCCCACACCCATGCACATATGGGCAGCACTAGTTGGACTT 13953
vi v i v v i ? v i
Lx8b_3end#LIN 1697 AGGCCACACATCCAAGAATATNTGGGCAGCACAAATTGGACTT 1739
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 32.18
Transitions / transversions = 2.00 (16/8)
Gap_init rate = 0.05 (5 / 92), avg. gap size = 1.00 (5 / 5)
454 14.29 0.00 0.00 UnnamedSequence 13902 13964 31846 + Lx8_3end LINE/L1 1684 1746 141
454 14.29 0.00 0.00 UnnamedSequence 13902 13964 (31846) Lx8_3end#LINE/L1 1684 1746 (141) m_b1s551i16
UnnamedSequen 13902 TCCAGTGGATAGCCCCACACCCATGCACATATGGGCAGCACTAGTTGGAC 13951
i i i i
Lx8_3end#LINE 1684 TCCAGTGGATGGCCCCACACCCATGCGCATACGGGCAGCACTAATTGGAC 1733
UnnamedSequen 13952 TTAGCAAGTCATT 13964
i iii i
Lx8_3end#LINE 1734 TCAGTGGGTTATT 1746
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 12.98
Transitions / transversions = 1.00 (9/0)
Gap_init rate = 0.00 (0 / 62), avg. gap size = 0.0 (0 / 0)
+ 1533 7.9 0.0 0.0 UnnamedSequence 13968 14157 (36407) C L1_Mur1 LINE/L1 (1234) 5592 5403 22
ANNOTATION EVIDENCE:
1533 7.89 0.00 0.00 UnnamedSequence 13968 14157 31653 C L1_Mur1_orf2 LINE/L1 4201 4390 294
1533 7.89 0.00 0.00 UnnamedSequence 13968 14157 (31653) C L1_Mur1_orf2#LINE/L1 (294) 4390 4201 m_b1s551i17
UnnamedSequen 13968 TCAGGTAGATTCATTTCCAATTTTCTGAGAAACCTCTAGATTGATTTCCA 14017
ii i i
C L1_Mur1_orf2# 4390 TCAGGTAGATCTATTTCCAATTTTCTGAGGAACCTCCAGATTGATTTCCA 4341
UnnamedSequen 14018 GAGTGGTTGTACCAGTTTGCAATCCTACCAGCAATGGAGGAGTGTTCCTC 14067
i
C L1_Mur1_orf2# 4340 GAGTGGTTGTACCAGTTTGCAATCCCACCAGCAATGGAGGAGTGTTCCTC 4291
UnnamedSequen 14068 TTTCTTCACATTCTTGCCAACATGTGCTGTCACCTGAATTTTTGATCTTA 14117
i i i? iv
C L1_Mur1_orf2# 4290 TTTCTCCACATCCTCNCCAACATGTGCTGTCACCTGAGGTTTTGATCTTA 4241
UnnamedSequen 14118 GTCATTCTGATTGGTATAAGGTAGAATCTTAGGGTTGTTT 14157
i i i i i
C L1_Mur1_orf2# 4240 GCCATTCTGATTGGTGTAAGGTGGAATCTCAGGGTCGTTT 4201
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 8.04
Transitions / transversions = 14.00 (14/1)
Gap_init rate = 0.00 (0 / 189), avg. gap size = 0.0 (0 / 0)
+ 1531 5.4 3.2 0.5 UnnamedSequence 14174 14359 (36205) + B2_Mm2 SINE/B2 1 191 (4) 23
ANNOTATION EVIDENCE:
1531 5.41 3.23 0.52 UnnamedSequence 14174 14359 35106 + B2_Mm2 SINE/B2 1 191 4
1531 5.41 3.23 0.52 UnnamedSequence 14174 14359 (35106) B2_Mm2#SINE/B2 1 191 (4) c_b1s355i1
UnnamedSequen 14174 GGAGCTGGAGAGATGACTCAGCAGTTAAGAGCACTGACTGGTCTTCCAGA 14223
i i i v
B2_Mm2#SINE/B 1 GGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTGCTCTTCCAGA 50
UnnamedSequen 14224 AGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGT 14273
i
B2_Mm2#SINE/B 51 GGTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGT 100
UnnamedSequen 14274 AATAAGATCTGATGCCCTCTTGTGGTGTGTCTGAAGACAGCTACAGTGTA 14323
ii v
B2_Mm2#SINE/B 101 AATGGGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTA 150
UnnamedSequen 14324 CT------CATAAATAAAATAAATAAACCTTAAAAAAAAAAA 14359
------ - i v
B2_Mm2#SINE/B 151 CTCACATACATAAAT-AAATAAATAAATCTTTAAAAAAAAAA 191
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 5.11
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.01 (2 / 185), avg. gap size = 3.50 (7 / 2)
+ 426 29.6 2.3 0.0 UnnamedSequence 14363 14494 (36070) C RMER5 LTR/ERV1 (168) 366 232 24
ANNOTATION EVIDENCE:
426 29.55 2.27 0.00 UnnamedSequence 14363 14494 31501 C RMER5 LTR/ERV1 232 366 168
426 29.55 2.27 0.00 UnnamedSequence 14363 14494 (31501) C RMER5#LTR/ERV1 (168) 366 232 m_b1s501i5
UnnamedSequen 14363 AAGTCTTATGTCAAGGCATTTAGTAAACACATTGGTAAGTACATCAG-TG 14411
v vi ? vv? i ii ? -?i
C RMER5#LTR/ERV 366 AAGTCATAAATCAAGGCANTTTTNAAATACATTGGTGGGNACATCAGANA 317
UnnamedSequen 14412 GGCGGTCACAAGAAG-C-AGAGCATCTTTGCTATAGGTTTCAGGCATTGT 14459
i iv - -i i v ? i ? ii iiii i
C RMER5#LTR/ERV 316 GGCGGTTACAGCAAGACGGGGGAANCTCTNCTATAGGCCTCAGATGCTAT 267
UnnamedSequen 14460 CTGATGATGCACCTAACCCTCAAGAGACTGGAGGC 14494
iiiv i i ii iii vviv i
C RMER5#LTR/ERV 266 CTGATGACATTCTTAGCTTTTGGGTTGGTGGAAGC 232
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 43.11
Transitions / transversions = 2.90 (29/10)
Gap_init rate = 0.02 (3 / 131), avg. gap size = 1.00 (3 / 3)
+ 280 16.0 36.8 0.0 UnnamedSequence 14495 14600 (35964) + Lx3_Mus LINE/L1 6852 6996 (13) 25
ANNOTATION EVIDENCE:
280 16.04 36.79 0.00 UnnamedSequence 14495 14600 31395 + Lx3_Mus_3end LINE/L1 1266 1410 13
280 16.04 36.79 0.00 UnnamedSequence 14495 14600 (31395) Lx3_Mus_3end#LINE/L1 1266 1410 (13) m_b1s551i18
UnnamedSequen 14495 CCCATGGAATTTAGAGGTCAAATGAGGTG--------------------- 14523
v i ii i ---------------------
Lx3_Mus_3end# 1266 CCCAGGGAGTTTAGAGGTCAGGTGGGGTGGGGGGTGGGGGCATCCACGTG 1315
UnnamedSequen 14524 ----------GGGGTGGGGAGGAGGTATGAGATGTGGAACAGTTGGGGGA 14563
---------- i i i i i i
Lx3_Mus_3end# 1316 GAGACGGGGTGGGGTGGGGAGGAGGTGTGGGATGTGGAGCAGTCGGAGGG 1365
UnnamedSequen 14564 TGAATG----GGGGCG----ATAAAATATGAAGTGAAAAAAAGAA 14600
i ---- ---- ii i v v
Lx3_Mus_3end# 1366 TGGATGGGGAGGGGCGGGGAATGGAATATGGAGTGTAAAAAATAA 1410
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 17.57
Transitions / transversions = 4.67 (14/3)
Gap_init rate = 0.04 (4 / 105), avg. gap size = 9.75 (39 / 4)
+ 45 17.8 1.1 0.0 UnnamedSequence 14602 14688 (35876) + GA-rich Low_complexity 1 88 (0) 26
ANNOTATION EVIDENCE:
45 17.75 1.15 0.00 UnnamedSequence 14602 14688 31307 + (AGAA)n Simple_repeat 1 88 0
45 17.75 1.15 0.00 UnnamedSequence 14602 14688 (31307) (AGAA)n#Simple_repeat 1 88 (0) m_b1s252i0
UnnamedSequen 14602 AGAGAGAGAGAAAGAAAGAAAGAAAGAAAGAAAGGAAGGAAGGAAGGAAG 14651
i i i i i i
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG 50
UnnamedSequen 14652 GAAGGAAGGAAGGAAGGAAGGAAGGAAGAAAG-AAGAA 14688
i i i i i i i -
(AGAA)n#Simpl 51 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAA 88
Matrix = Unknown
Transitions / transversions = 1.00 (13/0)
Gap_init rate = 0.01 (1 / 86), avg. gap size = 1.00 (1 / 1)
+ 272 23.8 9.0 2.1 UnnamedSequence 14696 14721 (35843) + Lx8 LINE/L1 7331 7355 (118) 27
ANNOTATION EVIDENCE:
272 23.81 9.02 2.11 UnnamedSequence 14696 14721 31465 + Lx8_3end LINE/L1 1745 1769 118
272 23.81 9.02 2.11 UnnamedSequence 14696 14721 (31465) Lx8_3end#LINE/L1 1745 1769 (118) m_b1s551i19
UnnamedSequen 14696 TTAAAGAAATGAAAGCAAAAACATGA 14721
i - iii ?i vvv
Lx8_3end#LINE 1745 TTAAAAAAA-GAGGACANGAAGTAGA 1769
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.96
Transitions / transversions = 1.67 (5/3)
Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1)
+ 1312 8.6 4.7 3.6 UnnamedSequence 14722 14913 (35651) + B2_Mm2 SINE/B2 2 195 (0) 28
ANNOTATION EVIDENCE:
1312 8.64 4.69 3.61 UnnamedSequence 14722 14913 34552 + B2_Mm2 SINE/B2 2 195 0
1312 8.64 4.69 3.61 UnnamedSequence 14722 14913 (34552) B2_Mm2#SINE/B2 2 195 (0) c_b1s355i2
UnnamedSequen 14722 GGGCTGGAGAGATGGCTCAGTGGTTAAAAGCACTGGCTCCTCTTTCAGAG 14771
i i i v i
B2_Mm2#SINE/B 2 GGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGACTGCTCTTCCAGAG 51
UnnamedSequen 14772 GTCATGAGTTCAATTCCCAGCAACCACATGGTGGCTTACAACCATCTGTA 14821
v i
B2_Mm2#SINE/B 52 GTCCTGAGTTCAATTCCCAGCAACCACATGGTGGCTCACAACCATCTGTA 101
UnnamedSequen 14822 ATGGGATCTGATGCCCTCTTCTGGTGTGT-------CAGCAACAGTGTGT 14864
------- v ii
B2_Mm2#SINE/B 102 ATGGGATCTGATGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGTAC 151
UnnamedSequen 14865 TCATATACATTAAACAAACAAACAAACAAACC--TAAAAACGAAACAAAA 14912
i ----- i i i i -- -- v
B2_Mm2#SINE/B 152 TCACATACAT-----AAATAAATAAATAAATCTTTAAAAA--AAAAAAAA 194
UnnamedSequen 14913 A 14913
B2_Mm2#SINE/B 195 A 195
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 8.74
Transitions / transversions = 3.00 (12/4)
Gap_init rate = 0.05 (9 / 191), avg. gap size = 1.78 (16 / 9)
+ 272 23.8 9.0 2.1 UnnamedSequence 14914 15019 (35545) + Lx8 LINE/L1 7356 7471 (2) 27
ANNOTATION EVIDENCE:
272 23.81 9.02 2.11 UnnamedSequence 14914 15019 31167 + Lx8_3end LINE/L1 1770 1885 2
272 23.81 9.02 2.11 UnnamedSequence 14914 15019 (31167) Lx8_3end#LINE/L1 1770 1885 (2) m_b1s551i19
UnnamedSequen 14914 CCCATGAAGTTTGGAAGAGGCAC-GTTAGGGGG---------GAGCTAGA 14953
vv - i v ?- i --------- i -
Lx8_3end#LINE 1770 GACATGAAGTT-GGGAGAGGGANAGTTGGGGGGATCTGGGGGGAGTT-GA 1817
UnnamedSequen 14954 AGAGGGGGGCT-AGATATACATGTTCATATTCCATTATATACATGCATGA 15002
i i iv -i iv i v v v v i i
Lx8_3end#LINE 1818 AGGGGAGGAATGGGATGAATATGATCAAAATACATTGTATACATGTATGA 1867
UnnamedSequen 15003 AAGTCTT-AAGCATAAAA 15019
v i- v
Lx8_3end#LINE 1868 AATTCTCAAAGAATAAAA 1885
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 29.96
Transitions / transversions = 1.09 (12/11)
Gap_init rate = 0.06 (6 / 105), avg. gap size = 2.33 (14 / 6)
+ 507 29.2 2.9 1.1 UnnamedSequence 15616 15790 (34774) C L1MD1 LINE/L1 (1160) 4986 4823 19
ANNOTATION EVIDENCE:
337 32.46 0.88 0.00 UnnamedSequence 15616 15729 30457 C L1_Rod_orf2 LINE/L1 3624 3738 907
337 32.46 0.88 0.00 UnnamedSequence 15616 15729 (30457) C L1_Rod_orf2#LINE/L1 (907) 3738 3624 m_b1s551i20
UnnamedSequen 15616 ATCCATTGAAACAAAATTGTTGTACAAAGTATAAGGCTTGAGTCCAAGCT 15665
vii vvv i v i i ivv iivi i i vi
C L1_Rod_orf2#L 3738 ATCCATTTGGAGTTAGTTTTTGTGCAAGGTGATAGATACGGGTCTAATTT 3689
UnnamedSequen 15666 CACTTTTCTGTCTCTGGATAGCTAATTTTCCTAGCACCATTTACTGAAAA 15715
i i iv v i v i i i ii i
C L1_Rod_orf2#L 3688 CATTCTTCTGCATGTGGACATCCAGTTTTCCCAGCACCATTTGTTGAAGA 3639
UnnamedSequen 15716 -ACTGTCTTACCTCC 15729
-i ? vi
C L1_Rod_orf2#L 3638 TGCTNTCTTTTCTCC 3624
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 43.64
Transitions / transversions = 1.85 (24/13)
Gap_init rate = 0.01 (1 / 113), avg. gap size = 1.00 (1 / 1)
507 28.92 3.11 1.22 UnnamedSequence 15630 15790 30396 C L1MD_orf2 LINE/L1 2714 2877 417
507 28.92 3.11 1.22 UnnamedSequence 15630 15790 (30396) C L1MD_orf2#LINE/L1 (417) 2877 2714 m_b1s551i21
UnnamedSequen 15630 AATTGTTGTACAAAGTATAAGGCTTGAGTCCAAGCTCACTTTTCTGTCTC 15679
v i i i i i ii v i i i i i v
C L1MD_orf2#LIN 2877 AATTTTTGTATAAGGTGTGAGGTTTAGGTCGAGGTTCATTTTTTTGCCTA 2828
UnnamedSequen 15680 TGGATAGCTAATTTTCCTAGCACCATTTACTGAAAA-ACTGTCTTACCTC 15728
iv i vii i ii -i i i v
C L1MD_orf2#LIN 2827 TGGATGTCCAATTGCTCCAGCACCATTTGTTGAAAAGGCTATCCTTCCTC 2778
UnnamedSequen 15729 C-TTCAA---GTTTTACACTTTTGTTTTACATAAGTTGAAGATGTTTACA 15774
- v ---v i i ivv v v iiv i iii
C L1MD_orf2#LIN 2777 CATTGAATTGCTTTTGCACCTTTGTCAAAAATCAGTTGGGCATATTTGTG 2728
UnnamedSequen 15775 TGATTGTCTATTCCTG 15790
i-- i
C L1MD_orf2#LIN 2727 TGG--GTCTATTTCTG 2714
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 38.81
Transitions / transversions = 2.54 (33/13)
Gap_init rate = 0.03 (5 / 160), avg. gap size = 1.40 (7 / 5)
+ 18 0.0 0.0 0.0 UnnamedSequence 15804 15826 (34738) + (CAC)n Simple_repeat 1 23 (0) 29
ANNOTATION EVIDENCE:
18 0.00 0.00 0.00 UnnamedSequence 15804 15826 30360 + (CAC)n Simple_repeat 1 23 0
18 0.00 0.00 0.00 UnnamedSequence 15804 15826 (30360) (CAC)n#Simple_repeat 1 23 (0) m_b1s252i1
UnnamedSequen 15804 CACCACCACCACCACCACCACCA 15826
(CAC)n#Simple 1 CACCACCACCACCACCACCACCA 23
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 22), avg. gap size = 0.0 (0 / 0)
+ 788 20.8 7.3 25.5 UnnamedSequence 15890 15969 (34595) C B3 SINE/B2 (5) 211 135 30
ANNOTATION EVIDENCE:
287 20.75 7.27 25.53 UnnamedSequence 15890 15969 30613 C B2_Mm2 SINE/B2 135 192 3
287 20.75 7.27 25.53 UnnamedSequence 15890 15969 (30613) C B2_Mm2#SINE/B2 (3) 192 135 m_b1s501i6
UnnamedSequen 15890 TTTTTTCAACTTTTAAAAGATTTAATTATTTTATTTTATATATATTAGTG 15939
---- v v - - i i v i
C B2_Mm2#SINE/B 192 TTTTTT----TTTTTAAAGATTTATTTATTT-ATTT-ATGTATGTGAGTA 149
UnnamedSequen 15940 TTTTGCCTTCACTATGTATGTTTACCATGG 15969
--------- i ivv i -------
C B2_Mm2#SINE/B 148 ---------CACTGTAGCTGTCT------- 135
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.62
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.28 (22 / 79), avg. gap size = 1.00 (22 / 22)
788 21.88 3.49 1.71 UnnamedSequence 15918 15969 30613 C B3 SINE/B2 159 211 5
788 21.88 3.49 1.71 UnnamedSequence 15918 15969 (30613) C B3#SINE/B2 (5) 211 159 m_b1s501i7
UnnamedSequen 15918 TTTTATTTTATATATATTAGTGTTTTGCCTTCAC-TATGTATGTTTACCA 15966
i i vi v i- v vi
C B3#SINE/B2 211 TTTTATTTTATGTGTATGGGTGTTTTGCCTGCATGTATGTCTGTGCACCA 162
UnnamedSequen 15967 TGG 15969
i v
C B3#SINE/B2 161 CGT 159
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 19.99
Transitions / transversions = 1.20 (6/5)
Gap_init rate = 0.02 (1 / 51), avg. gap size = 1.00 (1 / 1)
+ 3187 6.8 0.5 0.8 UnnamedSequence 15970 16366 (34198) + MTA_Mm LTR/ERVL-MaLR 1 396 (0) 31
ANNOTATION EVIDENCE:
3187 6.85 0.50 0.76 UnnamedSequence 15970 16366 32116 + MTA_Mm LTR/ERVL-MaLR 1 396 0
3187 6.85 0.50 0.76 UnnamedSequence 15970 16366 (32116) MTA_Mm#LTR/ERVL-MaLR 1 396 (0) c_b1s401i0
UnnamedSequen 15970 TGTACTGACTAGTTTTGTGTAAACTTGACACAGGCTGGAGTTATCACAGA 16019
i v -
MTA_Mm#LTR/ER 1 TGTACTGGCTAGTTTTGTGTCAACTTGACACAG-CTGGAGTTATCACAGA 49
UnnamedSequen 16020 GAAAGGAGCTTCAGTTGGGGAAACGCCTCCACAAGAGCCAACTCTAAGGC 16069
i i ii v v
MTA_Mm#LTR/ER 50 GAAAGGAGCTTCAGTTGAGGAAATGCCTCCATGAGATCCAACTGTAAGGC 99
UnnamedSequen 16070 ATTTTCTCATTTAGTGATCAAGGGG-AAAGGCCCCTTGTGGGTGGGACCA 16118
v -
MTA_Mm#LTR/ER 100 ATTTTCTCAATTAGTGATCAAGGGGGAAAGGCCCCTTGTGGGTGGGACCA 149
UnnamedSequen 16119 TCTCTGGGCTGGCAGTCTTGGGTTCTATAAGAGAGCAGGTTGAGCAAGCC 16168
i i
MTA_Mm#LTR/ER 150 TCTCTGGGCTGGTAGTCTTGGGTTCTATAAGAGAGCAGGCTGAGCAAGCC 199
UnnamedSequen 16169 AGGGGAAGCAAGCCAGTAAAGAACATCTCTCCACGGCCTCTGCTTCAGCT 16218
i i i v
MTA_Mm#LTR/ER 200 AGGGGAGGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGCT 249
UnnamedSequen 16219 CCTACTTCCTGACCTGCTTGAGTTCCAGTCCTGACATCCTTTGGTGATTA 16268
i v v
MTA_Mm#LTR/ER 250 CCTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTTGGTGATGA 299
UnnamedSequen 16269 ACAGCAAAGTGGAAAATGTAAGCTGAATAAACCCTTTCCTCACCAAC-TG 16317
ivi - i i v -
MTA_Mm#LTR/ER 300 ACAGCAGTATGG-AAGTGTAAGCCGAATAAACCCTTTCCTCCCCAACTTG 348
UnnamedSequen 16318 CTTCTTGGTTATGATGTTTTGTCCAGGAATAGGAACCCTGACTAAGACA 16366
i - v i
MTA_Mm#LTR/ER 349 CTTCTTGGTCATGATG-TTTGTGCAGGAATAGAAACCCTGACTAAGACA 396
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 6.97
Transitions / transversions = 1.70 (17/10)
Gap_init rate = 0.01 (5 / 396), avg. gap size = 1.00 (5 / 5)
+ 788 20.8 7.3 25.5 UnnamedSequence 16367 16505 (34059) C B3 SINE/B2 (58) 158 6 30
ANNOTATION EVIDENCE:
287 20.75 7.27 25.53 UnnamedSequence 16367 16505 30077 C B2_Mm2 SINE/B2 6 134 61
287 20.75 7.27 25.53 UnnamedSequence 16367 16505 (30077) C B2_Mm2#SINE/B2 (61) 134 6 m_b1s501i6
UnnamedSequen 16367 CATGATTATGCCCACAGAGATCAGAAGAAGTCATCGGGTTTCCTGGAACT 16416
- ------- ----i i v i i ii v ------
C B2_Mm2#SINE/B 134 CA-GA-------CACA----CCAGAAGAGGGCATCAGATCCCAT------ 103
UnnamedSequen 16417 AGAGTTTACAGGGAGTTTATGAGCCACCATGTGGGTGCTGGGCAC---AC 16463
------ ivi -i v v i---
C B2_Mm2#SINE/B 102 ------TACAGATGGTT-GTGAGCCACCATGTGGTTGCTGGGAATTGAAC 60
UnnamedSequen 16464 CCAGG-TCTCTAGCAAAAGCA------ACTCTAAACC----AAC--TCTC 16500
i -i i - i ------i v ---- i --
C B2_Mm2#SINE/B 59 TCAGGACCTCTGG-AAGAGCAGTCAGTGCTCTTAACCGCTGAGCCATCTC 11
UnnamedSequen 16501 TCAAG 16505
v
C B2_Mm2#SINE/B 10 TCCAG 6
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.62
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.22 (31 / 138), avg. gap size = 1.35 (42 / 31)
788 21.88 3.49 1.71 UnnamedSequence 16367 16485 30097 C B3 SINE/B2 38 158 58
788 21.88 3.49 1.71 UnnamedSequence 16367 16485 (30097) C B3#SINE/B2 (58) 158 38 m_b1s501i7
UnnamedSequen 16367 CATGATTA-TGCCCACAGAGATCAGAAGAAGTCATCGGGTTTCCTGGAAC 16415
i vi i- i i ii i v i i ii
C B3#SINE/B2 158 CGTGCCTGGTGCCCGCGGAGGCCAGAAGAGGGCGTCGGATCCCCTGGAAC 109
UnnamedSequen 16416 TAGAGTTTACAGGGAGTTTATGAGCCACCATGTGGGTGCTGGG---CACA 16462
i - ivi - i i --- iv
C B3#SINE/B2 108 TGGAG-TTACAGACGG-TTGTGAGCCGCCATGTGGGTGCTGGGAATCGAA 61
UnnamedSequen 16463 CCCAGGT-CTCTAGCAAAAGCAAC 16485
i - i - i i
C B3#SINE/B2 60 CCCGGGTCCTCTGG-AAGAGCAGC 38
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 19.99
Transitions / transversions = 5.50 (22/4)
Gap_init rate = 0.05 (6 / 118), avg. gap size = 1.33 (8 / 6)
+ 1713 20.4 8.2 10.5 UnnamedSequence 16632 16896 (33668) + RLTR20B4_MM LTR/ERVK 1 268 (298) 32
ANNOTATION EVIDENCE:
1713 20.44 8.19 10.50 UnnamedSequence 16632 16896 29873 + RLTR20B4_MM LTR/ERVK 1 268 298
1713 20.44 8.19 10.50 UnnamedSequence 16632 16896 (29873) RLTR20B4_MM#LTR/ERVK 1 268 (298) m_b1s501i8
UnnamedSequen 16632 TGTAGTAGCTTGTGTTCTCATGCTAATTATGTTACCCAAAA-CC------ 16674
ii - ------
RLTR20B4_MM#L 1 TGTAGCGGCTTGTGTTCTCATGCTAATTATGTTACCCAAAAACCTGTTTG 50
UnnamedSequen 16675 CAGTGTCCCACATGTAGG-CTAAAGGAAGCCTGCCCCCAATTGGCT---G 16720
i i - i i ---
RLTR20B4_MM#L 51 CAGTGTCCCGCACGTAGGACTAAAGGAAGCCTGCCCCCAGTTGGTTTTTG 100
UnnamedSequen 16721 --TGTTTGAGAAATAAAGTTGCCAGTGGCTAATGGC-GGGCATGGAGAC- 16766
-- v ii v i i - v -
RLTR20B4_MM#L 101 ACTGGTCAATAAATAAAGTTGCCAGCGGCCAATGGCTGGGCAGGGAGACA 150
UnnamedSequen 16767 ----------TTTTAGGATTCCCAGACAAGAAACCCAGGAGAGGGAAGAG 16806
---------- ------------ i - v?
RLTR20B4_MM#L 151 GAGGCGGGACTTTTAGGATTCCC------------CGGGA-AGGGACNAG 187
UnnamedSequen 16807 GGAGTCTGCCATGAGAAGGGCAACGGATGGAGCACACCAGGAAGAATGAG 16856
----- iv - ivi v iiv viv i v v iv v
RLTR20B4_MM#L 188 GGA-----CCGAG-GAAGGAGGAAGAGGGGATTCCGCCATGACGAGGGCG 231
UnnamedSequen 16857 GGTGAGATGGCCAATAT---ATAGGTGCAAAAGGAAAGTGTCG 16896
viv i v v iii---iv --- ii v ---
RLTR20B4_MM#L 232 TAGGAGACGGACCACGCCGGGAAGGTGCA---GGAGGGAG--- 268
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.44
Transitions / transversions = 1.35 (27/20)
Gap_init rate = 0.12 (33 / 264), avg. gap size = 1.61 (53 / 33)
+ 1167 9.0 0.7 0.0 UnnamedSequence 16897 17041 (33523) + B1_Mus2 SINE/Alu 1 146 (1) 33
ANNOTATION EVIDENCE:
1167 8.97 0.69 0.00 UnnamedSequence 16897 17041 32424 + B1_Mus2 SINE/Alu 1 146 1
1167 8.97 0.69 0.00 UnnamedSequence 16897 17041 (32424) B1_Mus2#SINE/Alu 1 146 (1) c_b1s355i3
UnnamedSequen 16897 AGCCAGGCGTGGTGGTGCACGTCTTTAATCTTAGCACTTAGGAGGCAGAG 16946
i i i ii ii
B1_Mus2#SINE/ 1 AGCCGGGCGTGGTGGCGCACGCCTTTAATCCCAGCACTCGGGAGGCAGAG 50
UnnamedSequen 16947 GCAGGGGGATTTCTGAGTTTGAAGCCAGCCTGGTCTACAAAGTCAGTTCC 16996
v i i i v
B1_Mus2#SINE/ 51 GCAGGCGGATTTCTGAGTTCGAGGCCAGCCTGGTCTACAGAGTGAGTTCC 100
UnnamedSequen 16997 AGGACAGCCAGGGCTACTCAGAGAAACCCTGTCTCG-AAAAACAAA 17041
v -
B1_Mus2#SINE/ 101 AGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCGAAAAAACAAA 146
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 6.75
Transitions / transversions = 3.33 (10/3)
Gap_init rate = 0.01 (1 / 144), avg. gap size = 1.00 (1 / 1)
+ 1713 20.4 8.2 10.5 UnnamedSequence 17042 17259 (33305) + RLTR20B4_MM LTR/ERVK 269 473 (93) 32
ANNOTATION EVIDENCE:
1713 20.44 8.19 10.50 UnnamedSequence 17042 17259 29510 + RLTR20B4_MM LTR/ERVK 269 473 93
1713 20.44 8.19 10.50 UnnamedSequence 17042 17259 (29510) RLTR20B4_MM#LTR/ERVK 269 473 (93) m_b1s501i8
UnnamedSequen 17042 CAAACAAACAAAACAAAACAAAACAAAACAAAAACAAAAACAAAAAAAAT 17091
- i iiv i ? ii-------------------i iivi iii-----
RLTR20B4_MM#L 269 -AGACGGCCGANATG-------------------TAGGTGCAGGG----- 293
UnnamedSequen 17092 GGGAAGCGGCCCCAAGAAGGGCTGCCCAGAAGGGTCCATGGGCAACAAAG 17141
i i - ? - i
RLTR20B4_MM#L 294 GGAAAGCGGCCCCAGGA-GGGCTGCCCAGNAGGGTCCA-GGGCAGCAAAG 341
UnnamedSequen 17142 ATAAAATATAGATTTAGTACGTATTAATTCAGAGATATT-AAAGGGAGAG 17190
? v i ii i-i i v
RLTR20B4_MM#L 342 ATAAAATATAGATTTAGNAAGTATTAACTCAGGAATATCGGAGGGGAGTG 391
UnnamedSequen 17191 TGTATTAGCCACCTGAACCCAAGGGATTAGCCCAGCCATTGAGCGAGCTA 17240
i v i vii-? v i vi?i
RLTR20B4_MM#L 392 TGTGTTAGCCACGTGGAGTT-NGGGAGTGGCCCAGCCATTGAGCTGNTTA 440
UnnamedSequen 17241 AGACATAGTAAAATATAAA--------------- 17259
i -v i---------------
RLTR20B4_MM#L 441 AGGCAT-TTAAAATATAAGGCTGCGTGTGTGTGT 473
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.44
Transitions / transversions = 3.44 (31/9)
Gap_init rate = 0.14 (31 / 217), avg. gap size = 1.45 (45 / 31)
+ 51 0.0 0.0 0.0 UnnamedSequence 17260 17303 (33261) + (GT)n Simple_repeat 1 44 (0) 34
ANNOTATION EVIDENCE:
51 0.00 0.00 0.00 UnnamedSequence 17260 17303 33261 + (GT)n Simple_repeat 1 44 0
51 0.00 0.00 0.00 UnnamedSequence 17260 17303 (33261) (GT)n#Simple_repeat 1 44 (0) c_b1s251i2
UnnamedSequen 17260 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 17303
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 1713 20.4 8.2 10.5 UnnamedSequence 17304 17392 (33172) + RLTR20B4_MM LTR/ERVK 474 561 (5) 32
ANNOTATION EVIDENCE:
1713 20.44 8.19 10.50 UnnamedSequence 17304 17392 29377 + RLTR20B4_MM LTR/ERVK 474 561 5
1713 20.44 8.19 10.50 UnnamedSequence 17304 17392 (29377) RLTR20B4_MM#LTR/ERVK 474 561 (5) m_b1s501i8
UnnamedSequen 17304 TTCCATCTG-GGATCCAGAACATTGGGGTGGGTGGCTAGGAGCAGCGCGT 17352
i ii - i i i ? i --- v i
RLTR20B4_MM#L 474 TTTCATTCGTGAATCCAGAGCACTNGGGCGGGTGGC---GAGAAGCGCGC 520
UnnamedSequen 17353 GCATCCTCTGGG-AGTTTAGAGCGCTCTAAT-TATTTACTGC 17392
i v i - v vvi i- - i
RLTR20B4_MM#L 521 GCACCCGCCGGGAAGTATAGAGCGGATTAACATA-TTACCGC 561
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.44
Transitions / transversions = 2.60 (13/5)
Gap_init rate = 0.08 (7 / 88), avg. gap size = 1.00 (7 / 7)
+ 439 27.6 8.6 1.6 UnnamedSequence 17416 17647 (32917) C L1MD1 LINE/L1 (1601) 4545 4298 19
ANNOTATION EVIDENCE:
439 27.60 8.62 1.61 UnnamedSequence 17416 17647 29122 C L1MD_orf2 LINE/L1 2189 2436 858
439 27.60 8.62 1.61 UnnamedSequence 17416 17647 (29122) C L1MD_orf2#LINE/L1 (858) 2436 2189 m_b1s551i22
UnnamedSequen 17416 TATAATAAGTCTTTTA-TCTACCAACATGGCACCTCTGTCCAGTTATTTC 17464
iv i ii - i iv i i iv v v v
C L1MD_orf2#LIN 2436 TATGTTGAGTCTTCCAATCCATGAACACGGTATGTCTCTCCATTTATTTA 2387
UnnamedSequen 17465 AGTCTACTTTA----CTT-----AGTATTGTTTAATATTTATCATAAAAG 17505
ii v i---- ----- ii v v i v i v v
C L1MD_orf2#LIN 2386 GATCTTCTTTGATTTCTTTCATCAGCGTTTTGTAGTTTTCAGCATACAAG 2337
UnnamedSequen 17506 TCCACATGCATGTTTTACTAGATTTATAACTTTGTGACTTC--------- 17546
-ii i ii v vv - i ---------
C L1MD_orf2#LIN 2336 TCC-TGTACATGTTTTGTTAGATTTATACCTAAGT-ATTTCATTTTTTTT 2289
UnnamedSequen 17547 TAAGTAACTACACACCTTAATGCATTTTCAATTTTTCTGTCATCA-GTGT 17595
i ii i ii v ivv v i i -- v ivi -
C L1MD_orf2#LIN 2288 TGAGCGATTGTAAATGGTATTGTATTTTTAATTT--CGGTTTCCACGTGT 2241
UnnamedSequen 17596 TAATTGCTCATATATAGAAATAAAATTTGTTTTTATATGTTTACCTTGTT 17645
v vi v vi i ? i v
C L1MD_orf2#LIN 2240 TCATTGCTAGTATATAGAAATACAATTGATTTTTGTATGTTNATCTTGTA 2191
UnnamedSequen 17646 TC 17647
C L1MD_orf2#LIN 2190 TC 2189
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 33.31
Transitions / transversions = 1.42 (37/26)
Gap_init rate = 0.04 (9 / 231), avg. gap size = 2.67 (24 / 9)
+ 761 19.4 11.0 0.0 UnnamedSequence 17649 17803 (32761) + ORR1C1 LTR/ERVL-MaLR 207 378 (0) 35
ANNOTATION EVIDENCE:
761 19.35 10.97 0.00 UnnamedSequence 17649 17803 28966 + ORR1C1 LTR/ERVL-MaLR 207 378 0
761 19.35 10.97 0.00 UnnamedSequence 17649 17803 (28966) ORR1C1#LTR/ERVL-MaLR 207 378 (0) m_b1s501i9
UnnamedSequen 17649 TTTCAGCTACTTCTCCAGCACAATATCTGACTGTGAGCTGTCATGGTACC 17698
i v i v i v i i v v
ORR1C1#LTR/ER 207 TCTCAGCTACTTCTCCAGCACCATGTCTGCCTGCGTGCCGCCATGCTCCC 256
UnnamedSequen 17699 TACCACGGTGACAATGGAAAAAACCTCTGAAACCATAAACAAGCCCCAAG 17748
ii i i i vv ii i ? v
ORR1C1#LTR/ER 257 CGCCATGATGATAATGGACTAAACCTCTGAAACTGTAAGCNAGCCCCAAT 306
UnnamedSequen 17749 CAAATGCT-------------GT----GCAGTTATGGTGTCCCTTCACAA 17781
i ------------- ---- ii i i i
ORR1C1#LTR/ER 307 TAAATGCTTTCCTTTATAAGAGTTGCCGTGGTCATGGTGTCTCTTCACAG 356
UnnamedSequen 17782 CAATAAAACACTGAGTAAGATA 17803
i v i
ORR1C1#LTR/ER 357 CAATAGAACACTGACTAAGACA 378
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 20.57
Transitions / transversions = 2.33 (21/9)
Gap_init rate = 0.01 (2 / 154), avg. gap size = 8.50 (17 / 2)
+ 248 32.2 11.9 4.9 UnnamedSequence 17804 18071 (32493) C L2 LINE/L2 (983) 2436 2151 36
ANNOTATION EVIDENCE:
248 32.18 11.94 4.90 UnnamedSequence 17804 18071 28698 C L2 LINE/L2 2151 2436 646
248 32.18 11.94 4.90 UnnamedSequence 17804 18071 (28698) C L2#LINE/L2 (646) 2436 2151 m_b1s601i0
UnnamedSequen 17804 GATGCCTCATTA-ATATCTACATGGAAATGATAAGTAGGTAGCCAGGTGT 17852
- - i i vi i vii i iii i i
C L2#LINE/L2 2436 GATGCCT-ATTAGACATCCAAGTGGAGATGTCGAGTAGGCAGTTGGATAT 2388
UnnamedSequen 17853 GAAAGTCATGTATTCTC-----AAGTCTGAGATAGAGACAGAAATTAGTG 17897
ivi vv vi vv----- i i i v i i v v v
C L2#LINE/L2 2387 ACGAGTCTGGAGTTCAGGGGAGAGGTCCGGGCTGGAGATATAAATTTGGG 2338
UnnamedSequen 17898 TATGGT--GCATAAAAGGAAAACGTTTTCTGCCATATTGTGGCACAAGAC 17945
vi vi -- v -- viiii vvv i----------
C L2#LINE/L2 2337 AGTCATCAGCATATA--GATGGTATTTAAAGCCATG----------AGAC 2300
UnnamedSequen 17946 TGAAGGACATCAC-AAAAGAATGC-TGTG--CAGAGAAGAGAG------C 17985
i v v -? ii i v- i--i i------
C L2#LINE/L2 2299 TGGATGAGATCACCNAGGGAGTGAGTGTAGATAGAGAAGAGAAGAGGTCC 2250
UnnamedSequen 17986 AAGACTTG----CTGTGAGTGTCCCCTTATTGGGAGGTTGATGGGA-GAC 18030
ivi ---- - i iiii vvii ?i i iv i - v
C L2#LINE/L2 2249 AAGGACTGAGCCCTG-GGGCACTCCAACGTTNAGAGGTCGGGGAGATGAG 2201
UnnamedSequen 18031 GATGAACCAGCCAAG--------GAAGGAGTGACAGGT-AGGTCGAAGGA 18071
v v -------- i i vi - v i
C L2#LINE/L2 2200 GAGGAACCAGCAAAGGAGACTGAGAAGGAGCGGCCAGTGAGGTAGGAGGA 2151
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 40.08
Transitions / transversions = 1.65 (51/31)
Gap_init rate = 0.09 (25 / 267), avg. gap size = 1.84 (46 / 25)
+ 15 5.5 0.0 0.0 UnnamedSequence 18117 18135 (32429) + (G)n Simple_repeat 1 19 (0) 37
ANNOTATION EVIDENCE:
15 5.48 0.00 0.00 UnnamedSequence 18117 18135 28634 + (G)n Simple_repeat 1 19 0
15 5.48 0.00 0.00 UnnamedSequence 18117 18135 (28634) (G)n#Simple_repeat 1 19 (0) m_b1s252i2
UnnamedSequen 18117 GGGGGCGGGGGGGGGGGGG 18135
v
(G)n#Simple_r 1 GGGGGGGGGGGGGGGGGGG 19
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.00 (0 / 18), avg. gap size = 0.0 (0 / 0)
+ 3347 6.3 0.3 0.0 UnnamedSequence 18372 19090 (31474) + L1MdV_III LINE/L1 897 1617 (5024) 38
ANNOTATION EVIDENCE:
3347 6.92 0.00 0.00 UnnamedSequence 18372 18819 27950 + L1MdV_III_5end LINE/L1 755 1202 0
3347 6.92 0.00 0.00 UnnamedSequence 18372 18819 (27950) L1MdV_III_5end#LINE/L1 755 1202 (0) m_b1s551i23
UnnamedSequen 18372 GGCAAGTAGCACTAGAAATAATCAGATGACAGGAGGCAAGCATATGAATA 18421
i i i i i i v i
L1MdV_III_5en 755 GGCAGGTAGCACTAGAGATAACCAGATGGCGGGAGGCAAGCGTAAGAACA 804
UnnamedSequen 18422 TAAGCAACAGAAACCACAGTTACTTGGCATCATCAAATCCCAATTCTCCC 18471
vi i v
L1MdV_III_5en 805 TAAGCAACAGAAACCAAGGTTACTTGGCATCATCAGAACCCAATTCTCCC 854
UnnamedSequen 18472 ACCATAGCAAGTCCTGGATGCACCATCACACTGGAAAAGCAAGATTAGGA 18521
i i v
L1MdV_III_5en 855 ACCATAGCAAGTCCTGGATACACCATCACACCGGAAAAGCAAGATTCGGA 904
UnnamedSequen 18522 TCTAAAATCACCTCTCATGATGATGATAGAGGACTTTAAGAAGGACATAA 18571
i
L1MdV_III_5en 905 TCTAAAATCACTTCTCATGATGATGATAGAGGACTTTAAGAAGGACATAA 954
UnnamedSequen 18572 ATAACTCCCTTAAAGAACTACACGAGAACACAGGTAAACAGGTACATGCC 18621
v v ? v v
L1MdV_III_5en 955 ATAACTCCCTTAAAGAAATACAGGAGAACACAGGTAAACAGNTAGAAGCC 1004
UnnamedSequen 18622 CTTAAAGAGGAAACACAAAAATCCCTTAAAGAATTACAGGAAAACACAAC 18671
i
L1MdV_III_5en 1005 CTTAAAGAGGAAACACAAAAATCCCTTAAAGAATTACAGGAAAACACAAT 1054
UnnamedSequen 18672 CAAACAGGTGAAGGAATTGAACAAAACCATCAAGGATCTAAAAATGAAAG 18721
i v v i i
L1MdV_III_5en 1055 CAAACAGGCGAAGGAAATGAACAAAACCATCCAGGATCTAAAAATGGAAA 1104
UnnamedSequen 18722 TAGAAACAATAAAGAAATCACAAAGGGAGACAACTCTGGAGATAGAAAAC 18771
i v
L1MdV_III_5en 1105 TAGAAACAATAAAGAAATCACAAAGGGAGACAACCCTGGAGTTAGAAAAC 1154
UnnamedSequen 18772 CTAGGAAAGAGATCAGGAGCCAGAGATGCAAGAATCACCAACAGAATA 18819
i v v
L1MdV_III_5en 1155 CTAGGAAAGAGATCAGGAGTCATAGATGCAAGCATCACCAACAGAATA 1202
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 6.41
Transitions / transversions = 1.38 (18/13)
Gap_init rate = 0.00 (0 / 447), avg. gap size = 0.0 (0 / 0)
3020 5.81 0.48 0.00 UnnamedSequence 18678 19090 27679 + L1Lx_II_orf2 LINE/L1 1 415 4269
3020 5.81 0.48 0.00 UnnamedSequence 18678 19090 (27679) L1Lx_II_orf2#LINE/L1 1 415 (4269) m_b1s551i24
UnnamedSequen 18678 GGTGAAGGAATTGAACAAAACCATCAAGGATCTAAAAATGAAAGTAGAAA 18727
v i
L1Lx_II_orf2# 1 GGTGAAGGAATTGAACAAAACCATCCAGGATCTAAAAATGGAAGTAGAAA 50
UnnamedSequen 18728 CAATAAAGAAATCACAAAGGGAGACAACTCTGGAGATAGAAAACCTAGGA 18777
i
L1Lx_II_orf2# 51 CAATAAAGAAATCACAAAGGGAGACAACCCTGGAGATAGAAAACCTAGGA 100
UnnamedSequen 18778 AAGAGATCAGGAGCCAGAGATGCAAGAATCACCAACAGAATACAAGAAAG 18827
i v v i v
L1Lx_II_orf2# 101 AAGAGATCAGGAGTCATAGATGCAAGCATCACCAACAGAATACAAGAGAT 150
UnnamedSequen 18828 AGAAGAGAGAATCTCAGGCACAGAAG-TACCATAGAAAACATTGATACAA 18876
ii - i
L1Lx_II_orf2# 151 AGAAGAGAGAATCTCAGGTGCAGAAGATACCATAGAAAACATTGACACAA 200
UnnamedSequen 18877 CAATCAAAGAAAATGTGAAACGCAAAAAGATCCTAACCCAAAACATCCAG 18926
i ii i ?
L1Lx_II_orf2# 201 CAGTCAAAGAAAATGCAAAATGCAAAAAGNTCCTAACCCAAAACATCCAG 250
UnnamedSequen 18927 GGAATCCAGGACACAATAAGAAGACCAAACCTAAGGATAATAGGTATAGA 18976
i i
L1Lx_II_orf2# 251 GAAATCCAGGACACAATGAGAAGACCAAACCTAAGGATAATAGGTATAGA 300
UnnamedSequen 18977 AGAGAGCTAAGATTCTCAACTTAAAGGGCCAGTAAATATCTTCAAGAAAA 19026
v i v
L1Lx_II_orf2# 301 AGAGAGCGAAGATTCCCAACTTAAAGGGCCAGTAAATATCTTCAACAAAA 350
UnnamedSequen 19027 TTATAGAAGAAAAG-TCCCTAATCTAAAGAAAGAGATGCCCATGAACATA 19075
v- i
L1Lx_II_orf2# 351 TTATAGAAGAAAACTTCCCTAACCTAAAGAAAGAGATGCCCATGAACATA 400
UnnamedSequen 19076 CAAGAAACCTACAAA 19090
i i
L1Lx_II_orf2# 401 CAAGAAGCCTACAGA 415
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 6.11
Transitions / transversions = 2.43 (17/7)
Gap_init rate = 0.00 (2 / 412), avg. gap size = 1.00 (2 / 2)
+ 2864 7.5 0.2 1.6 UnnamedSequence 19086 19478 (31086) + L1Lx_III LINE/L1 6200 6587 (47) 39 *
ANNOTATION EVIDENCE:
2864 7.50 0.25 1.55 UnnamedSequence 19086 19478 27291 + L1Lx_III_3end LINE/L1 617 1004 47
2864 7.50 0.25 1.55 UnnamedSequence 19086 19478 (27291) L1Lx_III_3end#LINE/L1 617 1004 (47) m_b1s551i25
UnnamedSequen 19086 ACAAATACAGAGGTGGATGCTCACAGACAACCATTGGACTGAGCACAGGG 19135
v v
L1Lx_III_3end 617 ACAAATACAGAGGTGGATGCTCTCAGCCAACCATTGGACTGAGCACAGGG 666
UnnamedSequen 19136 TCCCCAATGGAGGAGCTAGAGAAAGGACCCAAGGAGCTGAAGGGATTTAT 19185
i ii
L1Lx_III_3end 667 TCCCCAATGGAGGAGCTAGAGAAAGGACCCAAGGAGCTGAAGGGGTTTGC 716
UnnamedSequen 19186 AGCCC-ATAGGAGGAACAACCATATGAACTAACCAGTACCCCCAGAGCTC 19234
- v i
L1Lx_III_3end 717 AGCCCCATAGGAGGAACAACAATATGAACCAACCAGTACCCCCAGAGCTC 766
UnnamedSequen 19235 CCAGGGACTAAACCACTAGCCAAAGAGTACATATGGTGGGACTCATGGCT 19284
i i i v i
L1Lx_III_3end 767 CCAGGGACTAAACCACCAACCAAAGAGTACACATGGAGGGACCCATGGCT 816
UnnamedSequen 19285 CCAGCTGCATATGTAGCAGAGGATGGCCTTGTCAGACATCAATGAGAGGA 19334
i ? i
L1Lx_III_3end 817 CCAGCTGCATATGTAGCAGAGGATGGCCTTGTCGGNCATCAATGGGAGGA 866
UnnamedSequen 19335 CAGGCCCTTGGTCCTATGAAGGCTCTATGCCCCAGTGTAGCAGAATTCCA 19384
v i ? vi v
L1Lx_III_3end 867 GAGGCCCTTGGTCCTGTGAAGGCTCNATGCCCCAGTGTAGGGGAATGCCA 916
UnnamedSequen 19385 GGGCCAGGAAGTGGGAGTGGGTGGATTGGTGAGCAGGGGGAAGGGGGAGG 19434
i i i i
L1Lx_III_3end 917 GGGCCGGGAAGCGGGAGTGGGTGGGTTGGTGAGCAGGGGGAGGGGGGAGG 966
UnnamedSequen 19435 AGATGGGGAAGTGAATTTTCTGGAGGGGAAAACAGGAAAGGGAA 19478
i i ----- ii - v i
L1Lx_III_3end 967 GGATAGG-----GGGTTTTC-GGAGGGGAAACCAGGAAAGGGGA 1004
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 7.22
Transitions / transversions = 2.62 (21/8)
Gap_init rate = 0.02 (7 / 392), avg. gap size = 1.00 (7 / 7)
+ 2172 19.8 14.9 2.8 UnnamedSequence 19612 20213 (30351) C RLTR26_Mus LTR/ERVK (0) 673 1 40
ANNOTATION EVIDENCE:
2172 19.83 14.95 2.82 UnnamedSequence 19612 20213 28456 C RLTR26_Mus LTR/ERVK 1 673 0
2172 19.83 14.95 2.82 UnnamedSequence 19612 20213 (28456) C RLTR26_Mus#LTR/ERVK (0) 673 1 c_b1s401i1
UnnamedSequen 19612 TGTGGGCCTAGGTACCAGAAGTTTTCCACGGAGACCTCTATCCAGGCCGG 19661
i? i i i iv ? v
C RLTR26_Mus#LT 673 TGTGGGCCTGNGTACCAGAGGCTTTCCACGGAGATCTCTGGCCNGGCCTG 624
UnnamedSequen 19662 GTGGGAAGGCCCCAGCGA-GGGAAGTGAGTGCAGGCAGGGGGACGAAG-- 19708
v i ii i - i i i iv --
C RLTR26_Mus#LT 623 GTGCGAGGGTTCCGGCGAAGGGAAGCGAGTGCGGGCAGGGAGGGGAAGTC 574
UnnamedSequen 19709 -CATCTGCCACT-------------------------------------- 19719
- v i i --------------------------------------
C RLTR26_Mus#LT 573 GCTTCCGCCGCTTCCGCTGCTGCAGTTGGCTCCACCTCCGTCTCTGCCGT 524
UnnamedSequen 19720 -CCTTCCAGGTCCCTCGGTAACTCCAA-------TTCAGTGAGACAATTC 19761
- iv ? i?------- v v v iiv
C RLTR26_Mus#LT 523 GCCTTCCAGGTTACTCGGTNACTCCGNGCCGCCCTGCACTGAGTCGGGTC 474
UnnamedSequen 19762 T--CTCGGTAACTCCAATTCTGTGAG----ACAATTCAGTGAGGAAAACT 19805
v-- v ----- i i--- v ---- v vi -----
C RLTR26_Mus#LT 473 GGGCTGGG-----CCGAC---GAGAGGCCGACTAGCCAGTGAGGA----- 437
UnnamedSequen 19806 CGTGCG-------------CGGCTCTTCGGGAGAG---ATCTCTTCCCAA 19839
- ------------- v ---
C RLTR26_Mus#LT 436 -GTGCGGCGGAGCCTCAGGCGGCGCTTCGGGAGAGCAGATCTCTTCCCAA 388
UnnamedSequen 19840 GTGTTACAGCTCTTGGAACAAAAGGGTCAGACAAAGGAATAGTTTTCGCA 19889
i i i v i v i i
C RLTR26_Mus#LT 387 GTGTTACAGCTCTTAGGACAGAAGGCTCAGACGACGGAGTAGTTCTCGCA 338
UnnamedSequen 19890 TTCCTTTAAGTTCCTGCATGGCTC---TCCCTATATACAGTTCTGGCAGT 19936
iv -- v -i v v--- i i i -i
C RLTR26_Mus#LT 337 CACCTTTAA--TCCTTC-CGGATAGGATTCTTATATACAGTTTTGG-GGT 292
UnnamedSequen 19937 AATTTAGAGTTTGACAGCAAGCCCCTCTTGG-GGCTTGGGCTGAGAGTTT 19985
ii? i i i i iv i iiv- ? i
C RLTR26_Mus#LT 291 GGNTCAGGGTCTGACAGCAGGTACTTCTCATTGGCTTGGNCTGAGAGCTT 242
UnnamedSequen 19986 GGGGAAAACCTTATTTGCACGTGAGAGGGCTTGGTGCTGTTCCTAAGTGG 20035
v i i i i v i
C RLTR26_Mus#LT 241 TGGGGAAACCTTATTTGCATGTGGGAGGGCTTGGTGCTGCTCCTACGTGA 192
UnnamedSequen 20036 CTGATAGCCACGCCTCTC-CTGT-GAGGGTTGTGGGGGGCGGTAACTCCG 20083
i i vi - i- i i i v i v
C RLTR26_Mus#LT 191 CTGATGGCCACACACCTCTCTGCGGGGGGCTGTGGGAGGCTGTAGCTGCG 142
UnnamedSequen 20084 ACAGAAGCCA-GGGTCCAGGAGACTTGAGAGAACTCCTTCCATCCCAAGT 20132
i - i i v ivv v ? i v i
C RLTR26_Mus#LT 141 ACAGGAGCCAGGGGCCCAGGAGGCGTGGCCGAACACCTNCCGTCCCATGC 92
UnnamedSequen 20133 AAGTG--AATTATCA-CTACCGGCCC-CTGGGCTTCAAGATCTA-GCT-- 20175
i -- i i - i vi - i v v i ?- --
C RLTR26_Mus#LT 91 AGGTGGAAATCACCACCCACCGGGTCACCGGGGTTCCAGACCTNTGCTCG 42
UnnamedSequen 20176 ---GGAAACCAGGCTGTCTGCGCTGTAG-CCATTGCCCTACA 20213
--- ii i -ii - ii i
C RLTR26_Mus#LT 41 ACCGGGGACCAGGCTGTCTGTGC-ACAGCCCACCGCCCCACA 1
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 20.72
Transitions / transversions = 2.14 (79/37)
Gap_init rate = 0.07 (40 / 601), avg. gap size = 2.73 (109 / 40)
+ 366 26.3 3.5 8.1 UnnamedSequence 20299 20414 (30150) + MT2B LTR/ERVL 127 237 (364) 41 *
ANNOTATION EVIDENCE:
366 26.27 3.45 8.11 UnnamedSequence 20299 20414 26956 + MT2B LTR/ERVL 127 237 364
366 26.27 3.45 8.11 UnnamedSequence 20299 20414 (26956) MT2B#LTR/ERVL 127 237 (364) m_b1s501i10
UnnamedSequen 20299 ATGTGGGTTTTGACAAGTATAAAAGT-ATAAACATTTCAG---CAGATGT 20344
vi i i --i i ivi i- i v vi i --- iiiv
MT2B#LTR/ERVL 127 ATGGAGATCTTGA--GGCATAGTGGCCATGAAAAGCTTAGGCCCAGGCAA 174
UnnamedSequen 20345 AGTGGTACACACCTTTAATCCCAGCACTTGAGACAGAGGCAGGAGGATTT 20394
i i ----- i vi --
MT2B#LTR/ERVL 175 GGTGGTACACGCCTTTAATCCCAG-----GAGACAGAGGCAAGCAGA--T 217
UnnamedSequen 20395 TTCTGAGTTTAAAGTCAGCC 20414
i i i i
MT2B#LTR/ERVL 218 CTCTGAGTTCAAGGCCAGCC 237
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 32.91
Transitions / transversions = 3.67 (22/6)
Gap_init rate = 0.10 (11 / 115), avg. gap size = 1.18 (13 / 11)
+ 504 22.0 2.2 10.2 UnnamedSequence 20338 20474 (30090) + ORR1C1 LTR/ERVL-MaLR 651 777 (732) 35
ANNOTATION EVIDENCE:
504 21.96 2.19 10.24 UnnamedSequence 20338 20474 26896 + ORR1B1-int LTR/ERVL-MaLR 651 777 732
504 21.96 2.19 10.24 UnnamedSequence 20338 20474 (26896) ORR1B1-int#LTR/ERVL-MaLR 651 777 (732) m_b1s501i11
UnnamedSequen 20338 CAGATGTAGTGGTACACACCTTTAATCCCAGCACTT--GAGACAGAGGCA 20385
ii i i i-- i
ORR1B1-int#LT 651 CAGGCGTGGTGGTACACGCCTTTAATCCCAGCACTCAGGAGGCAGAGGCA 700
UnnamedSequen 20386 GGAGGATTTTTCTGAGTTTAAAGTCAGCCCCTGTTCTAT-GTATTAGCTC 20434
v -- i i i i -- v i- viiv i
ORR1B1-int#LT 701 GGCGGA--TCTCTGAGTTCAAGGCCAG--CCTGGTCTACAGAGCGAGTTC 746
UnnamedSequen 20435 CTAGAACAAAGAGACCCTAACTTTAAAGAGTCAAAGGAAA 20474
- i i------- i vi iiv -i
ORR1B1-int#LT 747 C-AGGACAG-------CCAAGCTTAGGCAGT-GAAGGAAA 777
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.59
Transitions / transversions = 3.50 (21/6)
Gap_init rate = 0.11 (15 / 136), avg. gap size = 1.07 (16 / 15)
+ 2310 15.4 5.3 3.3 UnnamedSequence 21104 21573 (28991) + Lx9 LINE/L1 6986 7464 (180) 42
ANNOTATION EVIDENCE:
2310 15.40 5.32 3.34 UnnamedSequence 21104 21573 25797 + Lx9_3end LINE/L1 1400 1878 180
2310 15.40 5.32 3.34 UnnamedSequence 21104 21573 (25797) Lx9_3end#LINE/L1 1400 1878 (180) m_b1s551i26
UnnamedSequen 21104 AGGACACTTCTCTTTGCAACAGATAATGACCATCACAGAAAAGCACAACC 21153
v iiiv i v
Lx9_3end#LINE 1400 AGGAAACTTCTCTTTGCAACAGACGGAGACCATTACAGAAAACCACAACC 1449
UnnamedSequen 21154 CATCAAAAGGCAGAGCTGTGAAGCACAGTTCCAATGAATACAGACAGGTA 21203
v v i i v i i i v----v
Lx9_3end#LINE 1450 GATCAAAATGCAGAGTTGTGGAGCCCAGTCCCAACGGATACAT----CTA 1495
UnnamedSequen 21204 CAGCACAACTCCTGCACCTAAGGCTCCGGGATCACTGCTGAAGAGGGGAA 21253
i? i v v i v iv
Lx9_3end#LINE 1496 CAANACAACTCCCGCACCTAAGGCTCAGGGAACATTGCGGAAGAGGGGGC 1545
UnnamedSequen 21254 AGAAAGCCTGTGCGAGCCAGAGGATCAGAGAGTTTGCTGTGAGACTGTGT 21303
i vi iv ? i i
Lx9_3end#LINE 1546 GGAAAGATTGTAAGAGCCAGAGGANCAGGGAGTTTGCTGTGAGATTGTGT 1595
UnnamedSequen 21304 GTCCTAGAAATGACAGAAGCTATACCCATAAAGTCTTACCAACATGACAG 21353
v ? v i i i v
Lx9_3end#LINE 1596 CTCCTAGNAATGTCAGAAGCTACACCCATAAAGTCTCACCAACATGGCTG 1645
UnnamedSequen 21354 CC---------------------CAACAACAATAGACATGCTGAAGTAGA 21382
--------------------- i v ii ? i
Lx9_3end#LINE 1646 CCTAAACATGAGCTGAACAAGGACGACACCAATAGACATGCCAANGTGGA 1695
UnnamedSequen 21383 TGGGAGAAAGCCCACAGAGCCTCAACACTACACAAAGAACTATAGGCAAC 21432
i i iii v i
Lx9_3end#LINE 1696 CGGGGGAAAGCCCACGAGGCCTCAACCCTACACAAAGAACTACAGGCAAC 1745
UnnamedSequen 21433 TAAGACCTGCAGAGAAAACGGAAAAATAATCACCTTCCCCAGGGAATAGC 21482
ivv v ivi- i i --- v
Lx9_3end#LINE 1746 TAAGGAATGCTGAGAGCG-GGAGAAATAGT---CTTCCCCAGGGAAGAGC 1791
UnnamedSequen 21483 ACGGCAATTGGTTA-CCAATACCAATACCAATGGTCAGTCCTGAAAAC-- 21529
iv - ----- i --
Lx9_3end#LINE 1792 ACACCAATTGGTTATCCAATACCA-----AATGGTCAGCCCTGAAAACAT 1836
UnnamedSequen 21530 ACACATTC-ACTAACATTCAGACTGAGCCTGAGCATGTTGTACTT 21573
i v - v - v v -- v i
Lx9_3end#LINE 1837 ATACATACAAGTAACATT-ATACGGA--CTGAGCAGGTTGTATTT 1878
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 15.49
Transitions / transversions = 1.33 (40/30)
Gap_init rate = 0.04 (20 / 469), avg. gap size = 2.05 (41 / 20)
+ 62 0.0 0.0 0.0 UnnamedSequence 21574 21626 (28938) + (AC)n Simple_repeat 1 53 (0) 43
ANNOTATION EVIDENCE:
62 0.00 0.00 0.00 UnnamedSequence 21574 21626 28938 + (AC)n Simple_repeat 1 53 0
62 0.00 0.00 0.00 UnnamedSequence 21574 21626 (28938) (AC)n#Simple_repeat 1 53 (0) c_b1s251i3
UnnamedSequen 21574 ACACACACACACACACACACACACACACACACACACACACACACACACAC 21623
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACACACACAC 50
UnnamedSequen 21624 ACA 21626
(AC)n#Simple_ 51 ACA 53
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 52), avg. gap size = 0.0 (0 / 0)
+ 17 4.0 3.9 0.0 UnnamedSequence 21685 21710 (28854) + (CAA)n Simple_repeat 1 27 (0) 44
ANNOTATION EVIDENCE:
17 3.96 3.85 0.00 UnnamedSequence 21685 21710 25712 + (CAA)n Simple_repeat 1 27 0
17 3.96 3.85 0.00 UnnamedSequence 21685 21710 (25712) (CAA)n#Simple_repeat 1 27 (0) m_b1s252i3
UnnamedSequen 21685 CAA-AACAACAACAACAACAACAAAAA 21710
- v
(CAA)n#Simple 1 CAACAACAACAACAACAACAACAACAA 27
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.04 (1 / 25), avg. gap size = 1.00 (1 / 1)
+ 455 23.0 26.4 0.0 UnnamedSequence 21717 21864 (28700) + B3 SINE/B2 29 215 (1) 45
ANNOTATION EVIDENCE:
455 22.97 26.35 0.00 UnnamedSequence 21717 21864 25558 + B3 SINE/B2 29 215 1
455 22.97 26.35 0.00 UnnamedSequence 21717 21864 (25558) B3#SINE/B2 29 215 (1) m_b1s501i12
UnnamedSequen 21717 GAGCACCAGCTTCTCTTTCAG---------GTTCAATTCCCAGCAGCCA- 21756
ii v i --------- i v -
B3#SINE/B2 29 GAGCACTGGCTGCTCTTCCAGAGGACCCGGGTTCGATTCCCAGCACCCAC 78
UnnamedSequen 21757 -----------------TCTGTGGCTCTAGTTTAAGGGTATCTGATGTC- 21788
----------------- ii i iv v i i i -
B3#SINE/B2 79 ATGGCGGCTCACAACCGTCTGTAACTCCAGTTCCAGGGGATCCGACGCCC 128
UnnamedSequen 21789 TCCTCTTACCTCCTCAAGCATCAAGAAAGCAC-------ACATTTGTACA 21831
i vi v ii i i v v ------- vvii
B3#SINE/B2 129 TCTTCTGGCCTCCGCGGGCACCAGGCACGCACGTGGTGCACAGACATACA 178
UnnamedSequen 21832 TGAAGGCAACACAGTCA----CATAAAATAAAATTAA 21864
v v vi ---- v
B3#SINE/B2 179 TGCAGGCAAAACACCCATACACATAAAATAAAAATAA 215
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 24.25
Transitions / transversions = 1.43 (20/14)
Gap_init rate = 0.03 (5 / 147), avg. gap size = 7.80 (39 / 5)
+ 525 26.2 0.0 0.0 UnnamedSequence 22122 22228 (28336) + B1_Mur3 SINE/Alu 43 149 (0) 46
ANNOTATION EVIDENCE:
525 26.17 0.00 0.00 UnnamedSequence 22122 22228 25194 + B1_Mur3 SINE/Alu 43 149 0
525 26.17 0.00 0.00 UnnamedSequence 22122 22228 (25194) B1_Mur3#SINE/Alu 43 149 (0) m_b1s501i13
UnnamedSequen 22122 AGAGAGAGAAATGCCTATCTTTATGAGTTCAAAGATAGCCTGGCCTATAG 22171
iv iv v vv i i i i vi i i
B1_Mur3#SINE/ 43 AGGCAGAGGCAGGCGGATCTCTGTGAGTTCGAGGCCAGCCTGGTCTACAG 92
UnnamedSequen 22172 AGCAAGTTCTAGGACAATTAAGGCTACACAGAAAATCCCTGTCTTGGAAA 22221
i i iii i i v iii
B1_Mur3#SINE/ 93 AGCGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGTCTCAAAAA 142
UnnamedSequen 22222 ACCAGAA 22228
v i
B1_Mur3#SINE/ 143 AACAAAA 149
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 30.85
Transitions / transversions = 2.50 (20/8)
Gap_init rate = 0.00 (0 / 106), avg. gap size = 0.0 (0 / 0)
+ 50 10.0 2.1 3.2 UnnamedSequence 22235 22328 (28236) + GA-rich Low_complexity 1 93 (0) 47
ANNOTATION EVIDENCE:
50 9.99 2.13 3.23 UnnamedSequence 22235 22328 25094 + (GGAGG)n Simple_repeat 1 93 0
50 9.99 2.13 3.23 UnnamedSequence 22235 22328 (25094) (GGAGG)n#Simple_repeat 1 93 (0) m_b1s252i4
UnnamedSequen 22235 GGA-GGAAGAGGAGGAGA-AGGAGGTAGAGGGAGAAGGGAAGGGGAGGGG 22282
- i i i -i -i - - i
(GGAGG)n#Simp 1 GGAGGGGAGGGGAGGGGAGGGGAGG-GGAGGG-G-AGGGGAGGGGAGGGG 47
UnnamedSequen 22283 AGAGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGAGAGGGGA 22328
i i
(GGAGG)n#Simp 48 AGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGAGGGGA 93
Matrix = Unknown
Transitions / transversions = 1.00 (8/0)
Gap_init rate = 0.05 (5 / 93), avg. gap size = 1.00 (5 / 5)
+ 712 24.1 10.2 2.7 UnnamedSequence 22401 22715 (27849) + L1MC LINE/L1 4094 4431 (1715) 48
ANNOTATION EVIDENCE:
712 24.13 10.16 2.66 UnnamedSequence 22401 22715 24707 + L1MC_orf2 LINE/L1 1985 2322 972
712 24.13 10.16 2.66 UnnamedSequence 22401 22715 (24707) L1MC_orf2#LINE/L1 1985 2322 (972) m_b1s551i27
UnnamedSequen 22401 CCTTCTCACTACTGTTTTTTAAACATCATAATGGAAATTTTAGGTAATAC 22450
i i vi i - i v i ii v i
L1MC_orf2#LIN 1985 CCCTCTCACCACTCCTTTTCAA-CATCGTACTGGAAGTCCTAGCTAATGC 2033
UnnamedSequen 22451 -----GAGAAGGAAAATAAATGAAAAA-ACACAGTGACTGGGAATGGTGA 22494
----- v i iv i ii- i -- i v iv
L1MC_orf2#LIN 2034 AATAAGACAAGAAAAGGAAATAAAAGGTATACAG--ATTGGGAAGGAAGA 2081
UnnamedSequen 22495 AA---AGCT-TGTTTGTTCACAGACAGCATAACTGTTTAATGTAGAAAAT 22540
--- i - v i iii i i i -
L1MC_orf2#LIN 2082 AATAAAACTGTCTTTGTTCGCAGATGACATGATTGTCTA-TGTAGAAAAT 2130
UnnamedSequen 22541 CCAAAAAGATAAACCAGAAAA----TGGAAGTCAAAAGG---TATAGTAA 22583
i ii vi v i ---- v v v v--- i
L1MC_orf2#LIN 2131 CCGAAAGAATCGACAAAAAAACTCCTGGAACTAATAAGCGATTATAGCAA 2180
UnnamedSequen 22584 AGTTGAAGGCTGCAGAGTTAATATGTGAAAGTTAA--GATTTTCTAC--- 22628
i v v i ii iii i -- v i i---
L1MC_orf2#LIN 2181 GGTTGCAGGATACAAGGTTAATATACAAAAGTCAATCGCTTTCCTATATA 2230
UnnamedSequen 22629 ----CAATCAACAAGAGAAAATTTGAA--TAAAAACCACAG----ATTTA 22668
---- v ?v -i -- - i----
L1MC_orf2#LIN 2231 CCAGCAATGAACAANTG-GAATTTGAAATTAAAAA-CACAATACCATTTA 2278
UnnamedSequen 22669 TACAAATACCCTTCAAAAGTGAGGCACGTAGGTAATAAAATATAACA 22715
i iv ii -i i iii v - - v
L1MC_orf2#LIN 2279 CATTAGCACCC-CCAAAAATGAAATACTTAGGT-AT-AAATCTAACA 2322
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.57
Transitions / transversions = 2.36 (52/22)
Gap_init rate = 0.06 (20 / 314), avg. gap size = 2.05 (41 / 20)
+ 415 28.5 2.7 12.0 UnnamedSequence 22770 23025 (27539) + RSINE1 SINE/B4 5 229 (63) 49
ANNOTATION EVIDENCE:
415 24.35 2.53 1.25 UnnamedSequence 22770 22848 24574 + RSINE1 SINE/B4 5 84 81
415 24.35 2.53 1.25 UnnamedSequence 22770 22848 (24574) RSINE1#SINE/B4 5 84 (81) m_b1s501i14
UnnamedSequen 22770 GCCAATGAGATGGCTTGGCAGATAAAAACACTTGCCACACAAGCCTGGCA 22819
iii ii i i ii i i - i i
RSINE1#SINE/B 5 GCCGGCGAGATGGCTCAGCGGGTAAAGGCGCTTGCCGC-CAAGCCTGACG 53
UnnamedSequen 22820 ACCTGAGTTTGATCTTTGGAA--CACAGGGT 22848
i iii i -- v
RSINE1#SINE/B 54 ACCTGAGTTCGATCCCCGGGACCCACATGGT 84
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 17.76
Transitions / transversions = 18.00 (18/1)
Gap_init rate = 0.03 (2 / 78), avg. gap size = 1.50 (3 / 2)
333 30.30 2.80 16.82 UnnamedSequence 22776 23025 24397 + B4 SINE/B4 10 229 63
333 30.30 2.80 16.82 UnnamedSequence 22776 23025 (24397) B4#SINE/B4 10 229 (63) m_b1s501i16
UnnamedSequen 22776 GAGATGGCTTGGCAGATAAAAACACTTGCCACACAAGCCTGGCAACCTGA 22825
ii iv i i-ii ?ii v ivi
B4#SINE/B4 10 GAGATGGCTCAGTCGGTAAAG-TGCTTGCCNTGCAAGCATGAGGACCTGA 58
UnnamedSequen 22826 GTTTGATCTTTGGAACACAGGGTTTTTTTTTTTTAAAGCTGGATATAG-G 22874
i iiii v v --------- vvv i iii i -
B4#SINE/B4 59 GTTCGATCCCCAGAACCCACG---------TAAAAAAGCCGGGCGTGGTG 99
UnnamedSequen 22875 GCACACATGTGTAATCCCACATGTAATTCCTACAGAAAGAGTGGAAGCAG 22924
i i iiv -ii ------ --------- v i
B4#SINE/B4 100 GCGCGCGCTTGTAATCCCA-GCG------CT---------GGGGAGGCAG 133
UnnamedSequen 22925 AAACAAGAGAATTACATGGAAGCTCAAGGGACAGATAGCCTGGAGTACAC 22974
i i v i i- v -i ivv v vi i vv v
B4#SINE/B4 134 AGACAGGCGGATC-CCTGG-GGCTCGCTGGCCAGCCAGCCTAGCCTACTC 181
UnnamedSequen 22975 AGCACAG---TAGG--AATAACAAGAGGGA-CCTGTCCTCAACAAAGCGA 23018
i i- ---i -- i ----- i - - - i -
B4#SINE/B4 182 GGCG-AGCTCCAGGCCAGT-----GAGAGACCCTGT-CTCAA-AAAAC-A 222
UnnamedSequen 23019 AGGGAGA 23025
vi
B4#SINE/B4 223 AGGTGGA 229
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 31.96
Transitions / transversions = 2.15 (43/20)
Gap_init rate = 0.16 (41 / 249), avg. gap size = 1.07 (44 / 41)
347 32.23 1.04 17.58 UnnamedSequence 22776 22967 24455 + B4A SINE/B4 10 174 118
347 32.23 1.04 17.58 UnnamedSequence 22776 22967 (24455) B4A#SINE/B4 10 174 (118) m_b1s501i15
UnnamedSequen 22776 GAGATGGCTTGGCAGATAAAAACACTTGCCACACAAGCCTGGCAACCTGA 22825
ii i? i i-ii i i v ivi
B4A#SINE/B4 10 GAGATGGCTCAGTNGGTAAAG-TGCTTGCCGCGCAAGCATGAGGACCTGA 58
UnnamedSequen 22826 GTTT-GATCTTTGGAACACAGGGTTTTTTTTTTTTAAAGCTGGATATAG- 22873
i- iiii v v v ---------- vv i iii i -
B4A#SINE/B4 59 GTTCGGATCCCCAGCACCCACG----------TAAAAAGCCGGGCGTGGC 98
UnnamedSequen 22874 GGCACACATGTGTAATCCCACATGTAATTCCTACAGAAAGAGTGGAAGCA 22923
i i iiv -ii ------ --------- v i i
B4A#SINE/B4 99 GGCGCGCGCCTGTAATCCCA-GCG------CT---------GGGGAGGCG 132
UnnamedSequen 22924 GAAACAAGAGAATTACATGGAAGCTCAAGGGACAGATAGCCTGG 22967
i i i i- v -i ivv v vi i
B4A#SINE/B4 133 GAGACAGGAGGATC-CCTGG-GGCTCGCTGGCCAGCCAGCCTAG 174
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 31.96
Transitions / transversions = 2.64 (37/14)
Gap_init rate = 0.16 (31 / 191), avg. gap size = 1.00 (31 / 31)
+ 92 8.5 1.1 4.1 UnnamedSequence 23072 23246 (27318) + (CA)n Simple_repeat 1 170 (0) 50
ANNOTATION EVIDENCE:
92 8.54 1.14 4.12 UnnamedSequence 23072 23246 27318 + (CA)n Simple_repeat 1 170 0
92 8.54 1.14 4.12 UnnamedSequence 23072 23246 (27318) (CA)n#Simple_repeat 1 170 (0) c_b1s251i4
UnnamedSequen 23072 CACACACATAC-CACACACACACACACACACACACACACACACACACACA 23120
i -
(CA)n#Simple_ 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50
UnnamedSequen 23121 CACACACACACACATATACACAGA-ATCACACACACAGAGCATCACACAT 23169
i i v - - v - - i
(CA)n#Simple_ 51 CACACACACACACACACACACACACA-CACACACACACA-CA-CACACAC 97
UnnamedSequen 23170 ACACACACACACACAGAGCATCACACACACACAGAGCATCATACACACAC 23219
v - - v - - i
(CA)n#Simple_ 98 ACACACACACACACACA-CA-CACACACACACACA-CA-CACACACACAC 143
UnnamedSequen 23220 ACAGTCACACACACGTACACACACACA 23246
vv ii
(CA)n#Simple_ 144 ACACACACACACACACACACACACACA 170
Matrix = Unknown
Transitions / transversions = 1.17 (7/6)
Gap_init rate = 0.05 (9 / 174), avg. gap size = 1.00 (9 / 9)
+ 26 0.0 0.0 0.0 UnnamedSequence 23247 23275 (27289) + (GA)n Simple_repeat 1 29 (0) 51
ANNOTATION EVIDENCE:
26 0.00 0.00 0.00 UnnamedSequence 23247 23275 24321 + (GA)n Simple_repeat 1 29 0
26 0.00 0.00 0.00 UnnamedSequence 23247 23275 (24321) (GA)n#Simple_repeat 1 29 (0) m_b1s252i5
UnnamedSequen 23247 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 23275
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAG 29
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 647 23.5 3.3 4.8 UnnamedSequence 23282 23491 (27073) + L1MC LINE/L1 4477 4683 (1463) 48
ANNOTATION EVIDENCE:
647 23.52 3.33 4.83 UnnamedSequence 23282 23491 24105 + L1MC_orf2 LINE/L1 2368 2574 720
647 23.52 3.33 4.83 UnnamedSequence 23282 23491 (24105) L1MC_orf2#LINE/L1 2368 2574 (720) m_b1s551i28
UnnamedSequen 23282 AAAAATATCAAAGA-GAT----ACAACCTGAGAGATATTCCATGTTCATT 23326
i v - ?---- i viv -
L1MC_orf2#LIN 2368 AAAGAAATCAAAGAAGANCTAAATAAATGGAGAGATATTCCATGTTCAT- 2416
UnnamedSequen 23327 TCATGATTGAGAAGACTCAGTATGGTCAAAACATCAGTTTTTTTCTCAAC 23376
---- iv ii i v i ii -- i i
L1MC_orf2#LIN 2417 ----GGATAGGAAGACTCAATATTGTCAAGATGTCAG--TTCTTCCCAAC 2460
UnnamedSequen 23377 TTGATCT-CAGATACAATATAGTGGCAAAGAAAATCCAAATGAATTATTT 23425
-i v ii i vv vv v iii i
L1MC_orf2#LIN 2461 TTGATCTATAGATTCAATGCAATCCCAATCAAAATCCCAGCAAGTTATTT 2510
UnnamedSequen 23426 TGT-TATATTTACAAATAGATCTCAAAGTTTTTTATACCAAGAAGTAAAA 23474
-v iv iv iii --- ivi i i
L1MC_orf2#LIN 2511 TGTGGATATCGACAAACTGATTCTAAAG---TTTATATGGAGAGGCAAAA 2557
UnnamedSequen 23475 GACTCTTAATAGCCAAC 23491
i vv
L1MC_orf2#LIN 2558 GACCCAGAATAGCCAAC 2574
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 28.42
Transitions / transversions = 1.76 (30/17)
Gap_init rate = 0.07 (14 / 209), avg. gap size = 1.21 (17 / 14)
+ 522 28.3 9.7 6.5 UnnamedSequence 23505 23827 (26737) + RMER15 LTR/ERVL 14 421 (154) 52
ANNOTATION EVIDENCE:
323 29.55 4.89 8.26 UnnamedSequence 23505 23729 23867 + RMER15 LTR/ERVL 14 231 344
323 29.55 4.89 8.26 UnnamedSequence 23505 23729 (23867) RMER15#LTR/ERVL 14 231 (344) m_b1s501i17
UnnamedSequen 23505 TTTCCTCTGA-ATTGAAACATTCCCTTCTGGAGGGAGG------AAGAAG 23547
i - v i v i ------ ---
RMER15#LTR/ER 14 TTTCCTCCGAGATTGAAACATTCCATCCTGCAGGGAAGCTCCTTAAG--- 60
UnnamedSequen 23548 GCTCAGGAGACTGAGTCAACAAACCCTAAA-AG-TCCAGGAAAACCT--A 23593
--- ----ii v - i v - - i iv i--
RMER15#LTR/ER 61 ---CAGGA----AGGTAAAC-AACTCAAAATAGCTTCAGGAAGTCCCTGA 102
UnnamedSequen 23594 AGCTTACAAGACTCATGAGGCCTCACCCAAGGTTATAGAAGATGTCAACA 23643
i v v i iv i v ---- ?vi iv v - i
RMER15#LTR/ER 103 AACTGACCAGATTCACTAGGCCCCTCCC----TNCCAGAGTAAG-CAATA 147
UnnamedSequen 23644 ATTGCTGGGGAGCGAGACTCCTGGACTGACCAAGCTGCCTAGAGGCAGCT 23693
vv vv v vv iii vii i vv i --i
RMER15#LTR/ER 148 AAAGCTGCTGAGAGTCACTCTCAGACAAGCCGAGCTGCAAAGAAG--ACT 195
UnnamedSequen 23694 CTCTGATCTGTTGTGCTACCTTCAAGTCCCAGGAAC 23729
vv i v vivv i vv vvv i
RMER15#LTR/ER 196 CTGAGACCAGACCAGCTGCCTGGAAGAAGCAGAAAC 231
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 36.43
Transitions / transversions = 0.85 (28/33)
Gap_init rate = 0.10 (23 / 224), avg. gap size = 1.26 (29 / 23)
522 27.94 10.98 5.99 UnnamedSequence 23573 23827 23769 + RMER15 LTR/ERVL 155 421 154
522 27.94 10.98 5.99 UnnamedSequence 23573 23827 (23769) RMER15#LTR/ERVL 155 421 (154) m_b1s501i18
UnnamedSequen 23573 CTAAAAGTC-----CAGGAAAACCTAAGCTT---ACAAGACTCATGAGGC 23614
i i ----- iv i -i v--- v - i
RMER15#LTR/ER 155 CTGAGAGTCACTCTCAGACAAGCC-GAGCTGCAAAGAAGACTC-TGAGAC 202
UnnamedSequen 23615 CTCACCCAAGGTTA--TAGAAGATGT------CAAC--AATTGCTGGGGA 23654
vv ---i i i-- i v i------ i -- ii iv i
RMER15#LTR/ER 203 CAGACC---AGCTGCCTGGAAGAAGCAGAAACCAGCCGAGCTGCCTGGAA 249
UnnamedSequen 23655 GCGAGACTCCTGGACTGACCAAGCTGCCTAGA---GGCAGCTCTCTGATC 23701
-- ii -- i ii ii ?ii i --- i - ii i
RMER15#LTR/ER 250 G--AGGTT--TAGACCAACTGAGNCACCTGGAAAGGACA-CTCTCCAACC 294
UnnamedSequen 23702 TGTTGTGCTACCTTCAAGTCC--CAG-GAACTTCAGGGTTACAGCTT--- 23745
v i v i iiv-- - vi i v iv ---
RMER15#LTR/ER 295 TGTTGAGCTGCCTGCAGGCTGTGCAGTGTGCTCCAGGTTCCCAGCTTTTG 344
UnnamedSequen 23746 -GAGTCATCACCCACACTGAGATAGGCTCTTTGGTGATGCAGCTGCCTTT 23794
- iii ii i i i -- i
RMER15#LTR/ER 345 TGAGCTGTCACCCATGCTGGGGTGGGCT--TTGGTGATGCAGCTGTCTTT 392
UnnamedSequen 23795 GAGTCATCCATGGACTCCCCTGCTTGCAACCCC 23827
iiv ---- i ivv i
RMER15#LTR/ER 393 GAGTCATTTCTG----CTCCTGTAAGTAACCCC 421
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 37.10
Transitions / transversions = 3.19 (51/16)
Gap_init rate = 0.10 (26 / 254), avg. gap size = 1.69 (44 / 26)
+ 897 24.0 3.2 3.6 UnnamedSequence 23845 24030 (26534) + RMER15-int LTR/ERVL 680 865 (4134) 52
ANNOTATION EVIDENCE:
897 23.97 3.25 3.62 UnnamedSequence 23845 24030 23960 + RMER15-int LTR/ERVL 680 865 4134
897 23.97 3.25 3.62 UnnamedSequence 23845 24030 (23960) RMER15-int#LTR/ERVL 680 865 (4134) m_b1s701i0
UnnamedSequen 23845 CAAGTTAAAACTGTGCTCAAAAATGCCCTTCTTGG-ATCTAAACACTTGG 23893
i i v v i -- i - i v
RMER15-int#LT 680 CAAATTAGATCTGTGCTAAAGA--GCCCTTCCTGGGATCCAAAAACTTGG 727
UnnamedSequen 23894 TACC--TGTGAAAGGCCAAATATTGAGAACAAATAGAGCAAGATG---AA 23938
v -- v iiii ii ? v i vi --- v ---
RMER15-int#LT 728 AACCCATGGGAAGAATCGGANAGTGAGGAAGAA---AGAAAGATGGTAAA 774
UnnamedSequen 23939 AGTGATCAAAGATACCCATCAGGTACAACCTTTCATACAGAAGAGAAAAA 23988
i vi v v i v ? i -- iii
RMER15-int#LT 775 AGCGATAGAAGATACCCCTCAGGTCCGACCTTTAATANAGAGGA--AGGG 822
UnnamedSequen 23989 AAAATCCATGCTT-AACATAGAGATGGGGGCTTTCATAATGGC 24030
i v - i iv i i v i
RMER15-int#LT 823 AAAATCCGTGATTCAGCATGCAGACGGGGGCCTTAACAATGGC 865
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.72
Transitions / transversions = 1.73 (26/15)
Gap_init rate = 0.06 (11 / 185), avg. gap size = 1.27 (14 / 11)
+ 3612 3.8 0.2 0.0 UnnamedSequence 24031 24425 (26139) + MTA_Mm LTR/ERVL-MaLR 1 396 (0) 53
ANNOTATION EVIDENCE:
3612 3.80 0.25 0.00 UnnamedSequence 24031 24425 24470 + MTA_Mm LTR/ERVL-MaLR 1 396 0
3612 3.80 0.25 0.00 UnnamedSequence 24031 24425 (24470) MTA_Mm#LTR/ERVL-MaLR 1 396 (0) c_b1s401i2
UnnamedSequen 24031 TGTACTGGCTAGTTTTGTGTCAACTTGACATAGCTGGAGTTATCACAGAG 24080
i
MTA_Mm#LTR/ER 1 TGTACTGGCTAGTTTTGTGTCAACTTGACACAGCTGGAGTTATCACAGAG 50
UnnamedSequen 24081 AAAGGAGCTTCAGTTGAAGAAATACCTCCATGAGATACAACTGTAAGGCA 24130
i i v
MTA_Mm#LTR/ER 51 AAAGGAGCTTCAGTTGAGGAAATGCCTCCATGAGATCCAACTGTAAGGCA 100
UnnamedSequen 24131 TTTTCTCAATTAGTGATCAAGGGGGAAAGGTCCCTTGTGGGTGGGACTAT 24180
i i
MTA_Mm#LTR/ER 101 TTTTCTCAATTAGTGATCAAGGGGGAAAGGCCCCTTGTGGGTGGGACCAT 150
UnnamedSequen 24181 CTCTGGCATGGTAGTCTTGGGTTCTATAAGAGAGCAGGCTGAGCAAGCCA 24230
vv
MTA_Mm#LTR/ER 151 CTCTGGGCTGGTAGTCTTGGGTTCTATAAGAGAGCAGGCTGAGCAAGCCA 200
UnnamedSequen 24231 GGGGAGGCAAGCCAGTAAAGAACATTCCTCCATGGCTTCTGCATCAGCTC 24280
i i
MTA_Mm#LTR/ER 201 GGGGAGGCAAGCCAGTAAAGAACATCCCTCCATGGCCTCTGCATCAGCTC 250
UnnamedSequen 24281 CTGCTCCCTGACCTGCTTGAGTTCCAGTCCTGACTTCC-TTGGTGATGAA 24329
i -
MTA_Mm#LTR/ER 251 CTGCTTCCTGACCTGCTTGAGTTCCAGTCCTGACTTCCTTTGGTGATGAA 300
UnnamedSequen 24330 CAGCAGCATGGAAGTGTAAGCCAAATAAATCCTTTCCTCCCCAACTTACT 24379
i i i i
MTA_Mm#LTR/ER 301 CAGCAGTATGGAAGTGTAAGCCGAATAAACCCTTTCCTCCCCAACTTGCT 350
UnnamedSequen 24380 TCTTGGTCATGATGTTTGTGCAGGAATAGAAACCCTGACTAAGACA 24425
MTA_Mm#LTR/ER 351 TCTTGGTCATGATGTTTGTGCAGGAATAGAAACCCTGACTAAGACA 396
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 3.68
Transitions / transversions = 4.00 (12/3)
Gap_init rate = 0.00 (1 / 394), avg. gap size = 1.00 (1 / 1)
+ 1519 27.2 17.0 2.3 UnnamedSequence 24426 25084 (25480) + RMER15-int LTR/ERVL 866 1619 (3380) 52
ANNOTATION EVIDENCE:
897 23.97 3.25 3.62 UnnamedSequence 24426 24515 23475 + RMER15-int LTR/ERVL 866 954 4045
897 23.97 3.25 3.62 UnnamedSequence 24426 24515 (23475) RMER15-int#LTR/ERVL 866 954 (4045) m_b1s701i0
UnnamedSequen 24426 ATGGCTCTAAGAAATCATGGGAATCCAGGAGTACTTAGTACTTGAACTGT 24475
vv -- vi i ii v vi i i? i i i
RMER15-int#LT 866 CAG--TACAGGAAACTATGGTAATCAGGGAATACTCNGCACCTGAACTGC 913
UnnamedSequen 24476 TTGAATTAGGACAAAACAC--AAAAGAACAATGAAAGAGCCT 24515
? i i- i vi-- vi i
RMER15-int#LT 914 TNGAATTGGGG-AAGACTTTTAAACAAGCAATGAAAGAGCCT 954
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 27.72
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.25 (5 / 4)
1519 27.66 9.31 2.13 UnnamedSequence 24516 25084 22906 + RMER15-int LTR/ERVL 1011 1619 3380
1519 27.66 9.31 2.13 UnnamedSequence 24516 25084 (22906) RMER15-int#LTR/ERVL 1011 1619 (3380) m_b1s701i1
UnnamedSequen 24516 GTGCTGC--AAGTGGAGGGAC--AATAATGTAACCATCCATCCCTTCATA 24561
i-- ii ii -- i i i i i v i
RMER15-int#LT 1011 GTGCTGTGGAAGCAGAGAAACTGAGTAATATAACTACCCATCCCTCCTTG 1060
UnnamedSequen 24562 GGACACAGAAGGCATAACCTGTAGCAACCTGAAGGAAACCAGCCCCTGAT 24611
i v ivv vi ivi i i i
RMER15-int#LT 1061 AGACAAAGGCTGCATAACCTGAGGCAATACGAGGGAAATCAGTCCCTGAT 1110
UnnamedSequen 24612 T--CTGGTTC----------------------TGTTATCAC-ATCTGACA 24636
v-- i ----------------------v i -iv vi
RMER15-int#LT 1111 GGACTGGCTCATANGAGCCATTAGGGACACTTGGTTATCGCCGGCTGAGG 1160
UnnamedSequen 24637 TCCCTCCATCTCCGAATGTCAAAAACTAGAAAACAAGAGAGAAAGAGCAG 24686
-- ---- i iii i i v i ii
RMER15-int#LT 1161 TCCC--CAT----GAATATCAGGGACTGGAAGACAATAGAGGAAGGACAG 1204
UnnamedSequen 24687 ACAG-ACAGCAGGAATTAG-CATGAGACTGGCAATGCTGTGTGCATATTT 24734
i iv- v vi i i -? vv ii i vvi vi v
RMER15-int#LT 1205 GCGTTACTGAGGGAACTGGGNATGAGAGAGGCGGTGTTTGATGCCCAGTT 1254
UnnamedSequen 24735 CACTGGGTCGAATGAGACT-TATT---AAGAAACTGATGCATTTGGAGAT 24780
i i ii ii - i --- i i v v v v ---i i
RMER15-int#LT 1255 CACCGGGCCAGATAGGACTGTGTTCACAGGAGAGTTAAGGA---AGAGGT 1301
UnnamedSequen 24781 TGTATTCA--------TTCAGGACTGGTATAAGGCTTAGTTGGCTTTGCT 24822
- --------i i ii viv
RMER15-int#LT 1302 TG-ATTCAGCAGGGACCTCGGGACTGGTATGGGGCTTTAGTGGCTTTGCT 1350
UnnamedSequen 24823 GAGTCCCATGATATGACAAG--CTCTATAAGGTATGAGAGGCTTTGGCAG 24870
i i i iv i? -- i i v
RMER15-int#LT 1351 GAGCCCCGTGGTGGGACGNGATCTTTATGAGGTAGGAGAGGCTTTGGCAG 1400
UnnamedSequen 24871 ACCCGAATTAACTAGATACACATATAAATTGAATTCATATAAAGTATTGA 24920
i i i v vi ivvi i i ?i i -- ii?i
RMER15-int#LT 1401 ATCTGAGTGACTTAGACCGGCATGTAAATCGNGTTCGTA--AAGTGCNAA 1448
UnnamedSequen 24921 AGCA---CAGAGAAGATGAGAGAAAAAGACAGCAGACAGTGGATCCCTGT 24967
---? ii i iiiv v ?- vi vvi
RMER15-int#LT 1449 AGCAATCNAGAGGGGATGAGAAAAGGGCAAAGCAGAN-GAAGAGGTCTGT 1497
UnnamedSequen 24968 CTGTGTTACTCAGAAACAA-----GCAAGATTGGCGCTGAGCTTGAGTCT 25012
i v i ii ii ----- v i ii iv ii
RMER15-int#LT 1498 CCGGGTCACTCGAAGGCAAATGTGGCAAGATTTGTGTCGAGCCGGAGTTC 1547
UnnamedSequen 25013 CCAGGGAAAGAATTGATAGAAAGTCAAAGTCCATGCCCATGAGGCTCTAG 25062
i i? i i v? ii ivi vi i
RMER15-int#LT 1548 CTAGGGAAAANATTGACAGAAAGCCAAATNCTGTGCTAGTGAGCTTCTGG 1597
UnnamedSequen 25063 AAGGCTTTACAGCCAGACTAGC 25084
v v v?
RMER15-int#LT 1598 AAGGCTTTAAAGCCTGAGNAGC 1619
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 32.68
Transitions / transversions = 2.35 (108/46)
Gap_init rate = 0.05 (26 / 568), avg. gap size = 2.54 (66 / 26)
+ 248 28.6 2.0 3.0 UnnamedSequence 25899 25999 (24565) + MER63D DNA/hAT-Tip100 5 104 (957) 54
ANNOTATION EVIDENCE:
248 28.58 1.98 3.00 UnnamedSequence 25899 25999 21991 + MER63D DNA/hAT-Tip100 5 104 957
248 28.58 1.98 3.00 UnnamedSequence 25899 25999 (21991) MER63D#DNA/hAT-Tip100 5 104 (957) m_b1s501i19
UnnamedSequen 25899 GGTACGCTGGAACAAACACAAACCATATAGTGAGATCCAAATGTTAAATT 25948
ii i vii v iv ivv v i v i v
MER63D#DNA/hA 5 GGTGTGCTGGAGCCGGCTCGTACCGGCTCGCGAGAGCCGATTGTTAAATT 54
UnnamedSequen 25949 T--AAGAACTGTTTCCAGCCAGTTGTTCAGACACATAGATTATATTAAAG 25996
-- i i - v v i - i vvv - v i
MER63D#DNA/hA 55 TTCAGGAATT-TTGCGAGCCGGTTGTT-AAACACAGCCATTAT-TAAAAA 101
UnnamedSequen 25997 TTA 25999
MER63D#DNA/hA 102 TTA 104
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 27.58
Transitions / transversions = 1.00 (14/14)
Gap_init rate = 0.04 (4 / 100), avg. gap size = 1.25 (5 / 4)
+ 1374 10.4 0.5 1.1 UnnamedSequence 26008 26192 (24372) + B2_Mm1t SINE/B2 1 184 (9) 55
ANNOTATION EVIDENCE:
1374 10.38 0.54 1.09 UnnamedSequence 26008 26192 23542 + B2_Mm1t SINE/B2 1 184 9
1374 10.38 0.54 1.09 UnnamedSequence 26008 26192 (23542) B2_Mm1t#SINE/B2 1 184 (9) c_b1s355i4
UnnamedSequen 26008 GGGGCTGGAGAGATCGCTCAGTGGATAAGAGCACT-GACTGCTCTTCTGA 26056
v v i i i- i
B2_Mm1t#SINE/ 1 GGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACCCGACTGCTCTTCCGA 50
UnnamedSequen 26057 AGATCCCGAGTTCAAATCCCAGCAACCACATGGTGGTTCACAACTATCTG 26106
i ? i i i
B2_Mm1t#SINE/ 51 AGGTCCNGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 100
UnnamedSequen 26107 CAGTGAGATCTCATGCCCTCTTCTGGTGTGTCTGAAGACAGCCACAGTGT 26156
i ii v i i
B2_Mm1t#SINE/ 101 TAACGAGATCTGACGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGT 150
UnnamedSequen 26157 ACTTACCTATAATAAATAAATAAAGACATTTAAAAA 26192
v -- iv
B2_Mm1t#SINE/ 151 ACTTACATATAATAAATAAATAA--ATCTTTAAAAA 184
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 8.48
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.02 (3 / 184), avg. gap size = 1.00 (3 / 3)
+ 476 17.4 1.2 0.0 UnnamedSequence 26227 26312 (24252) C B1_Mur3 SINE/Alu (1) 148 62 56
ANNOTATION EVIDENCE:
476 17.44 1.16 0.00 UnnamedSequence 26227 26312 21862 C B1_Mur3 SINE/Alu 62 148 1
476 17.44 1.16 0.00 UnnamedSequence 26227 26312 (21862) C B1_Mur3#SINE/Alu (1) 148 62 m_b1s501i21
UnnamedSequen 26227 TTTGTTTTTCT-AGACAGTGTTTCTCTGTCCAGGATTGGCTGTCCTGGAA 26275
i - v vi vvi
C B1_Mur3#SINE/ 148 TTTGTTTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAA 99
UnnamedSequen 26276 CTTGCTCTGTAAAGCAGGCTGGTCTCAAGCGCATAGA 26312
i i v i i i v i
C B1_Mur3#SINE/ 98 CTCGCTCTGTAGACCAGGCTGGCCTCGAACTCACAGA 62
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 17.30
Transitions / transversions = 1.50 (9/6)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1)
+ 31 21.6 2.1 3.2 UnnamedSequence 26331 26426 (24138) + A-rich Low_complexity 1 95 (0) 57
ANNOTATION EVIDENCE:
31 21.63 2.08 3.16 UnnamedSequence 26331 26426 21748 + (AAAGAAA)n Simple_repeat 1 95 0
31 21.63 2.08 3.16 UnnamedSequence 26331 26426 (21748) (AAAGAAA)n#Simple_repeat 1 95 (0) m_b1s252i8
UnnamedSequen 26331 AAAGAAAAAGGAAAAAAGAAAAGAGAAAAGAGGAAAAAAAAACTAAATAA 26380
i i - i i -v v
(AAAGAAA)n#Si 1 AAAGAAAAAAGAAAAAAGAAAAAAGAAAA-AAGAAAAAAGAA-AAAAGAA 48
UnnamedSequen 26381 AAATAAATATAAGAGTAAAGTAAACA-ACAACA-AAACAATAAAAAAG 26426
- i v v iv v v - v v - v v
(AAAGAAA)n#Si 49 AAA-AGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAG 95
Matrix = Unknown
Transitions / transversions = 0.55 (6/11)
Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5)
+ 5039 19.5 9.8 3.0 UnnamedSequence 26433 27699 (22865) C Lx6 LINE/L1 (465) 7231 5914 58
ANNOTATION EVIDENCE:
1622 19.10 18.59 0.00 UnnamedSequence 26433 26830 21344 C Lx7_3end LINE/L1 1174 1645 465
1622 19.10 18.59 0.00 UnnamedSequence 26433 26830 (21344) C Lx7_3end#LINE/L1 (465) 1645 1174 m_b1s551i29
UnnamedSequen 26433 CCTTTGGAGGAAATTAAGCTTCCATTTGCAAGTGTTTATCAGTTGGAAGT 26482
? i i ?i i ? i i v i ii
C Lx7_3end#LINE 1645 CCNTTGGAGAAAACTAANTTTTCNTTTGCGAGCGGTTATCAATTGGAGAT 1596
UnnamedSequen 26483 TGCTTCTGGCTTAGGAATGAGG-CACATGTCCACT-ATTCCTTTCGACTT 26530
v v i i - vii -vi i ii vi
C Lx7_3end#LINE 1595 AGCTTCTGGGTTAGGGATGGGGGCTTGTGTCCACTTCCTCCTCTCAGCGC 1546
UnnamedSequen 26531 CAGGACCCCATCTG--------------------GTGCACACTGCCTCAG 26560
ii -------------------- ii v
C Lx7_3end#LINE 1545 TGGGACCCCATCTGTGCAGACCCGTGCAGGCCCTGTGCATGCTGCCACAG 1496
UnnamedSequen 26561 TCTCTGGGATTT------------GGTTATGCTG-GTTTAGAGGACCCTG 26597
v v ------------ iv i - i i i i
C Lx7_3end#LINE 1495 TCTCTGTGAGTTCATATGTGCGTCGGTCCTGTTGTGTCTAGAAGGCCTTG 1446
UnnamedSequen 26598 TTTTCTTGGTGTCCATCACCCACTCTGGCTCTTACACTCTTTATGCCTCC 26647
i vi i v ? v
C Lx7_3end#LINE 1445 TTTCCTTGGTGTCCTCCATCCCCTCTGGCTCTTACANTCTTTCTGCCTCC 1396
UnnamedSequen 26648 TCTTCCTCCTACTTACATGACCTCTGAGGGAAGAGATTTGATAAAGATAT 26697
v vv v v v v i i i ii i
C Lx7_3end#LINE 1395 TCTTCCGCAGAGTTCCCTGAGCCCTGAGGGGAGGGATTTGATGGAGACAT 1346
UnnamedSequen 26698 CCCATTTAGG---GA----TCCAAGATCCCTCACTCTGTGT-TA-TGCTT 26738
--- ---- i i v i-i - iii
C Lx7_3end#LINE 1345 CCCATTTAGGACTGAGTGTTCCAAGGTCTCTCACTCTCTGCACATTGTCC 1296
UnnamedSequen 26739 GTCTGTGGTTCTCTGTATTTATTCCCATCTGCTACAGGAGGAAGATTCTA 26788
v v i i v v
C Lx7_3end#LINE 1295 GGCTGTGGGTCTCTGTATTTGTTCCCATCTGCTGCAGGAGGAAGCTTCTC 1246
UnnamedSequen 26789 ------------------------------GAGTATAACAGAATGTCACT 26808
------------------------------ i i
C Lx7_3end#LINE 1245 TGATGATGGCTGAGCAAGGCACTGATCTATGAGTATAGCAGAATGTCATT 1196
UnnamedSequen 26809 AGAAGTCATTTTATTGTTACAT 26830
i i i
C Lx7_3end#LINE 1195 AGGAGTCATTTTATTGCTACGT 1174
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 21.52
Transitions / transversions = 2.04 (51/25)
Gap_init rate = 0.03 (10 / 397), avg. gap size = 7.40 (74 / 10)
5039 19.73 5.80 4.36 UnnamedSequence 26545 27699 20475 C Lx6_3end LINE/L1 328 1498 376
5039 19.73 5.80 4.36 UnnamedSequence 26545 27699 (20475) C Lx6_3end#LINE/L1 (376) 1498 328 m_b1s551i30
UnnamedSequen 26545 GTGCACACTGCCTCAGTCTCTGGGA------------TTTGGTTATGCTG 26582
vii i v ------------i v i - i
C Lx6_3end#LINE 1498 GTGCTTGCTGCTTCAGTCTCTGTGAGTTCATATGAGCCTTGCTCA-GTTG 1450
UnnamedSequen 26583 GTTTAGAGGACCCTGTTTTCTTGGTGTCCATCACCCACTCTGGCTCTTAC 26632
i i i i i i vi i v
C Lx6_3end#LINE 1449 ATTCAGAGGGCCTTGTTCTCCTGGTGTCCTCCATCCCCTCTGGCTCTTAC 1400
UnnamedSequen 26633 ACTCTTTATGCCTCCTCTTCCTCCTACTTACATGACCTCTGAGGGAAGAG 26682
? vi v vviv v v v i i
C Lx6_3end#LINE 1399 ANTCTTTCCGCCTCCTCTTCCGCGGGGTTCCCTGAGCTCTGAGGGGAGGG 1350
UnnamedSequen 26683 ATTTGATAAAGATATCCCATTTAGGGAT-------CCAAGATCCCTCA-C 26724
ii i v ------- i i -
C Lx6_3end#LINE 1349 ATTTGATGGAGACATCCCATTTAGGGCTGAGTGTTCCAAGGTCTCTCATC 1300
UnnamedSequen 26725 TCTGTGTTATGCTTGTCTGTGGTTCTCTGTATTTATTCCCATCTGCTACA 26774
ii v ii v v i i i
C Lx6_3end#LINE 1299 TCTGCATAATGTCTGGCTGTGGGTCTCTGTATCTGTTCCCATCTGCTGCA 1250
UnnamedSequen 26775 GGAGGAAG-----------AT------------------TCTA-GAGTAT 26794
----------- ------------------ -
C Lx6_3end#LINE 1249 GGAGGAAGCCTCTCTGATGATGGCTGAACAAGGCACTGATCTATGAGTAT 1200
UnnamedSequen 26795 AACAGAATGTCACTAGAAGTCATTTTATTGTTACATATGATTCTCTCTCT 26844
i i i i i i ----------------
C Lx6_3end#LINE 1199 AGCAGAATATCATTAGGAGTCATTTTATCGCTAC---------------- 1166
UnnamedSequen 26845 CTCTTTCTCTCTCTCTCCTCCATTTTTTTAAAGAACAGTAGTATTTGGTT 26894
--- i -------------- ? -- v
C Lx6_3end#LINE 1165 ---TTTTT--------------TNTTTTTA--GACCAGTAGTATTTGGTT 1135
UnnamedSequen 26895 TTACCCAGGATCCCTGGGCTATGTAGTCTATGGTTCTTG-TCAGCTAAGC 26943
vi i i v v - v i
C Lx6_3end#LINE 1134 TTACCCTAGGTCTCTGGGCTATCTAGTCTCTGGTTCTTGGTCACCCAAGC 1085
UnnamedSequen 26944 AGTGTTGAGTATGGATTGCATCTCATGGGGTGAGGGTTTAGTTAAGCTAG 26993
i i i v i i i vv v i iii
C Lx6_3end#LINE 1084 AGTGTCGGGTATGGGTTCCATCTCGTGGAGTGGGCCTTAAGTCAAATCAG 1035
UnnamedSequen 26994 ATATTGGTTGGTTACTCCCACAAATTTTGTGCCACCATTGCATTTATGTA 27043
i i ii vi viii
C Lx6_3end#LINE 1034 ACATTGGTTGGCTACTCCCACAAGCTTTGTGCCACCATTGCCCTAGCATA 985
UnnamedSequen 27044 TCTTACAGGCAGAACATCATTGTAAATCAAAGATGTTGTGACTGGATTGG 27093
i i ?? ii i v i i
C Lx6_3end#LINE 984 TCTTGCAGGCAGGACANNATTGTAGGTCAAAGGTTTTGTGGCTGGGTTGG 935
UnnamedSequen 27094 TGCTTATGTTTCTCCTTTGGTAGTGTGAAGAGAACCTTCCTGTACCAAAG 27143
i i i iv v v i
C Lx6_3end#LINE 934 TGTTTACGTTTCTCTTTTGGTAGCCTGCAGAGTACCTTCCCGTACCAAAG 885
UnnamedSequen 27144 ACACTAGCACATATGCGTGAAGGTTCTATGTAGGTTCCAGCTTGACCTTT 27193
? v i v v i i iv i i i
C Lx6_3end#LINE 884 ANACTAGAACGTAGGGGTGAAGGCTCCATGTAGGCACCAGCTCGACTTCT 835
UnnamedSequen 27194 CTATGTTCGATGAGTTGTATATGTGTTGTCTTCAGCAATAGGGCTCTG-T 27242
i i i iv i ii -
C Lx6_3end#LINE 834 CCATGTTCAATGAGTTGTGTGGGTGTTGTCTTCAGCAATGGGGCCTTGCT 785
UnnamedSequen 27243 CTCATTTTGTGGAGAAGAAAGTATAATCTTGGCAACAGCCTGG---GTTT 27289
v v i iv vv vi ---
C Lx6_3end#LINE 784 GTCAGTTTGCGGAGAGCAACCTATTGTCTTGGCAACAGCCTGGGTTGTTT 735
UnnamedSequen 27290 GAGGATTCCCATAGGACCTCTTTGGACAATAACTCAATTAGATGTAACCC 27339
i i i i v i i
C Lx6_3end#LINE 734 GGGGATTTCCATGGGACCCCTTTGGCCAACAACTCAATTGGATGTAACCC 685
UnnamedSequen 27340 AGTCTTGGTCCTGGAAGCTTCATTTGGTGACAAAATATGGCTAGTTGGGG 27389
ii ?iv i i i v i i
C Lx6_3end#LINE 684 AGTCCCGNCACTGGAAGCTTCGTTTGGCGACAAGAGATGGCCAGTTGGGA 635
UnnamedSequen 27390 CTCTGTCTTCCCCAATTATTTGGTGGTTTCATTTATATCACCTTGGTATG 27439
i ? i - ? v ?i viv i vi i
C Lx6_3end#LINE 634 CTCCGTNTCCCCC-ATTATTNGGAGNCTTCATTAGGATCGCCTTCATATA 586
UnnamedSequen 27440 TGTGCATATTTTAGAAACCATCTACTATATTGTGTTTCTATACTATCCCT 27489
---- v i viv i ii i iv i i i
C Lx6_3end#LINE 585 T----AGATTTTAGGAAGTTTCCACTGCACTAGGTTTCCATACCACCCCT 540
UnnamedSequen 27490 CCGATGGCCCTTAATTTTAGCTGTCTTTTCCCATATTCCCTCCCTCTTCC 27539
vi v i ii i i ii i iv
C Lx6_3end#LINE 539 CAAATGCCCCTCAATTCCAGCTGTCTCTCCCCGCATTCTCTCCCTCCACC 490
UnnamedSequen 27540 CCATCTC-----CACTTGATCC-TCTCATTCCAG---CCA--TACCCCCA 27578
- ----- i - i i v --- --ii
C Lx6_3end#LINE 489 CC-TCTCCCCNTCACCTGATCCTTCCCGTTCCCGTCCCCACCCGCCCCCA 441
UnnamedSequen 27579 -TCCATCCATAACTATCTATTCTACCTCCCTTTCCTAGGGAAAGCTATCT 27627
- i i v- ii i i i v -----
C Lx6_3end#LINE 440 GTCCACCCGTAAA-ATCTATTCTATTTCCCCTTCCCAGGGAGATC----- 397
UnnamedSequen 27628 GACATGCCTCCCCTGATACACAGTCCCTTTATCTAAACTCTGTGGTTCTG 27677
-- v iv v? - vv i ? i v v v i
C Lx6_3end#LINE 396 --CATGCGTCCCCCTAGNC-CCTTCTCTNTACCTAACCTCTCTGGGTCTA 350
UnnamedSequen 27678 TGAATTGTAGTTTGGTTGTTAT 27699
i i i i i
C Lx6_3end#LINE 349 CGGATTGTAGCTTGGTTATCAT 328
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 21.53
Transitions / transversions = 2.21 (150/68)
Gap_init rate = 0.06 (65 / 1154), avg. gap size = 1.82 (118 / 65)
+ 1840 10.8 10.7 3.5 UnnamedSequence 27708 28025 (22539) + MTC LTR/ERVL-MaLR 12 351 (70) 59
ANNOTATION EVIDENCE:
1840 10.76 10.69 3.53 UnnamedSequence 27708 28025 20149 + MTC LTR/ERVL-MaLR 12 351 70
1840 10.76 10.69 3.53 UnnamedSequence 27708 28025 (20149) MTC#LTR/ERVL-MaLR 12 351 (70) m_b1s501i22
UnnamedSequen 27708 GTCTTATGTCATTTTGACACAAGC------------------------CT 27733
i vi ------------------------
MTC#LTR/ERVL- 12 GTTTTATGTCAACTTGACACAAGCTAGAGTCATCTGAGAGGAGGGAACCT 61
UnnamedSequen 27734 CAATTAAGAAAATGCCTCCATAGGATCGGGCTGTAGTCAGTCCCATTGTC 27783
i i v iv --- v
MTC#LTR/ERVL- 62 CAATTGAGAAAATGCCTCCATAAGATCGGGCTGTAGGCAAGCC---TGTA 108
UnnamedSequen 27784 AGGTATTTTCTTATTTAGTAATTGATG--------CCCCCTACAAGGTCA 27825
i i v i -------- ------ vi
MTC#LTR/ERVL- 109 GGGCATTTTCTTAATTAGTGATTGATGGGGGAGGGCCC------AGCCCA 152
UnnamedSequen 27826 TTTGTGTGGGTGGTGCCATCCCTGGCCATATGGTCCTGGGTTCTATAAGA 27875
--- v vvi
MTC#LTR/ERVL- 153 TT---GTGGGTGGTGCCATCCCTGGGCTGGTGGTCCTGGGTTCTATAAGA 199
UnnamedSequen 27876 AAGCAGACTGAACAAGCCATGGGGAGCAAGCCAGTAAGCAGCA-CTCTCC 27924
i i - i
MTC#LTR/ERVL- 200 AAGCAGGCTGAGCAAGCCATGGGGAGCAAGCCAGTAAGCAGCACCCCTCC 249
UnnamedSequen 27925 ATGGCTTCTATATCAGCTCCTGCCTCCAGGTTTCTGCCCTGCTTGAGTTC 27974
i ii i i
MTC#LTR/ERVL- 250 ATGGCCTCTGCATCAGCTCCTGCCTCCAGGTTCCTGCCCTGTTTGAGTTC 299
UnnamedSequen 27975 CT-CCCTGACTTCTTTTGATAATGAACAGTGATATGGAAGTGTAAGCCGA 28023
-i i i i ? i i
MTC#LTR/ERVL- 300 CTGTCCTGACTTCCTTCGATGATGAACNGTGATGTGGAAGTGTAAGCCAA 349
UnnamedSequen 28024 AT 28025
MTC#LTR/ERVL- 350 AT 351
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 11.50
Transitions / transversions = 2.67 (24/9)
Gap_init rate = 0.05 (16 / 317), avg. gap size = 2.88 (46 / 16)
+ 1374 10.4 0.5 1.1 UnnamedSequence 28138 28322 (22242) + B2_Mm1t SINE/B2 1 184 (9) 60
ANNOTATION EVIDENCE:
1374 10.38 0.54 1.09 UnnamedSequence 28138 28322 21412 + B2_Mm1t SINE/B2 1 184 9
1374 10.38 0.54 1.09 UnnamedSequence 28138 28322 (21412) B2_Mm1t#SINE/B2 1 184 (9) c_b1s355i5
UnnamedSequen 28138 GGGGCTGGAGAGATCGCTCAGTGGATAAGAGCACT-GACTGCTCTTCTGA 28186
v v i i i- i
B2_Mm1t#SINE/ 1 GGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACCCGACTGCTCTTCCGA 50
UnnamedSequen 28187 AGATCCCGAGTTCAAATCCCAGCAACCACATGGTGGTTCACAACTATCTG 28236
i ? i i i
B2_Mm1t#SINE/ 51 AGGTCCNGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 100
UnnamedSequen 28237 CAGTGAGATCTCATGCCCTCTTCTGGTGTGTCTGAAGACAGCCACAGTGT 28286
i ii v i i
B2_Mm1t#SINE/ 101 TAACGAGATCTGACGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGT 150
UnnamedSequen 28287 ACTTACCTATAATAAATAAATAAAGACATTTAAAAA 28322
v -- iv
B2_Mm1t#SINE/ 151 ACTTACATATAATAAATAAATAA--ATCTTTAAAAA 184
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 8.48
Transitions / transversions = 2.80 (14/5)
Gap_init rate = 0.02 (3 / 184), avg. gap size = 1.00 (3 / 3)
+ 476 17.4 1.2 0.0 UnnamedSequence 28357 28442 (22122) C B1_Mur3 SINE/Alu (1) 148 62 61
ANNOTATION EVIDENCE:
476 17.44 1.16 0.00 UnnamedSequence 28357 28442 19916 C B1_Mur3 SINE/Alu 62 148 1
476 17.44 1.16 0.00 UnnamedSequence 28357 28442 (19916) C B1_Mur3#SINE/Alu (1) 148 62 m_b1s501i24
UnnamedSequen 28357 TTTGTTTTTCT-AGACAGTGTTTCTCTGTCCAGGATTGGCTGTCCTGGAA 28405
i - v vi vvi
C B1_Mur3#SINE/ 148 TTTGTTTTTTTGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAA 99
UnnamedSequen 28406 CTTGCTCTGTAAAGCAGGCTGGTCTCAAGCGCATAGA 28442
i i v i i i v i
C B1_Mur3#SINE/ 98 CTCGCTCTGTAGACCAGGCTGGCCTCGAACTCACAGA 62
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 17.30
Transitions / transversions = 1.50 (9/6)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1)
+ 31 21.6 2.1 3.2 UnnamedSequence 28461 28556 (22008) + A-rich Low_complexity 1 95 (0) 62
ANNOTATION EVIDENCE:
31 21.63 2.08 3.16 UnnamedSequence 28461 28556 19802 + (AAAGAAA)n Simple_repeat 1 95 0
31 21.63 2.08 3.16 UnnamedSequence 28461 28556 (19802) (AAAGAAA)n#Simple_repeat 1 95 (0) m_b1s252i11
UnnamedSequen 28461 AAAGAAAAAGGAAAAAAGAAAAGAGAAAAGAGGAAAAAAAAACTAAATAA 28510
i i - i i -v v
(AAAGAAA)n#Si 1 AAAGAAAAAAGAAAAAAGAAAAAAGAAAA-AAGAAAAAAGAA-AAAAGAA 48
UnnamedSequen 28511 AAATAAATATAAGAGTAAAGTAAACA-ACAACA-AAACAATAAAAAAG 28556
- i v v iv v v - v v - v v
(AAAGAAA)n#Si 49 AAA-AGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAG 95
Matrix = Unknown
Transitions / transversions = 0.55 (6/11)
Gap_init rate = 0.05 (5 / 95), avg. gap size = 1.00 (5 / 5)
+ 5029 19.7 9.8 3.0 UnnamedSequence 28563 29829 (20735) C Lx6 LINE/L1 (465) 7231 5914 63
ANNOTATION EVIDENCE:
1584 19.35 18.59 0.00 UnnamedSequence 28563 28960 19398 C Lx7_3end LINE/L1 1174 1645 465
1584 19.35 18.59 0.00 UnnamedSequence 28563 28960 (19398) C Lx7_3end#LINE/L1 (465) 1645 1174 m_b1s551i31
UnnamedSequen 28563 CCTTTGGAGGAAATTAAGCTTCCATTTGCAAGTGTTTATCAGTTGGAAGT 28612
? i i ?i i ? i i v i ii
C Lx7_3end#LINE 1645 CCNTTGGAGAAAACTAANTTTTCNTTTGCGAGCGGTTATCAATTGGAGAT 1596
UnnamedSequen 28613 TGCTTCTGGCTTAGGAATGAGG-CACATGGCCACT-ATTCCTTTCGACTT 28660
v v i i - vii v -vi i ii vi
C Lx7_3end#LINE 1595 AGCTTCTGGGTTAGGGATGGGGGCTTGTGTCCACTTCCTCCTCTCAGCGC 1546
UnnamedSequen 28661 CAGGACCCCATCTG--------------------GTGCACACTGCCTCAG 28690
ii -------------------- ii v
C Lx7_3end#LINE 1545 TGGGACCCCATCTGTGCAGACCCGTGCAGGCCCTGTGCATGCTGCCACAG 1496
UnnamedSequen 28691 TCTCTG-----------G-GCTTTGGTTATGCTG-GTTTAGAGGACCCTG 28727
----------- - v i iv i - i i i i
C Lx7_3end#LINE 1495 TCTCTGTGAGTTCATATGTGCGTCGGTCCTGTTGTGTCTAGAAGGCCTTG 1446
UnnamedSequen 28728 TTTTCTTGGTGTCCATCACCCACTCTGGCTCTTACACTCTTTATGCCTCC 28777
i vi i v ? v
C Lx7_3end#LINE 1445 TTTCCTTGGTGTCCTCCATCCCCTCTGGCTCTTACANTCTTTCTGCCTCC 1396
UnnamedSequen 28778 TCTTCCTCCTACTTACATGACCTCTGAGGGAAGAGATTTGATAAAGATAT 28827
v vv v v v v i i i ii i
C Lx7_3end#LINE 1395 TCTTCCGCAGAGTTCCCTGAGCCCTGAGGGGAGGGATTTGATGGAGACAT 1346
UnnamedSequen 28828 CCCATTTAGG---GA----TCCAAGATCCCTCACTCTGTGT-TA-TGCTT 28868
--- ---- i i v i-i - iii
C Lx7_3end#LINE 1345 CCCATTTAGGACTGAGTGTTCCAAGGTCTCTCACTCTCTGCACATTGTCC 1296
UnnamedSequen 28869 GTCTGTGGTTCTCTGTATTTATTCCCATCTGCTACAGGAGGAAGATTCTA 28918
v v i i v v
C Lx7_3end#LINE 1295 GGCTGTGGGTCTCTGTATTTGTTCCCATCTGCTGCAGGAGGAAGCTTCTC 1246
UnnamedSequen 28919 ------------------------------GAGTATAACAGAATGTCACT 28938
------------------------------ i i
C Lx7_3end#LINE 1245 TGATGATGGCTGAGCAAGGCACTGATCTATGAGTATAGCAGAATGTCATT 1196
UnnamedSequen 28939 AGAAGTCATTTTATTGTTACAT 28960
i i i
C Lx7_3end#LINE 1195 AGGAGTCATTTTATTGCTACGT 1174
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 21.55
Transitions / transversions = 2.08 (52/25)
Gap_init rate = 0.03 (11 / 397), avg. gap size = 6.73 (74 / 11)
5029 19.82 5.80 4.36 UnnamedSequence 28675 29829 18529 C Lx6_3end LINE/L1 328 1498 376
5029 19.82 5.80 4.36 UnnamedSequence 28675 29829 (18529) C Lx6_3end#LINE/L1 (376) 1498 328 m_b1s551i32
UnnamedSequen 28675 GTGCACACTGCCTCAGTCTCTG------------GGCTTTGGTTATGCTG 28712
vii i ------------i i v i - i
C Lx6_3end#LINE 1498 GTGCTTGCTGCTTCAGTCTCTGTGAGTTCATATGAGCCTTGCTCA-GTTG 1450
UnnamedSequen 28713 GTTTAGAGGACCCTGTTTTCTTGGTGTCCATCACCCACTCTGGCTCTTAC 28762
i i i i i i vi i v
C Lx6_3end#LINE 1449 ATTCAGAGGGCCTTGTTCTCCTGGTGTCCTCCATCCCCTCTGGCTCTTAC 1400
UnnamedSequen 28763 ACTCTTTATGCCTCCTCTTCCTCCTACTTACATGACCTCTGAGGGAAGAG 28812
? vi v vviv v v v i i
C Lx6_3end#LINE 1399 ANTCTTTCCGCCTCCTCTTCCGCGGGGTTCCCTGAGCTCTGAGGGGAGGG 1350
UnnamedSequen 28813 ATTTGATAAAGATATCCCATTTAGGGAT-------CCAAGATCCCTCA-C 28854
ii i v ------- i i -
C Lx6_3end#LINE 1349 ATTTGATGGAGACATCCCATTTAGGGCTGAGTGTTCCAAGGTCTCTCATC 1300
UnnamedSequen 28855 TCTGTGTTATGCTTGTCTGTGGTTCTCTGTATTTATTCCCATCTGCTACA 28904
ii v ii v v i i i
C Lx6_3end#LINE 1299 TCTGCATAATGTCTGGCTGTGGGTCTCTGTATCTGTTCCCATCTGCTGCA 1250
UnnamedSequen 28905 GGAGGAAG-----------AT------------------TCTA-GAGTAT 28924
----------- ------------------ -
C Lx6_3end#LINE 1249 GGAGGAAGCCTCTCTGATGATGGCTGAACAAGGCACTGATCTATGAGTAT 1200
UnnamedSequen 28925 AACAGAATGTCACTAGAAGTCATTTTATTGTTACATATGATTCTCTCTCT 28974
i i i i i i ----------------
C Lx6_3end#LINE 1199 AGCAGAATATCATTAGGAGTCATTTTATCGCTAC---------------- 1166
UnnamedSequen 28975 CTCTTTCTCTCTCTCTCCTCCATTTTTTTAAAGAACAGTAGTATTTGGTT 29024
--- i -------------- ? -- v
C Lx6_3end#LINE 1165 ---TTTTT--------------TNTTTTTA--GACCAGTAGTATTTGGTT 1135
UnnamedSequen 29025 TTACCCAGGATCCCTGGGCTATGTAGTCTATGGTTCTTG-TCAGCTAAGC 29073
vi i i v v - v i
C Lx6_3end#LINE 1134 TTACCCTAGGTCTCTGGGCTATCTAGTCTCTGGTTCTTGGTCACCCAAGC 1085
UnnamedSequen 29074 AGTGTTGAGTATGGATTGCATCTCATGGGGTGAGGGTTTAGTTAAGCTAG 29123
i i i v i i i vv v i iii
C Lx6_3end#LINE 1084 AGTGTCGGGTATGGGTTCCATCTCGTGGAGTGGGCCTTAAGTCAAATCAG 1035
UnnamedSequen 29124 ATATTGGTTGGTTACTCCCACAAATTTTGTGCCACCATTGCATTTATGTA 29173
i i ii vi viii
C Lx6_3end#LINE 1034 ACATTGGTTGGCTACTCCCACAAGCTTTGTGCCACCATTGCCCTAGCATA 985
UnnamedSequen 29174 TCTTACAGGCAGAACATCATTGTAAATCAAAGATGTTGTGACTGGATTGG 29223
i i ?? ii i v i i
C Lx6_3end#LINE 984 TCTTGCAGGCAGGACANNATTGTAGGTCAAAGGTTTTGTGGCTGGGTTGG 935
UnnamedSequen 29224 TGCTTATGTTTCTCCTTTGGTAGTGTGAAGAGAACCTTCCTGTACCAAAG 29273
i i i iv v v i
C Lx6_3end#LINE 934 TGTTTACGTTTCTCTTTTGGTAGCCTGCAGAGTACCTTCCCGTACCAAAG 885
UnnamedSequen 29274 ACACTAGCACATATGCGTGAAGGTTCTATGTAGGTTCCAGCTTGACCTTT 29323
? v i v v i i iv i i i
C Lx6_3end#LINE 884 ANACTAGAACGTAGGGGTGAAGGCTCCATGTAGGCACCAGCTCGACTTCT 835
UnnamedSequen 29324 CTATGTTCGATGAGTTGTATATGTGTTGTCTTCAGCAATAGGGCTCTG-T 29372
i i i iv i ii -
C Lx6_3end#LINE 834 CCATGTTCAATGAGTTGTGTGGGTGTTGTCTTCAGCAATGGGGCCTTGCT 785
UnnamedSequen 29373 CTCATTTTGTGGAGAAGAAAGTATAATCTTGGCAACAGCCTGG---GTTT 29419
v v i iv vv vi ---
C Lx6_3end#LINE 784 GTCAGTTTGCGGAGAGCAACCTATTGTCTTGGCAACAGCCTGGGTTGTTT 735
UnnamedSequen 29420 GAGGATTCCCATAGGACCTCTTTGGACAATAACTCAATTAGATGTAACCC 29469
i i i i v i i
C Lx6_3end#LINE 734 GGGGATTTCCATGGGACCCCTTTGGCCAACAACTCAATTGGATGTAACCC 685
UnnamedSequen 29470 AGTCTTGGTCCTGGAAGCTTCATTTGGTGACAAAATATGGCTAGTTGGGG 29519
ii ?iv i i i v i i
C Lx6_3end#LINE 684 AGTCCCGNCACTGGAAGCTTCGTTTGGCGACAAGAGATGGCCAGTTGGGA 635
UnnamedSequen 29520 CTCTGTCTTCCCCAATTATTTGGTGGTTTCATTTATATCACCTTGGTATG 29569
i ? i - ? v ?i viv i vi i
C Lx6_3end#LINE 634 CTCCGTNTCCCCC-ATTATTNGGAGNCTTCATTAGGATCGCCTTCATATA 586
UnnamedSequen 29570 TGTGCATATTTTAGAAACCATCTACTATATTGTGTTTCTATACTATCCCT 29619
---- v i viv i ii i iv i i i
C Lx6_3end#LINE 585 T----AGATTTTAGGAAGTTTCCACTGCACTAGGTTTCCATACCACCCCT 540
UnnamedSequen 29620 CCGATGGCCCTTAATTTTAGCTGTCTTTTCCCATATTCCCTCCCTCTTCC 29669
vi v i ii i i ii i iv
C Lx6_3end#LINE 539 CAAATGCCCCTCAATTCCAGCTGTCTCTCCCCGCATTCTCTCCCTCCACC 490
UnnamedSequen 29670 CCATCTC-----CACTTGATCC-TCTCATTCCAG---CCA--TACCCCCA 29708
- ----- i - i i v --- --ii
C Lx6_3end#LINE 489 CC-TCTCCCCNTCACCTGATCCTTCCCGTTCCCGTCCCCACCCGCCCCCA 441
UnnamedSequen 29709 -TCCATCCATAACTATCTATTCTACCTCCCTTTCCTAGGGAAAGCTATCT 29757
- i i v- ii i i i v -----
C Lx6_3end#LINE 440 GTCCACCCGTAAA-ATCTATTCTATTTCCCCTTCCCAGGGAGATC----- 397
UnnamedSequen 29758 GACATGCCTTCCCTGATACACAGTCCCTTTATCTAAACTCTGTGGTTCTG 29807
-- v i iv v? - vv i ? i v v v i
C Lx6_3end#LINE 396 --CATGCGTCCCCCTAGNC-CCTTCTCTNTACCTAACCTCTCTGGGTCTA 350
UnnamedSequen 29808 TGAATTGTAGTTTGGTTGTTAT 29829
i i i i i
C Lx6_3end#LINE 349 CGGATTGTAGCTTGGTTATCAT 328
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 21.68
Transitions / transversions = 2.27 (152/67)
Gap_init rate = 0.06 (65 / 1154), avg. gap size = 1.82 (118 / 65)
+ 1840 10.8 10.7 3.5 UnnamedSequence 29838 30155 (20409) + MTC LTR/ERVL-MaLR 12 351 (70) 64
ANNOTATION EVIDENCE:
1840 10.76 10.69 3.53 UnnamedSequence 29838 30155 18203 + MTC LTR/ERVL-MaLR 12 351 70
1840 10.76 10.69 3.53 UnnamedSequence 29838 30155 (18203) MTC#LTR/ERVL-MaLR 12 351 (70) m_b1s501i25
UnnamedSequen 29838 GTCTTATGTCATTTTGACACAAGC------------------------CT 29863
i vi ------------------------
MTC#LTR/ERVL- 12 GTTTTATGTCAACTTGACACAAGCTAGAGTCATCTGAGAGGAGGGAACCT 61
UnnamedSequen 29864 CAATTAAGAAAATGCCTCCATAGGATCGGGCTGTAGTCAGTCCCATTGTC 29913
i i v iv --- v
MTC#LTR/ERVL- 62 CAATTGAGAAAATGCCTCCATAAGATCGGGCTGTAGGCAAGCC---TGTA 108
UnnamedSequen 29914 AGGTATTTTCTTATTTAGTAATTGATG--------CCCCCTACAAGGTCA 29955
i i v i -------- ------ vi
MTC#LTR/ERVL- 109 GGGCATTTTCTTAATTAGTGATTGATGGGGGAGGGCCC------AGCCCA 152
UnnamedSequen 29956 TTTGTGTGGGTGGTGCCATCCCTGGCCATATGGTCCTGGGTTCTATAAGA 30005
--- v vvi
MTC#LTR/ERVL- 153 TT---GTGGGTGGTGCCATCCCTGGGCTGGTGGTCCTGGGTTCTATAAGA 199
UnnamedSequen 30006 AAGCAGACTGAACAAGCCATGGGGAGCAAGCCAGTAAGCAGCA-CTCTCC 30054
i i - i
MTC#LTR/ERVL- 200 AAGCAGGCTGAGCAAGCCATGGGGAGCAAGCCAGTAAGCAGCACCCCTCC 249
UnnamedSequen 30055 ATGGCTTCTATATCAGCTCCTGCCTCCAGGTTTCTGCCCTGCTTGAGTTC 30104
i ii i i
MTC#LTR/ERVL- 250 ATGGCCTCTGCATCAGCTCCTGCCTCCAGGTTCCTGCCCTGTTTGAGTTC 299
UnnamedSequen 30105 CT-CCCTGACTTCTTTTGATAATGAACAGTGATATGGAAGTGTAAGCCGA 30153
-i i i i ? i i
MTC#LTR/ERVL- 300 CTGTCCTGACTTCCTTCGATGATGAACNGTGATGTGGAAGTGTAAGCCAA 349
UnnamedSequen 30154 AT 30155
MTC#LTR/ERVL- 350 AT 351
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 11.50
Transitions / transversions = 2.67 (24/9)
Gap_init rate = 0.05 (16 / 317), avg. gap size = 2.88 (46 / 16)
+ 1941 16.9 13.0 0.9 UnnamedSequence 30338 30469 (20095) C MTC LTR/ERVL-MaLR (0) 421 266 65
ANNOTATION EVIDENCE:
1941 16.92 13.03 0.95 UnnamedSequence 30338 30469 19002 C MTC LTR/ERVL-MaLR 266 421 0
1941 16.92 13.03 0.95 UnnamedSequence 30338 30469 (19002) C MTC#LTR/ERVL-MaLR (0) 421 266 c_b1s401i3
UnnamedSequen 30338 TGTTTTAGTTAGAGTTTCTAGTTGCTGTGACCAA-CACCATGACCAAAAA 30386
i i ? - iv - --
C MTC#LTR/ERVL- 421 TGTCTTAGTTAGGGTTNCTA-TTGCTGTGATGAAACACCATGACCAAA-- 375
UnnamedSequen 30387 GCAAGTTGGGGAGGAAAGGATTTATTTGACTTACACTTCCATATAACTGT 30436
? i i i v ?
C MTC#LTR/ERVL- 374 GCAANTTGGGGAGGAAAGGGTTTATTTGGCTTACACTTCCACATCACNGT 325
UnnamedSequen 30437 TCATCATCAAAAGAAATCAGGACAGAAACCCG------------------ 30468
i i i i i i------------------
C MTC#LTR/ERVL- 324 TCATCATCGAAGGAAGTCAGGACAGGAACTCAAACAGGGCAGGAACCTGG 275
UnnamedSequen 30469 --------G 30469
--------
C MTC#LTR/ERVL- 274 AGGCAGGAG 266
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 19.22
Transitions / transversions = 6.00 (12/2)
Gap_init rate = 0.05 (6 / 131), avg. gap size = 5.00 (30 / 6)
+ 243 0.0 0.0 0.0 UnnamedSequence 30470 30678 (19886) + (GGGCA)n Simple_repeat 1 209 (0) 66
ANNOTATION EVIDENCE:
243 0.00 0.00 0.00 UnnamedSequence 30470 30678 19886 + (GGGCA)n Simple_repeat 1 209 0
243 0.00 0.00 0.00 UnnamedSequence 30470 30678 (19886) (GGGCA)n#Simple_repeat 1 209 (0) c_b1s251i5
UnnamedSequen 30470 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 30519
(GGGCA)n#Simp 1 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 50
UnnamedSequen 30520 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 30569
(GGGCA)n#Simp 51 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 100
UnnamedSequen 30570 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 30619
(GGGCA)n#Simp 101 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 150
UnnamedSequen 30620 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 30669
(GGGCA)n#Simp 151 GGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCAGGGCA 200
UnnamedSequen 30670 GGGCAGGGC 30678
(GGGCA)n#Simp 201 GGGCAGGGC 209
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 208), avg. gap size = 0.0 (0 / 0)
+ 1941 16.9 13.0 0.9 UnnamedSequence 30679 30921 (19643) C MTC LTR/ERVL-MaLR (156) 265 2 65
ANNOTATION EVIDENCE:
1941 16.92 13.03 0.95 UnnamedSequence 30679 30921 18550 C MTC LTR/ERVL-MaLR 2 265 156
1941 16.92 13.03 0.95 UnnamedSequence 30679 30921 (18550) C MTC#LTR/ERVL-MaLR (156) 265 2 c_b1s401i3
UnnamedSequen 30679 TGATGTAG-CGTCACTGAGGAGTCCTGCTTCCTACTTTGCTTCCCATGGG 30727
i -v i iv i v v ivi i v
C MTC#LTR/ERVL- 265 TGATGCAGAGGCCATGGAGGGGTGCTGCTTACTGGCTTGCTCCCCATGGC 216
UnnamedSequen 30728 TGGATCAGCCTGCTTTCTTATAGATCCCAAAACCA--------GGGATAC 30769
v v v ii -------- iv
C MTC#LTR/ERVL- 215 TTGCTCAGCCTGCTTTCTTATAGAACCCAGGACCACCAGCCCAGGGATGG 166
UnnamedSequen 30770 CACCGCCTACAATGGCCTGGACCTTCCTCCATTGATCGCTCATTGAGAAA 30819
i i v i i i ii i v i
C MTC#LTR/ERVL- 165 CACCACCCACAATGGGCTGGGCCCTCCCCCATCAATCACTAATTAAGAAA 116
UnnamedSequen 30820 ATGCCTTAGAA-------------CTGACTCTCATAGAGGCATTTCCTCA 30856
i v i------------- i - i i i
C MTC#LTR/ERVL- 115 ATGCCCTACAGGCTTGCCTACAGCCCGA-TCTTATGGAGGCATTTTCTCA 67
UnnamedSequen 30857 ACTGAGCCTCCTTCCTCTCTGATGACTCTAGCTTTTGTCAAGATGACATA 30906
i vi i v v v
C MTC#LTR/ERVL- 66 ATTGAGGTTCCCTCCTCTCAGATGACTCTAGCTTGTGTCAAGTTGACATA 17
UnnamedSequen 30907 AAATCAACCAGTACA 30921
ii i i
C MTC#LTR/ERVL- 16 AAACTAGCCAGCACA 2
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 19.22
Transitions / transversions = 1.88 (32/17)
Gap_init rate = 0.02 (4 / 242), avg. gap size = 5.75 (23 / 4)
+ 788 22.6 8.0 1.8 UnnamedSequence 31352 31563 (19001) + MTD LTR/ERVL-MaLR 195 419 (0) 67
ANNOTATION EVIDENCE:
788 22.57 8.02 1.78 UnnamedSequence 31352 31563 17378 + MTD LTR/ERVL-MaLR 195 419 0
788 22.57 8.02 1.78 UnnamedSequence 31352 31563 (17378) MTD#LTR/ERVL-MaLR 195 419 (0) m_b1s501i26
UnnamedSequen 31352 TATGGAAGCTAGCTGCGCATGAGCCA---GGA-------AGTGAGCAGCT 31391
v i vi v -- --- ------- i v
MTD#LTR/ERVL- 195 TAAGAAAGCAGGCTGAGCA--AGCCATGGGGAGCAAGCCAGTAAGCAGCG 242
UnnamedSequen 31392 CTTCTGAAAATCTTCTGA---AATTTCTGCTTCTGTCATTCCTGC-TTGG 31437
i i vv viv i v--- i i i iiv-i - i
MTD#LTR/ERVL- 243 TTCCTCCATGGCCTCTGCTTCAGTTCCTGCCTCCAG-GTTCCTGCCTTGA 291
UnnamedSequen 31438 GTTTCTGCTCTCACTTCCCTCAGCAATGAACTATGACCTGGAAGTGTGAG 31487
i i v i ii i i v i
MTD#LTR/ERVL- 292 GTTCCTGCCCTGACTTCCCTCGGTGATGGACTGTGACCTGGAACTGTAAG 341
UnnamedSequen 31488 TCGAA-TAAGCCCTTCCCTCTCCTAAGCTGTTTTTGGTCATGATG-TTTA 31535
ii - i i i - i i i -
MTD#LTR/ERVL- 342 CTGAAATAAACCCTTTCCTCCCC-AAGTTGCTTTTGGTCATGGTGTTTTA 390
UnnamedSequen 31536 CCACAGCAACAGAAAGCA-AACAAGGACA 31563
i i v v- v
MTD#LTR/ERVL- 391 TCACAGCAATAGAAACCCTAACTAGGACA 419
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 27.09
Transitions / transversions = 2.13 (32/15)
Gap_init rate = 0.05 (11 / 211), avg. gap size = 1.91 (21 / 11)
+ 20 21.4 8.6 0.0 UnnamedSequence 32055 32092 (18472) + (AGAACA)n Simple_repeat 1 87 (0) 68
ANNOTATION EVIDENCE:
20 21.35 8.64 0.00 UnnamedSequence 32055 32135 16806 + (AGAACA)n Simple_repeat 1 88 0
20 21.35 8.64 0.00 UnnamedSequence 32055 32135 (16806) (AGAACA)n#Simple_repeat 1 88 (0) m_b1s252i12
UnnamedSequen 32055 AGAACAACAACAAGAAGAAGAAGAGGAGTAGGAGGCAG-A-AAGAA-AA- 32100
v v v i ii i ivv - - - -
(AGAACA)n#Sim 1 AGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAACAAG 50
UnnamedSequen 32101 AAC-AGACAAACAACAAAAACAA-AACAA-AACAAAAA 32135
- vv v i - - i
(AGAACA)n#Sim 51 AACAAGAACAAGAACAAGAACAAGAACAAGAACAAGAA 88
Matrix = Unknown
Transitions / transversions = 0.88 (7/8)
Gap_init rate = 0.09 (7 / 80), avg. gap size = 1.00 (7 / 7)
+ 18 10.8 4.8 2.3 UnnamedSequence 32093 32134 (18430) + A-rich Low_complexity 1 43 (0) 69
ANNOTATION EVIDENCE:
18 10.81 4.76 2.33 UnnamedSequence 32093 32134 16807 + (AAACA)n Simple_repeat 1 43 0
18 10.81 4.76 2.33 UnnamedSequence 32093 32134 (16807) (AAACA)n#Simple_repeat 1 43 (0) m_b1s252i13
UnnamedSequen 32093 AAAGAAAA-AACAGACAAACAACA-AAAACAAAACAAAACAAAA 32134
v - v v - v -
(AAACA)n#Simp 1 AAACAAAACAAAACA-AAACAAAACAAAACAAAACAAAACAAAA 43
Matrix = Unknown
Transitions / transversions = 0.00 (0/4)
Gap_init rate = 0.07 (3 / 41), avg. gap size = 1.00 (3 / 3)
+ 241 28.4 14.4 1.7 UnnamedSequence 32632 32733 (17831) C MLT1D LTR/ERVL-MaLR (0) 505 391 70
ANNOTATION EVIDENCE:
241 28.37 14.42 1.71 UnnamedSequence 32632 32735 16206 C MLT1D LTR/ERVL-MaLR 389 505 0
241 28.37 14.42 1.71 UnnamedSequence 32632 32735 (16206) C MLT1D#LTR/ERVL-MaLR (0) 505 389 m_b1s501i27
UnnamedSequen 32632 TGTATTAATTTCCT---GCTGTGACAATGAATGTCCTAAAATACA----T 32674
i --- ivii ii vv vv ivi ----i
C MLT1D#LTR/ERV 505 TGTATTAGTTTCCTATTGCTGCTGTAACAAATTACCACAAACTTAGTGGC 456
UnnamedSequen 32675 TTAAGACCATGTAAATTCATT--------GTTCTGGAGCTCACACGTACA 32716
i v iii i -------- v v v v -
C MLT1D#LTR/ERV 455 TTAAAACAACACAAATTTATTATCTTACAGTTCTGGAGGTCAGAAGTCC- 407
UnnamedSequen 32717 AAAAATAGATCTTACTGGG 32735
-i i i i
C MLT1D#LTR/ERV 406 -GAAATGGGTCTCACTGGG 389
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 35.35
Transitions / transversions = 1.64 (18/11)
Gap_init rate = 0.05 (5 / 103), avg. gap size = 3.40 (17 / 5)
+ 1363 1.9 0.0 0.0 UnnamedSequence 32734 32892 (17672) + B2_Mm1a SINE/B2 1 159 (34) 71
ANNOTATION EVIDENCE:
1363 1.89 0.00 0.00 UnnamedSequence 32734 32892 16049 + B2_Mm1a SINE/B2 1 159 34
1363 1.89 0.00 0.00 UnnamedSequence 32734 32892 (16049) B2_Mm1a#SINE/B2 1 159 (34) m_b1s501i28
UnnamedSequen 32734 GGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCTGA 32783
i
B2_Mm1a#SINE/ 1 GGGGCTGGTGAGATGGCTCAGTGGGTAAGAGCACCCGACTGCTCTTCCGA 50
UnnamedSequen 32784 AGGTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 32833
B2_Mm1a#SINE/ 51 AGGTCCGGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 100
UnnamedSequen 32834 TAATGTGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGT 32883
i v
B2_Mm1a#SINE/ 101 TAACGAGATCTGACTCCCTCTTCTGGAGTGTCTGAAGACAGCTACAGTGT 150
UnnamedSequen 32884 ACTTACATA 32892
B2_Mm1a#SINE/ 151 ACTTACATA 159
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 0.76
Transitions / transversions = 2.00 (2/1)
Gap_init rate = 0.00 (0 / 158), avg. gap size = 0.0 (0 / 0)
+ 34 0.0 0.0 0.0 UnnamedSequence 32893 32924 (17640) + (AAAT)n Simple_repeat 1 32 (0) 72
ANNOTATION EVIDENCE:
34 0.00 0.00 0.00 UnnamedSequence 32893 32924 17640 + (AAAT)n Simple_repeat 1 32 0
34 0.00 0.00 0.00 UnnamedSequence 32893 32924 (17640) (AAAT)n#Simple_repeat 1 32 (0) c_b1s251i6
UnnamedSequen 32893 AAATAAATAAATAAATAAATAAATAAATAAAT 32924
(AAAT)n#Simpl 1 AAATAAATAAATAAATAAATAAATAAATAAAT 32
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 31), avg. gap size = 0.0 (0 / 0)
+ 1143 10.1 0.0 8.3 UnnamedSequence 32925 32959 (17605) + B2_Mm2 SINE/B2 159 179 (16) 73
ANNOTATION EVIDENCE:
1143 10.07 0.00 8.33 UnnamedSequence 32925 32959 16013 + B2_Mm2 SINE/B2 159 179 16
1143 10.07 0.00 8.33 UnnamedSequence 32925 32959 (16013) B2_Mm2#SINE/B2 159 179 (16) m_b1s501i29
UnnamedSequen 32925 CTGTTTGTTTTAAAATAAAAAAAAAAATAGATCTT 32959
-------------- v v i
B2_Mm2#SINE/B 159 --------------ATAAATAAATAAATAAATCTT 179
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 10.24
Transitions / transversions = 0.50 (1/2)
Gap_init rate = 0.41 (14 / 34), avg. gap size = 1.00 (14 / 14)
+ 511 31.3 12.3 4.3 UnnamedSequence 32949 33208 (17356) C MLT1D LTR/ERVL-MaLR (100) 405 126 70 *
ANNOTATION EVIDENCE:
511 31.34 12.31 4.29 UnnamedSequence 32949 33208 15764 C MLT1D LTR/ERVL-MaLR 126 405 100
511 31.34 12.31 4.29 UnnamedSequence 32949 33208 (15764) C MLT1D#LTR/ERVL-MaLR (100) 405 126 m_b1s501i30
UnnamedSequen 32949 AAATAGATCTTACTTTGCTGCAAATCCCTGCATAGACAGCAC-ACATTCC 32997
i i i vv i- vvv ii v i vi -i i
C MLT1D#LTR/ERV 405 AAATGGGTCTCACTGGGCTA-AAATCAAGGTGTCGGCAGGGCTGCGTTCC 357
UnnamedSequen 32998 TTTTGGAGACTCT-GGGAATAGT---------TATTTTTTATA--TTTTA 33035
i i - i v i --------- iii vi -- i
C MLT1D#LTR/ERV 356 TTCTGGAGGCTCTAGGGGAGAATCCGTTTCCTTGCCTTTTCCAGCTTCTA 307
UnnamedSequen 33036 GAGTCTATACATGCTCTTTGGCTTCCGCCCCACCCCACCTTTCCTACATT 33085
v iiiv iiii i ivi ----i ---- v i
C MLT1D#LTR/ERV 306 GAGGCCGCCCGCATTCCTTGGCTCGTG----GCCCC----TTCCTCCATC 265
UnnamedSequen 33086 TTAAAACCTAGCTATATTG-------GGCTAAATCTGCTTC-------AT 33121
v v i v ii i ------- i i--- ------- i
C MLT1D#LTR/ERV 264 TTCAAAGCCAGCAACGTCGTCACTCCGACC---TCTGCTTCCGTCGTCAC 218
UnnamedSequen 33122 ATTATTCTCTCTGATTGT---CTTCCTG--TCCCACGTCTAAGGATCCCG 33166
iviii i v --- i -- v v v i iv
C MLT1D#LTR/ERV 217 ATCTCCTTCTCTGACTCTGACCCTCCTGCCTCCCTCTTATAAGGACCCTT 168
UnnamedSequen 33167 AGGATGGCAGCAGGCCCACCTGGATAAACCAGGATAATCTTC 33208
iv vi vii i v i
C MLT1D#LTR/ERV 167 GTGATTACATTGGGCCCACCCGGATAATCCAGGATAATCTCC 126
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 37.79
Transitions / transversions = 2.00 (52/26)
Gap_init rate = 0.08 (20 / 259), avg. gap size = 2.20 (44 / 20)
+ 29 0.0 7.0 2.2 UnnamedSequence 33475 33517 (17047) + (AAAAT)n Simple_repeat 1 45 (0) 74
ANNOTATION EVIDENCE:
29 0.00 6.98 2.22 UnnamedSequence 33475 33517 17047 + (AAAAT)n Simple_repeat 1 45 0
29 0.00 6.98 2.22 UnnamedSequence 33475 33517 (17047) (AAAAT)n#Simple_repeat 1 45 (0) c_b1s251i7
UnnamedSequen 33475 AAAAT-AAA-AAAATAAAATAAAATAAAATAATAAT-AAATAAAAT 33517
- - - -
(AAAAT)n#Simp 1 AAAATAAAATAAAATAAAATAAAATAAAATAA-AATAAAATAAAAT 45
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4)
+ 1795 16.6 15.0 1.2 UnnamedSequence 33545 33911 (16653) + MTC LTR/ERVL-MaLR 5 421 (0) 75
ANNOTATION EVIDENCE:
1795 16.55 14.99 1.20 UnnamedSequence 33545 33911 15633 + MTC LTR/ERVL-MaLR 5 421 0
1795 16.55 14.99 1.20 UnnamedSequence 33545 33911 (15633) MTC#LTR/ERVL-MaLR 5 421 (0) c_b1s401i4
UnnamedSequen 33545 CTGGCTAGTTTTGTGTCAAC----------CTATGGT----TGAGAGGAA 33580
i ---------- vi ---- i
MTC#LTR/ERVL- 5 CTGGCTAGTTTTATGTCAACTTGACACAAGCTAGAGTCATCTGAGAGGAG 54
UnnamedSequen 33581 AGAACCTCAATTGAGAAAATAAATGTCTCTATAAGATGGGGCTGCAAGCA 33630
i ---- i i v i i
MTC#LTR/ERVL- 55 GGAACCTCAATTGAGA----AAATGCCTCCATAAGATCGGGCTGTAGGCA 100
UnnamedSequen 33631 AGCTTGTA-GGCATTTTCTTAA--------------------GCTCATCT 33659
i - -------------------- i v i
MTC#LTR/ERVL- 101 AGCCTGTAGGGCATTTTCTTAATTAGTGATTGATGGGGGAGGGCCCAGCC 150
UnnamedSequen 33660 CATCCTGGGT--------------GCTGTTGGTCCTGAGTTCTATAAGAA 33695
iv -------------- v i
MTC#LTR/ERVL- 151 CATTGTGGGTGGTGCCATCCCTGGGCTGGTGGTCCTGGGTTCTATAAGAA 200
UnnamedSequen 33696 AGCAGGCTAAGCAAGCCAT-AGAAGCAAGCCATTAAGCAGCAGTTCTCCA 33744
i -i i v vii
MTC#LTR/ERVL- 201 AGCAGGCTGAGCAAGCCATGGGGAGCAAGCCAGTAAGCAGCACCCCTCCA 250
UnnamedSequen 33745 TGGCCTCTGCATCGGTTCCTGCCTCCAGGTTCCCACCGGATTTGAGCTCC 33794
i i ii vvi i
MTC#LTR/ERVL- 251 TGGCCTCTGCATCAGCTCCTGCCTCCAGGTTCCTGCCCTGTTTGAGTTCC 300
UnnamedSequen 33795 TGCCTTGGCTTCCCTCAGTGGAGTACGATCCAGGGTAA---TAA--TAAA 33839
i i i i ii iv v ?i vvv v v --- --i
MTC#LTR/ERVL- 301 TGTCCTGACTTCCTTCGATGATGAACNGTGATGTGGAAGTGTAAGCCAAA 350
UnnamedSequen 33840 TAAACCCTTTCCTCCCCAAGTTGCTCTGGTCCTTGATATTTCATCAAGTC 33889
? i v- i i viv
MTC#LTR/ERVL- 351 TAAACCCTTTCCTCCCCAANTTGCTTTGGTCA-TGGTGTTTCATCACAGC 399
UnnamedSequen 33890 ATTGAAAACCCTAACTAAGATA 33911
v ii? i
MTC#LTR/ERVL- 400 AATAGNAACCCTAACTAAGACA 421
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 18.93
Transitions / transversions = 2.00 (40/20)
Gap_init rate = 0.04 (13 / 366), avg. gap size = 4.62 (60 / 13)
+ 29 13.3 0.0 4.9 UnnamedSequence 34127 34190 (16374) + (TTTTGT)n Simple_repeat 1 61 (0) 76
ANNOTATION EVIDENCE:
29 13.26 0.00 4.92 UnnamedSequence 34127 34190 15190 + (TTTTGT)n Simple_repeat 1 61 0
29 13.26 0.00 4.92 UnnamedSequence 34127 34190 (15190) (TTTTGT)n#Simple_repeat 1 61 (0) m_b1s252i15
UnnamedSequen 34127 TTTTCTTTTGGTTTTGGTTTTGGTTTTTGTTGTTGTTGTTGTTGTTTGTT 34176
v v v v v v - -
(TTTTGT)n#Sim 1 TTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTT-TTTG-T 48
UnnamedSequen 34177 TGTTTGTTTTTCTT 34190
- v
(TTTTGT)n#Sim 49 T-TTTGTTTTTGTT 61
Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.05 (3 / 63), avg. gap size = 1.00 (3 / 3)
+ 1413 11.0 1.1 0.0 UnnamedSequence 34255 34445 (16119) + B2_Mm1t SINE/B2 1 193 (0) 77
ANNOTATION EVIDENCE:
1413 10.99 1.05 0.00 UnnamedSequence 34255 34445 15570 + B2_Mm1t SINE/B2 1 193 0
1413 10.99 1.05 0.00 UnnamedSequence 34255 34445 (15570) B2_Mm1t#SINE/B2 1 193 (0) c_b1s355i6
UnnamedSequen 34255 GGGACTGGAGAGATGGCTTAGTGGTTAAGAGCACT-GATTGCTCTTCCAA 34303
i v i i v i- i i
B2_Mm1t#SINE/ 1 GGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACCCGACTGCTCTTCCGA 50
UnnamedSequen 34304 AGGTCCTGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 34353
?
B2_Mm1t#SINE/ 51 AGGTCCNGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 100
UnnamedSequen 34354 TAATGAGATCTGACACCTTCTTCTGGTGCATCTGAAGTCAGCTATGGTGT 34403
i i i ii v ii
B2_Mm1t#SINE/ 101 TAACGAGATCTGACGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGT 150
UnnamedSequen 34404 ACTTATATATAAC-AATAAATACATCTTTAAAAAATATAAAAA 34445
i i- v v v
B2_Mm1t#SINE/ 151 ACTTACATATAATAAATAAATAAATCTTTAAAAAAAAAAAAAA 193
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 9.85
Transitions / transversions = 2.50 (15/6)
Gap_init rate = 0.01 (2 / 190), avg. gap size = 1.00 (2 / 2)
+ 202 32.1 1.8 0.0 UnnamedSequence 34623 34678 (15886) C MIRb SINE/MIR (92) 176 120 78
ANNOTATION EVIDENCE:
202 32.14 1.79 0.00 UnnamedSequence 34623 34678 14892 C MIRb SINE/MIR 120 176 92
202 32.14 1.79 0.00 UnnamedSequence 34623 34678 (14892) C MIRb#SINE/MIR (92) 176 120 m_b1s601i1
UnnamedSequen 34623 ACCTTGCAAAGTAGGCCTCAG-GCTCCCATTTTACCAATGAGGAGCCTAA 34671
i i i iv i v-iii vi iv i
C MIRb#SINE/MIR 176 ACCCTGCGAGGTAGGTATTATTATCCCCATTTTACAGATGAGGAAACTGA 127
UnnamedSequen 34672 GGTTTGG 34678
i ii
C MIRb#SINE/MIR 126 GGCTCAG 120
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 42.60
Transitions / transversions = 3.50 (14/4)
Gap_init rate = 0.02 (1 / 55), avg. gap size = 1.00 (1 / 1)
+ 16 0.0 0.0 0.0 UnnamedSequence 34815 34832 (15732) + (T)n Simple_repeat 1 18 (0) 79
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 UnnamedSequence 34815 34832 14738 + (T)n Simple_repeat 1 18 0
16 0.00 0.00 0.00 UnnamedSequence 34815 34832 (14738) (T)n#Simple_repeat 1 18 (0) m_b1s252i16
UnnamedSequen 34815 TTTTTTTTTTTTTTTTTT 34832
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTT 18
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 17), avg. gap size = 0.0 (0 / 0)
+ 1287 11.9 1.2 1.9 UnnamedSequence 34870 35086 (15478) + B2_Mm1t SINE/B2 1 213 (3) 80
ANNOTATION EVIDENCE:
756 25.28 5.07 7.04 UnnamedSequence 34870 35086 14484 + B3 SINE/B2 1 213 3
756 25.28 5.07 7.04 UnnamedSequence 34870 35086 (14484) B3#SINE/B2 1 213 (3) m_b1s501i32
UnnamedSequen 34870 GGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACTGATTGCTCTTCTGAA 34919
i ii iii
B3#SINE/B2 1 GGGGCTGGAGAGATGGCTCAGCGGTTAAGAGCACTGGCTGCTCTTCCAGA 50
UnnamedSequen 34920 GGTCCTGAGTTCAAATTCCAGTAACCACATGGTGGCTCACAACCATCCAT 34969
v i i i v i i v i i ii
B3#SINE/B2 51 GGACCCGGGTTCGATTCCCAGCACCCACATGGCGGCTCACAACCGTCTGT 100
UnnamedSequen 34970 AAT-----------GAGATCTGATGCCCTTTTCTGGGGTGTCTGAAGACA 35008
i----------- i i i i -- iv i vi i
B3#SINE/B2 101 AACTCCAGTTCCAGGGGATCCGACGCCCTCTTCT--GGCCTCCGCGGGCA 148
UnnamedSequen 35009 GCTAAAGTGTACTTACATATAATAAATAAATATAAACAATTAAAACAATT 35058
v --- - i --i ii ii iv i i i -- - vv ii --
B3#SINE/B2 149 CC---AG-GCAC--GCACGTGGTGCACAGACAT--AC-ATGCAGGCAA-- 187
UnnamedSequen 35059 AATAGCAACACACAGGTAGAATAAATAT 35086
i v v i -- i v
B3#SINE/B2 188 AACACCCATACACA--TAAAATAAAAAT 213
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 24.44
Transitions / transversions = 3.25 (39/12)
Gap_init rate = 0.07 (16 / 216), avg. gap size = 1.62 (26 / 16)
1287 9.74 0.53 1.08 UnnamedSequence 34870 35056 14514 + B2_Mm1t SINE/B2 1 186 7
1287 9.74 0.53 1.08 UnnamedSequence 34870 35056 (14514) B2_Mm1t#SINE/B2 1 186 (7) m_b1s501i31
UnnamedSequen 34870 GGGGCTGGAGAGATGGCTCAGTGGTTAAGAGCACT-GATTGCTCTTCTGA 34918
v i v i- i i
B2_Mm1t#SINE/ 1 GGGGCTGGTGAGATGGCTCAGCGGGTAAGAGCACCCGACTGCTCTTCCGA 50
UnnamedSequen 34919 AGGTCCTGAGTTCAAATTCCAGTAACCACATGGTGGCTCACAACCATCCA 34968
? i i i
B2_Mm1t#SINE/ 51 AGGTCCNGAGTTCAAATCCCAGCAACCACATGGTGGCTCACAACCATCCG 100
UnnamedSequen 34969 TAATGAGATCTGATGCCCTTTTCTGGGGTGTCTGAAGACAGCTAAAGTGT 35018
i i i v v
B2_Mm1t#SINE/ 101 TAACGAGATCTGACGCCCTCTTCTGGTGTGTCTGAAGACAGCTACAGTGT 150
UnnamedSequen 35019 ACTTACATATAATAAATAAATATAAACAATTAAAACAA 35056
-- ivv v
B2_Mm1t#SINE/ 151 ACTTACATATAATAAATAA--ATAAATCTTTAAAAAAA 186
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 7.73
Transitions / transversions = 1.57 (11/7)
Gap_init rate = 0.02 (3 / 186), avg. gap size = 1.00 (3 / 3)
+ 694 28.7 2.1 4.8 UnnamedSequence 35319 35512 (15052) C B3A SINE/B2 (3) 195 7 81
ANNOTATION EVIDENCE:
694 28.69 2.06 4.76 UnnamedSequence 35319 35512 14058 C B3A SINE/B2 7 195 3
694 28.69 2.06 4.76 UnnamedSequence 35319 35512 (14058) C B3A#SINE/B2 (3) 195 7 m_b1s501i33
UnnamedSequen 35319 ATTTTAGTTTTTTTATGTGTATGTGTATGTGTATTTGTGTGTG--TGTCC 35366
vi v i i i i ii v ? i -- i
C B3A#SINE/B2 195 ATTTTTATTTTATTGTGTGTGTGTGTGTGCGCGTGTGNGTGCGGGTGCCC 146
UnnamedSequen 35367 GTGAAAGCTAGAAGATGCCATTGGATCCC-TGCAGTTTTAAT-ACAAGAT 35414
i i i i v v i i - v i vv i - i vv
C B3A#SINE/B2 145 GCGGAGGCCAGAAGAGGGCGTCGGATCCCCTGGAGCTGGAGTTACAGGCG 96
UnnamedSequen 35415 GTTGTGAACCTCCTAATGTGTACAGCATGAGTGCTAGGAACTGAAATCTG 35464
i v ii i ---------i i i v v
C B3A#SINE/B2 95 GTTGTGAGCCGCCCGACGTG---------GGTGCTGGGAACCGAACTCGG 55
UnnamedSequen 35465 GTCCTTCAAAGGAGTAGCAAATGCTTTTCATTGCGGAGCCATCTTCCC 35512
iiiv i i ii i v ii v ii
C B3A#SINE/B2 54 GTCCTCTGCAAGAGCAGCAAGCGCTCTTAACCGCTGAGCCATCTCTCC 7
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 28.63
Transitions / transversions = 2.31 (37/16)
Gap_init rate = 0.06 (12 / 193), avg. gap size = 1.08 (13 / 12)
+ 288 29.2 7.4 0.6 UnnamedSequence 36047 36194 (14370) C L1ME4b LINE/L1 (393) 5752 5595 82
ANNOTATION EVIDENCE:
288 29.23 7.43 0.63 UnnamedSequence 36047 36194 13376 C L1ME4b_3end LINE/L1 342 499 393
288 29.23 7.43 0.63 UnnamedSequence 36047 36194 (13376) C L1ME4b_3end#LINE/L1 (393) 499 342 m_b1s551i33
UnnamedSequen 36047 ATGATCATTGAAGT-GTTAC--ATCTTTTATTATTACGAG----GCTTCA 36089
iv v i - v -- ii i i---- v
C L1ME4b_3end#L 499 ATGGACATTTAGGTTGTTTCCAATCTTTTGCTATTACAAACAATGCTGCA 450
UnnamedSequen 36090 G-GGGTGATGCTAGTAAACTGGCTATTTTACCAATGTGAAGCTGCATCTA 36138
i- ii i i- v v ivv ii ii vv viiv ii i
C L1ME4b_3end#L 449 ATGAATAAC-CTTGTACATACGTCATTTCGCACATGTGCGAGTATATCTG 401
UnnamedSequen 36139 TAGAATAAATTTC-AGAAGTTGAATTGCTTAGTCAAAGAG-ATATCC-CC 36185
i i - v vi i - i v -ii
C L1ME4b_3end#L 400 TAGGATAAATTCCTAGAAGTGGAATTGCTGGGTCAAAGGGTATGTGCATT 351
UnnamedSequen 36186 TGTAATTTT 36194
C L1ME4b_3end#L 350 TGTAATTTT 342
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 36.25
Transitions / transversions = 1.87 (28/15)
Gap_init rate = 0.05 (8 / 147), avg. gap size = 1.50 (12 / 8)
+ 623 16.6 13.8 11.4 UnnamedSequence 36340 36570 (13994) C Lx5 LINE/L1 (0) 7050 6815 83
ANNOTATION EVIDENCE:
623 16.62 13.85 11.44 UnnamedSequence 36340 36570 13000 C Lx5_3end LINE/L1 1229 1464 0
623 16.62 13.85 11.44 UnnamedSequence 36340 36570 (13000) C Lx5_3end#LINE/L1 (0) 1464 1229 m_b1s551i34
UnnamedSequen 36340 TTTATATATTTATTTACTTTACAACCTATTATCAG-------TCCTTCCT 36382
v i v iiv vv ------- i
C Lx5_3end#LINE 1464 TTTATTTATTTATTCACTTTACATCCCGATCGCAGCNCCCCCTCCCTCCT 1415
UnnamedSequen 36383 CTTCTCCCAGT---ACCCCCA-----------------TCCCCCCTCCT- 36411
i --- i ----------------- i-
C Lx5_3end#LINE 1414 CTCCTCCCAGTCCCACCCTCACAAACCCCTCCCCCCATTCCCCCCTCCCC 1365
UnnamedSequen 36412 ---TCCTTTGAGAAGGGGAAGCCCCACTCTGAGTGTCAGTCCCCATCCCC 36458
--- i? - i i ii ?-- --
C Lx5_3end#LINE 1364 TTCTCCTCNGAGAAGGGGAAGCCCC-CCCTGGGTACCAN--CCCA--CCC 1320
UnnamedSequen 36459 TTACTTCTCCACCGCACTATCCCTTCACATCACGTCACAGAGGAACTAGA 36508
vi ---------------------- v i ? vi i i
C Lx5_3end#LINE 1319 TGGC----------------------ACATCAAGTCGCNGCAGGACTAGG 1292
UnnamedSequen 36509 CA-ATCCTCTCCCACTGAGCCCAGACAAGGCTGTCCATTTATGGATGGGG 36557
i- v v i v v ivi?
C Lx5_3end#LINE 1291 CGCATCCTCTCCCACTGAGGCCAGACAAGGCAGCCCAGTTAGGGGAANGG 1242
UnnamedSequen 36558 GATCCACAGGCAG 36570
?
C Lx5_3end#LINE 1241 GATCCANAGGCAG 1229
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 17.77
Transitions / transversions = 1.62 (21/13)
Gap_init rate = 0.14 (33 / 230), avg. gap size = 1.79 (59 / 33)
+ 36 6.7 0.0 0.0 UnnamedSequence 36638 36684 (13880) + (TGA)n Simple_repeat 1 47 (0) 84
ANNOTATION EVIDENCE:
36 6.71 0.00 0.00 UnnamedSequence 36638 36684 13880 + (TGA)n Simple_repeat 1 47 0
36 6.71 0.00 0.00 UnnamedSequence 36638 36684 (13880) (TGA)n#Simple_repeat 1 47 (0) c_b1s251i8
UnnamedSequen 36638 TGATGATGTTGATGATGTTGATGATGATGATGTTGATGATGATGATG 36684
v v v
(TGA)n#Simple 1 TGATGATGATGATGATGATGATGATGATGATGATGATGATGATGATG 47
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 955 16.4 0.0 1.4 UnnamedSequence 36686 36833 (13731) C B1_Mur2 SINE/Alu (1) 148 3 85
ANNOTATION EVIDENCE:
955 16.45 0.00 1.37 UnnamedSequence 36686 36833 13228 C B1_Mur2 SINE/Alu 3 148 1
955 16.45 0.00 1.37 UnnamedSequence 36686 36833 (13228) C B1_Mur2#SINE/Alu (1) 148 3 c_b1s355i7
UnnamedSequen 36686 TTTGTTTTGTTTTGAGACAGGGTATCTCTATGTAGCCCTAGCTGTCCTGG 36735
-- v v i
C B1_Mur2#SINE/ 148 TTTGTTTT--TTTGAGACAGGGTCTCACTATGTAGCCCTGGCTGTCCTGG 101
UnnamedSequen 36736 AACTTGCTATGTAGACCAGGCTGGTCTCAAGCTTACAGAGGTCTGCCTGC 36785
i i i i i i i
C B1_Mur2#SINE/ 100 AACTCGCTATGTAGACCAGGCTGGCCTCGAACTCACAGAGATCCGCCTGC 51
UnnamedSequen 36786 CTCTGCCTTCGGAGTCCTGGGACTGAAAGTATAAACCGCCACTCCTGG 36833
i v v i i i ii ivi i v i
C B1_Mur2#SINE/ 50 CTCTGCCTCCCGAGTGCTGGGATTAAAGGCGTGCGCCACCACGCCCGG 3
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 14.08
Transitions / transversions = 3.00 (18/6)
Gap_init rate = 0.01 (2 / 147), avg. gap size = 1.00 (2 / 2)
+ 945 8.1 0.6 10.7 UnnamedSequence 36959 37123 (13441) + L1MdFanc_II LINE/L1 6418 6567 (6) 86
ANNOTATION EVIDENCE:
945 8.14 0.61 10.67 UnnamedSequence 36959 37123 12804 + L1MdFanc_II_3end LINE/L1 832 981 6
945 8.14 0.61 10.67 UnnamedSequence 36959 37123 (12804) L1MdFanc_II_3end#LINE/L1 832 981 (6) c_b1s451i3
UnnamedSequen 36959 TGGTTTGCTGGGAAGATT-TATGACCCAGTACAGGGGAATGCCAGGGACA 37007
i -- v - v v
L1MdFanc_II_3 832 TGGTCT--TGCGAAGATTATATGCCCCAGTACAGGGGAATGCCAGGGCCA 879
UnnamedSequen 37008 GGAAGCGGGAGTGGGTGGGCTGGGAAGCAGGGTGGGAGGTGGGTGGGGGG 37057
i i i i ------------
L1MdFanc_II_3 880 GGAAGCGGGAGTGGGTGGGTTGGGGAGCAGGGCGGGGG------------ 917
UnnamedSequen 37058 TTGAGGGTATAGGGGACTTTCAGGATAGCATTTGAAGTGTAAATGAGGAA 37107
-- i i i
L1MdFanc_II_3 918 --GAGGGTATAGGGGACTTTCGGGATAGCATTTGAAATGTAAATGAAGAA 965
UnnamedSequen 37108 AATATCTAGTAAAAAA 37123
i
L1MdFanc_II_3 966 AATATCTAATAAAAAA 981
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 7.24
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.10 (17 / 164), avg. gap size = 1.00 (17 / 17)
+ 62 4.8 0.0 0.0 UnnamedSequence 37517 37582 (12982) + (TA)n Simple_repeat 1 66 (0) 87
ANNOTATION EVIDENCE:
62 4.77 0.00 0.00 UnnamedSequence 37517 37582 12982 + (TA)n Simple_repeat 1 66 0
62 4.77 0.00 0.00 UnnamedSequence 37517 37582 (12982) (TA)n#Simple_repeat 1 66 (0) c_b1s251i9
UnnamedSequen 37517 TATATATATATATATATATATGTATATATATATATATATATATATATATA 37566
i
(TA)n#Simple_ 1 TATATATATATATATATATATATATATATATATATATATATATATATATA 50
UnnamedSequen 37567 TATATACACATATATA 37582
i i
(TA)n#Simple_ 51 TATATATATATATATA 66
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 65), avg. gap size = 0.0 (0 / 0)
+ 267 19.7 0.0 1.5 UnnamedSequence 37584 37650 (12914) C RLTR17B_Mm LTR/ERVK (370) 432 367 88
ANNOTATION EVIDENCE:
267 19.70 0.00 1.52 UnnamedSequence 37584 37650 12342 C RLTR17B_Mm LTR/ERVK 367 432 370
267 19.70 0.00 1.52 UnnamedSequence 37584 37650 (12342) C RLTR17B_Mm#LTR/ERVK (370) 432 367 m_b1s501i34
UnnamedSequen 37584 ACACACACACACATATATATACTATGTATATGTATACACATATGTATATG 37633
? i ?i - ii ? i ?ii i i
C RLTR17B_Mm#LT 432 ANACACACATACATNCATATAC-ACATNTATATATACACATNCATACATA 384
UnnamedSequen 37634 TGTATATATCTATATAT 37650
ii i v
C RLTR17B_Mm#LT 383 TACATACATATATATAT 367
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 26.63
Transitions / transversions = 12.00 (12/1)
Gap_init rate = 0.02 (1 / 66), avg. gap size = 1.00 (1 / 1)
+ 943 13.3 7.1 4.0 UnnamedSequence 38148 38501 (12063) + Lx4A LINE/L1 6629 7057 (1) 89
ANNOTATION EVIDENCE:
891 9.87 2.70 4.11 UnnamedSequence 38148 38295 11697 + Lx4A_3end LINE/L1 1043 1188 284
891 9.87 2.70 4.11 UnnamedSequence 38148 38295 (11697) Lx4A_3end#LINE/L1 1043 1188 (284) m_b1s551i35
UnnamedSequen 38148 TTGCAGGGGCCCCAACGGGGATAGGAACTCCACAGGAAGAC----AGAGT 38193
-- i v ----
Lx4A_3end#LIN 1043 TTGC--GGGCCCCGAAGGGGATAGGAACTCCACAGGAAGACCAACAGAGT 1090
UnnamedSequen 38194 CAACTAACCTGAACCCATGGGGCTCTAAGAGTCTGAACCACCAACCAAAG 38243
i v v ?
Lx4A_3end#LIN 1091 CAACTAACCTGGACCCTTGGGGCTCTCAGAGNCTGAACCACCAACCAAAG 1140
UnnamedSequen 38244 ACCATATACCGGCTGGATCTAGGCTTCCTCGCACGCACGTGTGCAGCAGA 38293
v i v i i i---- i i i
Lx4A_3end#LIN 1141 AACATACACGGGCTGGACCTAGGCCTCCC----CGCACATATGTAGCAGA 1186
UnnamedSequen 38294 TG 38295
Lx4A_3end#LIN 1187 TG 1188
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 9.99
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.05 (7 / 147), avg. gap size = 1.43 (10 / 7)
868 19.63 10.36 6.57 UnnamedSequence 38164 38501 11491 + Lx2B2_3end LINE/L1 1052 1401 0
868 19.63 10.36 6.57 UnnamedSequence 38164 38501 (11491) Lx2B2_3end#LINE/L1 1052 1401 (0) m_b1s551i36
UnnamedSequen 38164 GGGGATAGGAACTCCACAGGAAGAC----AGAGTCAACTAACCTGAACCC 38209
i v i i ---- v i i
Lx2B2_3end#LI 1052 GGGGATGGCAACCCCATAGGAAGACCAACAGTGTCAACTAACCCGGACCC 1101
UnnamedSequen 38210 ATGGG-GCTCTAAGAGTCTGAACCACCAACCAAAGACCATATACCGGCTG 38258
v - iv v i i v i v
Lx2B2_3end#LI 1102 CTGGGAGCTCCCAGAGACTAAGCCACCAACCAAAGAGCATACACGGGCTG 1151
UnnamedSequen 38259 GATCTAGGCTTCCTCGCACGCACGTGTGCAGCAGATGGGGTCTGCTCTGT 38308
vi v? -- i --- i i i --- v -----
Lx2B2_3end#LI 1152 GTCCGNGGC--CCCCG---GCACATATGTAGCAGA---GGACTGC----- 1188
UnnamedSequen 38309 CCGGCCGTCTTGTCTGGTCTCAATGGGAGAGGAAGTGCCTAAGCCTCGCA 38358
-------- i i v i v - i
Lx2B2_3end#LI 1189 --------CTTGTCTGGCCTCAGTGGGAGAGGATGCGCCTAATCCT-GTA 1229
UnnamedSequen 38359 GAGAGTTGAAGTGCCAGGGTTGGGGGATACCCAG-----------GGGGT 38397
v v iv vv i vi -----------
Lx2B2_3end#LI 1230 GAGACTTGATGCCCCAGGGAAGGGGGATGCCGGGTGGGTGGGAGTGGGGT 1279
UnnamedSequen 38398 CC----CCACCCGCTCAGAGGAGAAGGGGA--GGGAA--GGATG------ 38433
vv----v v v -- -- i ------
Lx2B2_3end#LI 1280 GGGGGAGCACCCTCTCAGAGGCGAAGGGGAGGGGGAATGGGGTGAAGAAC 1329
UnnamedSequen 38434 --TGGGAAGGTGTGACTGGGAGAGGCAGGAAG---TGGTATATAAAAAGA 38478
-- i - v i i vi v v--- v i v i
Lx2B2_3end#LI 1330 TCTGGGAGGG-GGGACCGGGAGGGGGGGCAACATTTGGAATGTAAATAAA 1378
UnnamedSequen 38479 AAAAAAAAGTAAAAAAGAAAAAA 38501
v v v v i
Lx2B2_3end#LI 1379 TAAAATAATTAATAAAAAAAAAA 1401
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 21.81
Transitions / transversions = 0.88 (29/33)
Gap_init rate = 0.09 (32 / 337), avg. gap size = 1.81 (58 / 32)
943 11.16 7.07 2.60 UnnamedSequence 38311 38494 11498 + Lx4A_3end LINE/L1 1280 1471 1
943 11.16 7.07 2.60 UnnamedSequence 38311 38494 (11498) Lx4A_3end#LINE/L1 1280 1471 (1) m_b1s551i37
UnnamedSequen 38311 GGCCGTCTTGTCTGGTCTCAATGGGAGAGGAAGTGCCTAAGCCTCGCAGA 38360
i i i i ? i -
Lx4A_3end#LIN 1280 GGCTGCCTTGTCTGGCCTCAGTGGGAGAGGANGCGCCTA-GCCTCGCAGA 1328
UnnamedSequen 38361 GAGTTGAAGTGCCAGGGTTGGGGGATACCCAGGGGGTCCCCACCCGCTCA 38410
v ? v v
Lx4A_3end#LIN 1329 GACTTGANGTGCCAGGGTGGGGGGATACCCAGGGGGGCCCCACCCGCTCA 1378
UnnamedSequen 38411 GAGGAGAAGGGGA----------GGGAAGGA-TGTGGGAAGGTGTGACTG 38449
---------- - i v i
Lx4A_3end#LIN 1379 GAGGAGAAGGGGAGGGGGGATGGGGGAAGGATTGTGGGAGGGGGTGACCG 1428
UnnamedSequen 38450 GGA--GAGGCAGGAAGTGGTATATAAAAAGAAAAAAAAAGTAAAAAA 38494
-- i vi i v i iv ---- v
Lx4A_3end#LIN 1429 GGAGGGGGGCAGTGAGCGGGATGTAAAGTG----AATAAGTAAAAAA 1471
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 10.51
Transitions / transversions = 1.50 (12/8)
Gap_init rate = 0.04 (8 / 183), avg. gap size = 2.25 (18 / 8)
+ 68 0.0 0.0 5.3 UnnamedSequence 38511 38589 (11975) + (AAACC)n Simple_repeat 1 75 (0) 90
ANNOTATION EVIDENCE:
68 0.00 0.00 5.33 UnnamedSequence 38511 38589 11975 + (AAACC)n Simple_repeat 1 75 0
68 0.00 0.00 5.33 UnnamedSequence 38511 38589 (11975) (AAACC)n#Simple_repeat 1 75 (0) c_b1s251i10
UnnamedSequen 38511 AAACCAAACCAAACCGTTTAAACCAAACCAAACCAAACCAAACCAAACCA 38560
----
(AAACC)n#Simp 1 AAACCAAACCAAACC----AAACCAAACCAAACCAAACCAAACCAAACCA 46
UnnamedSequen 38561 AACCAAACCAAACCAAACCAAACCAAACC 38589
(AAACC)n#Simp 47 AACCAAACCAAACCAAACCAAACCAAACC 75
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.05 (4 / 78), avg. gap size = 1.00 (4 / 4)
+ 65 0.0 0.0 0.0 UnnamedSequence 38961 39015 (11549) + (TG)n Simple_repeat 1 55 (0) 91
ANNOTATION EVIDENCE:
65 0.00 0.00 0.00 UnnamedSequence 38961 39015 11549 + (TG)n Simple_repeat 1 55 0
65 0.00 0.00 0.00 UnnamedSequence 38961 39015 (11549) (TG)n#Simple_repeat 1 55 (0) c_b1s251i11
UnnamedSequen 38961 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 39010
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG 50
UnnamedSequen 39011 TGTGT 39015
(TG)n#Simple_ 51 TGTGT 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 233 27.0 9.2 2.1 UnnamedSequence 39315 39401 (11163) C B1F SINE/Alu (52) 97 5 92
ANNOTATION EVIDENCE:
233 27.02 9.20 2.15 UnnamedSequence 39315 39401 10723 C B1F SINE/Alu 5 97 52
233 27.02 9.20 2.15 UnnamedSequence 39315 39401 (10723) C B1F#SINE/Alu (52) 97 5 m_b1s501i35
UnnamedSequen 39315 TCACTGTGGAGCCCACGTTGACCTGGAACTCACAG------TTCTGCCCT 39358
i v v i i v i ------ i ii
C B1F#SINE/Alu 97 TCACTATGTAGCCCAGGCTGGCCTCGAACTCACGGCAATCCTCCTGCCTC 48
UnnamedSequen 39359 GGAAT-TCAAGTGGACT-GGAGTACACGTGTATGCCACCCTGACC 39401
i vv -i i -- - v v i iv vi v
C B1F#SINE/Alu 47 AGCCTCCCGAGTG--CTGGGATTACAGGCGTGAGCCACCACGCCC 5
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 27.39
Transitions / transversions = 1.30 (13/10)
Gap_init rate = 0.06 (5 / 86), avg. gap size = 2.00 (10 / 5)
+ 246 13.2 10.7 5.1 UnnamedSequence 39582 39637 (10927) + RLTR20A3_MM LTR/ERVK 426 484 (64) 93
ANNOTATION EVIDENCE:
246 13.17 10.71 5.08 UnnamedSequence 39582 39637 10487 + RLTR20A3_MM LTR/ERVK 426 484 64
246 13.17 10.71 5.08 UnnamedSequence 39582 39637 (10487) RLTR20A3_MM#LTR/ERVK 426 484 (64) m_b1s501i36
UnnamedSequen 39582 AGTTGGTGTGTGTGTGTGTGTGTGTGTGTATA-CTTTCAT-----AATTA 39625
i i i i- ----- i-
RLTR20A3_MM#L 426 AGCTGGCGTGTGTGTGTGTGTGTGTGTGTGTGTCTTTCATTCGCGAATC- 474
UnnamedSequen 39626 AGCAAAGAGCCC 39637
-- i i
RLTR20A3_MM#L 475 --CAGAGAGCTC 484
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 13.08
Transitions / transversions = 1.00 (7/0)
Gap_init rate = 0.09 (5 / 55), avg. gap size = 1.80 (9 / 5)
+ 236 29.9 7.9 12.9 UnnamedSequence 40113 40404 (10160) C LTR103b_Mam LTR/ERV1 (54) 494 216 94
ANNOTATION EVIDENCE:
236 29.89 7.88 12.90 UnnamedSequence 40113 40404 9720 C LTR103b_Mam LTR/ERV1 216 494 54
236 29.89 7.88 12.90 UnnamedSequence 40113 40404 (9720) C LTR103b_Mam#LTR/ERV1 (54) 494 216 m_b1s501i37
UnnamedSequen 40113 ACGGTGCTACAGAGGGGTAGTTTCAGAAGAAACAGAAGTT----TCCAAA 40158
ii ---------- i i v i i----
C LTR103b_Mam#L 494 ACGGTGTCACA----------TCCAAAAGAAACACAAATCCGACTCCAAA 455
UnnamedSequen 40159 CACCTTCTGTAAAATGATATAGAAATGGAAGCTTCAGTGAGAGTTT---G 40205
vi ? -- v i i i -------v i v ii ---
C LTR103b_Mam#L 454 AGCNTT--GAAAAGTAATGTAGA-------TCTTTACTGAAGGTTTCTTG 414
UnnamedSequen 40206 GGGA--CAGAGGAAAGCATT---TC-TATGCTAAAAATCAGTTGACATTT 40249
-- i i ii vi --- -i ii?i v v v i--i v ii
C LTR103b_Mam#L 413 GGGAGGCGGAGAAGGGGGTTACATCGCACANCACACAGCAA--AACTTCC 366
UnnamedSequen 40250 TAAAAAGTATCTTTAT---TTTATTTTTTTAAACAATCCAGCCATTATTC 40296
viv v--- i v i i ------- -- vvi
C LTR103b_Mam#L 365 TAAAAATCCTCTTTAAACATCTCTCTCTTT-------CC--CCAAAGTTC 325
UnnamedSequen 40297 C---CTTCGCGGCCGCCTTCGCTCAGTTTCTCATGCCATTCCTTTCCTGT 40343
--- i i v i--- viii - v vi vii ?vi
C LTR103b_Mam#L 324 CACTCCTCACGGCAGCT---GCTCCACCTCTC-TCCCTCTCCACCCCNTC 279
UnnamedSequen 40344 CCAGGTCCCTCCCTCCCTCCCTCCCTCCTTCTGCTCCC---TCCCTCT-G 40389
i ii - ? i vv i?i v ii --- -?
C LTR103b_Mam#L 278 TCAAATCC-TCNCCCCAGCTNCCCCTCCTTCTCCCTCCGNNTCCCTCTCN 230
UnnamedSequen 40390 CTCCCTCCCGTGATT 40404
ii - ?
C LTR103b_Mam#L 229 CCTCCTCCC-TGNTT 216
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 40.54
Transitions / transversions = 2.04 (51/25)
Gap_init rate = 0.15 (45 / 291), avg. gap size = 1.31 (59 / 45)
+ 1136 7.4 0.0 0.0 UnnamedSequence 41466 41600 (8964) C B1_Mus1 SINE/Alu (11) 137 3 95
ANNOTATION EVIDENCE:
1136 7.41 0.00 0.00 UnnamedSequence 41466 41600 8658 C B1_Mus1 SINE/Alu 3 137 11
1136 7.41 0.00 0.00 UnnamedSequence 41466 41600 (8658) C B1_Mus1#SINE/Alu (11) 137 3 c_b1s355i8
UnnamedSequen 41466 CAAAGCAGGGTTTCTCTGTGTAGCCCTGGCAGTCCTGGAACTCACTTTGT 41515
i ii v i
C B1_Mus1#SINE/ 137 CGAGACAGGGTTTCTCTGTGTAGCCCTGGCTGTCCTGGAACTCACTCTGT 88
UnnamedSequen 41516 AGACCAGGCTGGCCTCAAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAG 41565
i
C B1_Mus1#SINE/ 87 AGACCAGGCTGGCCTCGAACTCAGAAATCCGCCTGCCTCTGCCTCCCAAG 38
UnnamedSequen 41566 TGCTAGGACTAAAGGCGTGTGCCACCACTGCCCGG 41600
i i i i
C B1_Mus1#SINE/ 37 TGCTGGGATTAAAGGCGTGCGCCACCACCGCCCGG 3
Matrix = 18p41g.matrix
Kimura (with divCpGMod) = 4.95
Transitions / transversions = 9.00 (9/1)
Gap_init rate = 0.00 (0 / 134), avg. gap size = 0.0 (0 / 0)
+ 600 25.6 7.3 2.9 UnnamedSequence 41783 41947 (8617) C B3A SINE/B2 (25) 173 2 96
ANNOTATION EVIDENCE:
600 25.59 7.27 2.91 UnnamedSequence 41783 41947 8311 C B3A SINE/B2 2 173 25
600 25.59 7.27 2.91 UnnamedSequence 41783 41947 (8311) C B3A#SINE/B2 (25) 173 2 m_b1s501i38
UnnamedSequen 41783 GTGTATACAC---CGCTTGCACGGTGCTCACAGAGGTCACA----GGCAT 41825
i i i ---i ?v i- i i i i v ---- i
C B3A#SINE/B2 173 GTGTGTGCGCGTGTGNGTGCG-GGTGCCCGCGGAGGCCAGAAGAGGGCGT 125
UnnamedSequen 41826 CGAATTCCCAGGAGCTGAAATTCCAGGCTGATATAAGCTTCCTCAAGTGG 41875
i i v i i v v v i i iv iv v
C B3A#SINE/B2 124 CGGATCCCCTGGAGCTGGAGTTACAGGCGGTTGTGAGCCGCCCGACGTGG 75
UnnamedSequen 41876 GTGTTGGGAATT---TTTGAGTTTTACCTCAGGAAAAGCAG--GGCACTC 41920
i ii---i i i ---- v v i --i i
C B3A#SINE/B2 74 GTGCTGGGAACCGAACTCGGGT----CCTCTGCAAGAGCAGCAAGCGCTC 29
UnnamedSequen 41921 TTAACAGCTGAGCCACGTCTCCAGCCC 41947
v iv
C B3A#SINE/B2 28 TTAACCGCTGAGCCATCTCTCCAGCCC 2
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.80
Transitions / transversions = 2.15 (28/13)
Gap_init rate = 0.05 (9 / 164), avg. gap size = 1.89 (17 / 9)
+ 19 0.0 0.0 0.0 UnnamedSequence 42207 42230 (8334) + (GGCG)n Simple_repeat 1 24 (0) 97
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 UnnamedSequence 42207 42230 8028 + (GGCG)n Simple_repeat 1 24 0
19 0.00 0.00 0.00 UnnamedSequence 42207 42230 (8028) (GGCG)n#Simple_repeat 1 24 (0) m_b1s252i17
UnnamedSequen 42207 GGCGGGCGGGCGGGCGGGCGGGCG 42230
(GGCG)n#Simpl 1 GGCGGGCGGGCGGGCGGGCGGGCG 24
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 314 31.3 13.7 7.6 UnnamedSequence 43383 43593 (6971) + MLT1D LTR/ERVL-MaLR 262 484 (21) 98
ANNOTATION EVIDENCE:
314 31.29 13.74 7.62 UnnamedSequence 43383 43593 6665 + MLT1D LTR/ERVL-MaLR 262 484 21
314 31.29 13.74 7.62 UnnamedSequence 43383 43593 (6665) MLT1D#LTR/ERVL-MaLR 262 484 (21) m_b1s501i39
UnnamedSequen 43383 GAAGATATAAGCAGAGACACAGAGGTCAGAGAGATGTCGGCATCCTGGGC 43432
iv i v i i - vii i ii - iv iv ---
MLT1D#LTR/ERV 262 GAAGATGGAGGAAGGGGC-CACGAGCCAAGGA-ATGCGGGCGGCCT---C 306
UnnamedSequen 43433 CAACAACAGACACTAAGCTAGAATA---AAGAAAGCCCATTCTGGCTTTT 43479
i i----------- i v --- i i vv vv i vv
MLT1D#LTR/ERV 307 TAG-----------AAGCTGGAAAAGGCAAGGAAACGGATTCTCCCCTAG 345
UnnamedSequen 43480 AGCCTTCTAAAGGAATGGAGCCCT-CCG---------------------- 43506
i vi i v - ----------------------
MLT1D#LTR/ERV 346 AGCCTCCAGAAGGAACGCAGCCCTGCCGACACCTTGATTTTAGCCCAGTG 395
UnnamedSequen 43507 -GACTCATTTTAGACACCCGGCTCCTATAATTACACAATGATAATTTTGT 43555
- i ii vi i i ii i v i ii vi i v
MLT1D#LTR/ERV 396 AGACCCATTTCGGACTTCTGACCTCCAGAACTGTAAGATAATAAATTTGT 445
UnnamedSequen 43556 GTTTGTTTT-AGTCATGAAATGTGTGGCAACTGATT-CAG 43593
- - i iv i v i i vi -
MLT1D#LTR/ERV 446 G-TTGTTTTAAGCCACTAAGTTTGTGGTAATTTGTTACAG 484
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 38.15
Transitions / transversions = 1.90 (40/21)
Gap_init rate = 0.11 (23 / 210), avg. gap size = 2.00 (46 / 23)
+ 1301 22.0 12.7 4.6 UnnamedSequence 43614 43975 (6589) C MTD LTR/ERVL-MaLR (0) 419 30 99
ANNOTATION EVIDENCE:
1301 22.01 12.71 4.62 UnnamedSequence 43614 43975 6283 C MTD LTR/ERVL-MaLR 30 419 0
1301 22.01 12.71 4.62 UnnamedSequence 43614 43975 (6283) C MTD#LTR/ERVL-MaLR (0) 419 30 m_b1s501i40
UnnamedSequen 43614 TGTTTTAGTT-TGCTTTCTATTGCTATAACAAAG-GCCATGACCAAAAGT 43661
ii -v v i i i i-i i
C MTD#LTR/ERVL- 419 TGTCCTAGTTAGGGTTTCTATTGCTGTGATAAAACACCATGACCAAAAGC 370
UnnamedSequen 43662 ATCCT-GGGAAGAAAGGAT-------AA---------------CACAGGT 43688
v i - i i ------- i--------------- vi
C MTD#LTR/ERVL- 369 AACTTGGGGAGGAAAGGGTTTATTTCAGCTTACAGTTCCAGGTCACAGTC 320
UnnamedSequen 43689 CATCCCTGAGGGAAGGCAAGGCAGGAACTCAAGCTGTACAGGAACCTGCA 43738
v i v i ----i v
C MTD#LTR/ERVL- 319 CATCACCGAGGGAAGTCAGGGCAGGAACTCAAG----GCAGGAACCTGGA 274
UnnamedSequen 43739 GGAAAGGACTGCTGAAGCGGA--CAATGGAGGGGCACT-CTCAC------ 43779
v i i --- i -- v ii i - i ------
C MTD#LTR/ERVL- 273 GGCAGGAA---CTGAAGCAGAGGCCATGGAGGAACGCTGCTTACTGGCTT 227
UnnamedSequen 43780 --------TGGCTTGCTCAGCTTGCTTTTTTA----ATGCAGGCAAACCA 43817
-------- i i ---- iv ---
C MTD#LTR/ERVL- 226 GCTCCCCATGGCTTGCTCAGCCTGCTTTCTTATACNACCCAGG---ACCA 180
UnnamedSequen 43818 ACTAACGGTCTAAGGGTCGCATTGACCACATTGAGTTGGATCCTCCTATA 43867
v ---- i i i v ii v v i i ii i i
C MTD#LTR/ERVL- 179 CCT----GCCCAGGGGTGGCACCGCCCACAGTGGGCTGGGCCCTCCCACA 134
UnnamedSequen 43868 TCAATCAGAAACCAAGAAAGTGTGCCTCCCAAGGATTTGCCTACAGGCCA 43917
vv i i ----i vi i i
C MTD#LTR/ERVL- 133 TCAATCATCAATCAAGAAAATG----CCCCACAGACTTGCCCACAGGCCA 88
UnnamedSequen 43918 ATATGGTGATTACAATTTTTTAATTAAGGTACCTTCTTTCCAAATTACTC 43967
v i ivvi v i i i v i i i v
C MTD#LTR/ERVL- 87 ATCTGATGGAGGCATTTTCTCAATTGAGGTTCCCTCTTCCCAGATGACTC 38
UnnamedSequen 43968 TAGTTTGT 43975
i
C MTD#LTR/ERVL- 37 TAGCTTGT 30
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 25.85
Transitions / transversions = 2.30 (53/23)
Gap_init rate = 0.08 (28 / 361), avg. gap size = 2.29 (64 / 28)
+ 558 28.9 6.8 2.4 UnnamedSequence 43997 44159 (6405) + ID_B1 SINE/B4 37 206 (18) 100
ANNOTATION EVIDENCE:
558 28.90 6.75 2.35 UnnamedSequence 43997 44159 6099 + ID_B1 SINE/B4 37 206 18
558 28.90 6.75 2.35 UnnamedSequence 43997 44159 (6099) ID_B1#SINE/B4 37 206 (18) m_b1s501i41
UnnamedSequen 43997 CCTAGCATATGAAAGAGACTCTGGGTTCAAACTGCAACACTGCAGGAACC 44046
-- v v ii i i v iv i i vi v
ID_B1#SINE/B4 37 CCTAGCAT--GCACGAAGCCCTGGGTTCGATCCCCAGCACCGCATAAAAC 84
UnnamedSequen 44047 C-----------TGCATACCTGTATCCTCAACACCCAGGGTGTAGAGGCA 44085
-----------i ii vi i i i i iv i
ID_B1#SINE/B4 85 CGGGCGTGGTGGCGCACGCCTGTAATCCCAGCACTCGGGAGGTGGAGGCA 134
UnnamedSequen 44086 GGAGGTTTAGAATTTCAAAGTCACCTTCAGGTACAGATATTGTCCTGGAA 44135
v i v i i i i v -- vi vvi v i
ID_B1#SINE/B4 135 GGAGGATCAGAAGTTCAAGGTCATCCTCGGCTAC--ATAGCGAGTTCGAG 182
UnnamedSequen 44136 GCCAATGTGAGCTGCATGAGACCC 44159
iiv i i
ID_B1#SINE/B4 183 GCCAGCCTGGGCTACATGAGACCC 206
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 30.95
Transitions / transversions = 1.88 (30/16)
Gap_init rate = 0.03 (5 / 162), avg. gap size = 3.00 (15 / 5)
+ 307 15.8 19.5 0.0 UnnamedSequence 44181 44262 (6302) + Lx6 LINE/L1 7358 7455 (5) 101
ANNOTATION EVIDENCE:
307 15.85 19.51 0.00 UnnamedSequence 44181 44262 5996 + Lx6_3end LINE/L1 1772 1869 5
307 15.85 19.51 0.00 UnnamedSequence 44181 44262 (5996) Lx6_3end#LINE/L1 1772 1869 (5) m_b1s551i38
UnnamedSequen 44181 GAGGGGAGGAGGGGAAGGACTAGGAGG-------------GAAACTGTAA 44217
v i i i -------------
Lx6_3end#LINE 1772 GAGGGGAGGTGGGGAGGAACTGGGAGGAGTAGAGGGAGGGGAAACTGTAA 1821
UnnamedSequen 44218 TCAGGATGTGTTATATGACAAAAA---CTATTTTACATAAAAGGAAAA 44262
i i i v i--- vv i i
Lx6_3end#LINE 1822 TCAGGATATATTGTATGAGAAAAGAATCTATTTTCAATAAAAGAAGAA 1869
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 18.19
Transitions / transversions = 2.25 (9/4)
Gap_init rate = 0.02 (2 / 81), avg. gap size = 8.00 (16 / 2)
+ 504 1.6 1.6 0.0 UnnamedSequence 44289 44352 (6212) + B1_Mus2 SINE/Alu 83 147 (0) 102
ANNOTATION EVIDENCE:
504 1.56 1.56 0.00 UnnamedSequence 44289 44352 5906 + B1_Mus2 SINE/Alu 83 147 0
504 1.56 1.56 0.00 UnnamedSequence 44289 44352 (5906) B1_Mus2#SINE/Alu 83 147 (0) m_b1s501i42
UnnamedSequen 44289 GTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGT 44338
B1_Mus2#SINE/ 83 GTCTACAGAGTGAGTTCCAGGACAGCCAGGGCTACACAGAGAAACCCTGT 132
UnnamedSequen 44339 CTC-AAAAAATAAAA 44352
- i
B1_Mus2#SINE/ 133 CTCGAAAAAACAAAA 147
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 1.59
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.02 (1 / 63), avg. gap size = 1.00 (1 / 1)
+ 33 8.4 6.2 1.5 UnnamedSequence 44353 44417 (6147) + GA-rich Low_complexity 1 68 (0) 103
ANNOTATION EVIDENCE:
33 8.41 6.15 1.47 UnnamedSequence 44353 44417 5841 + (AGAA)n Simple_repeat 1 68 0
33 8.41 6.15 1.47 UnnamedSequence 44353 44417 (5841) (AGAA)n#Simple_repeat 1 68 (0) m_b1s252i18
UnnamedSequen 44353 AGAAAAAAAGAAA-AAAGAAAAAGAAG-AAGAGAGAAAGAAAGAAAGAAA 44400
i - i - - i
(AGAA)n#Simpl 1 AGAAAGAAAGAAAGAAAGAAAGA-AAGAAAGAAAGAAAGAAAGAAAGAAA 49
UnnamedSequen 44401 G-AA-AAAGAACGAACGAA 44417
- - v v
(AGAA)n#Simpl 50 GAAAGAAAGAAAGAAAGAA 68
Matrix = Unknown
Transitions / transversions = 1.50 (3/2)
Gap_init rate = 0.08 (5 / 64), avg. gap size = 1.00 (5 / 5)
+ 12 14.4 0.0 0.0 UnnamedSequence 44534 44557 (6007) + (CAA)n Simple_repeat 1 24 (0) 104
ANNOTATION EVIDENCE:
12 14.38 0.00 0.00 UnnamedSequence 44534 44557 5701 + (CAA)n Simple_repeat 1 24 0
12 14.38 0.00 0.00 UnnamedSequence 44534 44557 (5701) (CAA)n#Simple_repeat 1 24 (0) m_b1s252i19
UnnamedSequen 44534 CAACAACAACAACAGCAGCAGCAA 44557
i i i
(CAA)n#Simple 1 CAACAACAACAACAACAACAACAA 24
Matrix = Unknown
Transitions / transversions = 1.00 (3/0)
Gap_init rate = 0.00 (0 / 23), avg. gap size = 0.0 (0 / 0)
+ 180 24.5 8.2 0.0 UnnamedSequence 44650 44698 (5866) + Tigger19b DNA/TcMar-Tigger 122 174 (376) 105
ANNOTATION EVIDENCE:
180 24.49 8.16 0.00 UnnamedSequence 44650 44698 5560 + Tigger19b DNA/TcMar-Tigger 122 174 376
180 24.49 8.16 0.00 UnnamedSequence 44650 44698 (5560) Tigger19b#DNA/TcMar-Tigger 122 174 (376) m_b1s601i2
UnnamedSequen 44650 CATCTTAGCTCCCTCCGTCCG-TCTAC---CAGAGAGGCATTCTGAAATG 44695
i i iii- i --- i vi i iv
Tigger19b#DNA 122 CATCTCAGCTCCCTCTGTTTACTCTGCACGCAGAGAAGCCCTTTGAAACC 171
UnnamedSequen 44696 CAA 44698
Tigger19b#DNA 172 CAA 174
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 31.93
Transitions / transversions = 5.00 (10/2)
Gap_init rate = 0.04 (2 / 48), avg. gap size = 2.00 (4 / 2)
+ 401 24.3 4.4 5.4 UnnamedSequence 44749 44861 (5703) + B3 SINE/B2 105 216 (0) 106
ANNOTATION EVIDENCE:
401 24.31 4.42 5.36 UnnamedSequence 44749 44861 5397 + B3 SINE/B2 105 216 0
401 24.31 4.42 5.36 UnnamedSequence 44749 44861 (5397) B3#SINE/B2 105 216 (0) m_b1s501i43
UnnamedSequen 44749 CCAGTTCTGGGGGACCTCACACC---TTTTGGCCTTGGGTGGACATCACG 44795
ii i iv i --- i iv -i i i v
B3#SINE/B2 105 CCAGTTCCAGGGGATCCGACGCCCTCTTCTGGCCTCCG-CGGGCACCAGG 153
UnnamedSequen 44796 AATACATGTGCTGAA--GATATACATTCAGGTAAAACACCTACACACAAG 44843
v ii i v v -- i v i i i ----
B3#SINE/B2 154 CACGCACGTGGTGCACAGACATACATGCAGGCAAAACACCCATACA---- 199
UnnamedSequen 44844 TCATAAACTAATAATAAA 44861
- v v
B3#SINE/B2 200 -CATAAAATAAAAATAAA 216
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 23.59
Transitions / transversions = 1.89 (17/9)
Gap_init rate = 0.07 (8 / 112), avg. gap size = 1.38 (11 / 8)
+ 541 25.0 5.3 3.7 UnnamedSequence 45081 45213 (5351) + RSINE1 SINE/B4 3 137 (28) 107
ANNOTATION EVIDENCE:
541 24.98 5.26 3.70 UnnamedSequence 45081 45213 5045 + RSINE1 SINE/B4 3 137 28
541 24.98 5.26 3.70 UnnamedSequence 45081 45213 (5045) RSINE1#SINE/B4 3 137 (28) m_b1s501i44
UnnamedSequen 45081 GGGTATGCAAGATGGCTCTGCAGGTAACAAACAGGC-TTTGCTGTCAAGT 45129
ivv i v i ----- -i i i i
RSINE1#SINE/B 3 GGGCCGGCGAGATGGCTCAGCGGGTAA-----AGGCGCTTGCCGCCAAGC 47
UnnamedSequen 45130 CTGACA--CTG---TCCATTTTCCAGATTCATATGGTGAAAAGACGGAAC 45174
i-- --- v iii vi ii i i i vi
RSINE1#SINE/B 48 CTGACGACCTGAGTTCGATCCCCGGGACCCACATGGTGGAAGGAGAGAAC 97
UnnamedSequen 45175 TACATCCCATAAGTTGTCCTCTGACCTCCACACACA-GCC 45213
iivv ii i i-
RSINE1#SINE/B 98 CGACTCCCGCAAGTTGTCCTCTGACCTCCACACGCGCGCC 137
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 22.87
Transitions / transversions = 3.00 (24/8)
Gap_init rate = 0.07 (9 / 132), avg. gap size = 1.33 (12 / 9)
+ 20 8.6 2.6 2.6 UnnamedSequence 45724 45762 (4802) + (CAAA)n Simple_repeat 1 39 (0) 108
ANNOTATION EVIDENCE:
20 8.63 2.56 2.56 UnnamedSequence 45724 45762 4496 + (CAAA)n Simple_repeat 1 39 0
20 8.63 2.56 2.56 UnnamedSequence 45724 45762 (4496) (CAAA)n#Simple_repeat 1 39 (0) m_b1s252i20
UnnamedSequen 45724 CAAAAAAACCAAACAAACAAAAAAAGAAACAAA-AAACAA 45762
v - v v -
(CAAA)n#Simpl 1 CAAACAAA-CAAACAAACAAACAAACAAACAAACAAACAA 39
Matrix = Unknown
Transitions / transversions = 0.00 (0/3)
Gap_init rate = 0.05 (2 / 38), avg. gap size = 1.00 (2 / 2)
+ 14 0.0 0.0 8.3 UnnamedSequence 45906 45931 (4633) + (TCCC)n Simple_repeat 1 24 (0) 109
ANNOTATION EVIDENCE:
14 0.00 0.00 8.33 UnnamedSequence 45906 45931 4327 + (TCCC)n Simple_repeat 1 24 0
14 0.00 0.00 8.33 UnnamedSequence 45906 45931 (4327) (TCCC)n#Simple_repeat 1 24 (0) m_b1s252i22
UnnamedSequen 45906 TCCCTCCCTCCCTCCCTTCTCCTCCC 45931
- -
(TCCC)n#Simpl 1 TCCCTCCCTCCCTCCC-TC-CCTCCC 24
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.08 (2 / 25), avg. gap size = 1.00 (2 / 2)
+ 65 0.0 0.0 0.0 UnnamedSequence 45941 45995 (4569) + (GT)n Simple_repeat 1 55 (0) 110
ANNOTATION EVIDENCE:
65 0.00 0.00 0.00 UnnamedSequence 45941 45995 4569 + (GT)n Simple_repeat 1 55 0
65 0.00 0.00 0.00 UnnamedSequence 45941 45995 (4569) (GT)n#Simple_repeat 1 55 (0) c_b1s251i12
UnnamedSequen 45941 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 45990
(GT)n#Simple_ 1 GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 50
UnnamedSequen 45991 GTGTG 45995
(GT)n#Simple_ 51 GTGTG 55
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 54), avg. gap size = 0.0 (0 / 0)
+ 422 8.8 0.0 0.0 UnnamedSequence 46367 46446 (4118) + Lx3_Mus LINE/L1 6015 6094 (915) 111
ANNOTATION EVIDENCE:
422 8.75 0.00 0.00 UnnamedSequence 46367 46446 3866 + Lx3_Mus_3end LINE/L1 429 508 915
422 8.75 0.00 0.00 UnnamedSequence 46367 46446 (3866) Lx3_Mus_3end#LINE/L1 429 508 (915) m_b1s551i39
UnnamedSequen 46367 GAAGAAAGCAATCACAAGTGGGGAGGGAGGGAGGGACCTGGGAGGGAAAG 46416
Lx3_Mus_3end# 429 GAAGAAAGCAATCACAAGTGGGGAGGGAGGGAGGGACCTGGGAGGGAAAG 478
UnnamedSequen 46417 TAGAAGGGTTGGGGAGGGAGTTGGGGAGAA 46446
i v v i ? v i i
Lx3_Mus_3end# 479 TGGACGGGGTGGGGGGGNAGTGGGGGGGGA 508
Matrix = 20p41g.matrix
Kimura (with divCpGMod) = 9.47
Transitions / transversions = 1.33 (4/3)
Gap_init rate = 0.00 (0 / 79), avg. gap size = 0.0 (0 / 0)
+ 323 24.7 5.6 1.1 UnnamedSequence 46627 46716 (3848) C PB1D9 SINE/Alu (3) 117 24 112
ANNOTATION EVIDENCE:
323 24.70 5.56 1.06 UnnamedSequence 46627 46716 3596 C PB1D9 SINE/Alu 24 117 3
323 24.70 5.56 1.06 UnnamedSequence 46627 46716 (3596) C PB1D9#SINE/Alu (3) 117 24 m_b1s501i45
UnnamedSequen 46627 TGTTTCT---ATACAGGGTTTTCTCTATGTCATCCCTGCTGACCTAGAAC 46673
i --- v i - v i vii iv i v
C PB1D9#SINE/Al 117 TGTTTTTTTGAGACAGGGTCT-CACTGTGTAGCCCTGGCTGGCCTCGAAC 69
UnnamedSequen 46674 TGA-AAAGATTAGTTTGCCTCTGTCTCTTGA-TTCTGGGATTAAA 46716
v - i iv ii i ii - v
C PB1D9#SINE/Al 68 TCACAGAGATCCGCCTGCCTCTGCCTCCCGAGTGCTGGGATTAAA 24
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 29.20
Transitions / transversions = 1.75 (14/8)
Gap_init rate = 0.04 (4 / 89), avg. gap size = 1.50 (6 / 4)
+ 90 0.0 0.0 0.0 UnnamedSequence 46765 46843 (3721) + (CTCTT)n Simple_repeat 1 79 (0) 113
ANNOTATION EVIDENCE:
90 0.00 0.00 0.00 UnnamedSequence 46765 46843 3721 + (CTCTT)n Simple_repeat 1 79 0
90 0.00 0.00 0.00 UnnamedSequence 46765 46843 (3721) (CTCTT)n#Simple_repeat 1 79 (0) c_b1s251i13
UnnamedSequen 46765 CTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT 46814
(CTCTT)n#Simp 1 CTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTTCTCTT 50
UnnamedSequen 46815 CTCTTCTCTTCTCTTCTCTTCTCTTCTCT 46843
(CTCTT)n#Simp 51 CTCTTCTCTTCTCTTCTCTTCTCTTCTCT 79
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 78), avg. gap size = 0.0 (0 / 0)
+ 47 1.2 10.8 1.1 UnnamedSequence 46857 46939 (3625) + (CTC)n Simple_repeat 1 91 (0) 114
ANNOTATION EVIDENCE:
47 1.24 10.84 1.10 UnnamedSequence 46857 46939 3625 + (CTC)n Simple_repeat 1 91 0
47 1.24 10.84 1.10 UnnamedSequence 46857 46939 (3625) (CTC)n#Simple_repeat 1 91 (0) c_b1s251i14
UnnamedSequen 46857 CTCC-CCTCC-CCTCC-CCTCC-CCTCTCTCCTCCTCCTCCTCCTCCTCC 46902
- - - - -
(CTC)n#Simple 1 CTCCTCCTCCTCCTCCTCCTCCTCCTC-CTCCTCCTCCTCCTCCTCCTCC 49
UnnamedSequen 46903 TCTTCCTCCT-CTCCT-CTCCT-CTCCT-CTCCT-CTCCTCC 46939
i - - - - -
(CTC)n#Simple 50 TCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCCTCC 91
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.12 (10 / 82), avg. gap size = 1.00 (10 / 10)
+ 11 15.0 8.8 5.1 UnnamedSequence 47086 47142 (3422) + (ACTGCAA)n Simple_repeat 1 59 (0) 115
ANNOTATION EVIDENCE:
11 15.00 8.77 5.08 UnnamedSequence 47086 47142 3330 + (ACTGCAA)n Simple_repeat 1 59 0
11 15.00 8.77 5.08 UnnamedSequence 47086 47142 (3330) (ACTGCAA)n#Simple_repeat 1 59 (0) m_b1s252i23
UnnamedSequen 47086 ACTCCAAA-GGCAAACTTC--TCAGC-AACTGGTAACACTGCAAA-TGTT 47130
v -v v --v v - - i - - -i
(ACTGCAA)n#Si 1 ACTGCAAACTGCAAACTGCAAACTGCAAACT-GCAA-ACTGCAAACTG-C 47
UnnamedSequen 47131 AAACTGCAAACT 47142
(ACTGCAA)n#Si 48 AAACTGCAAACT 59
Matrix = Unknown
Transitions / transversions = 0.40 (2/5)
Gap_init rate = 0.12 (7 / 56), avg. gap size = 1.14 (8 / 7)
+ 16 4.1 0.0 3.9 UnnamedSequence 47636 47662 (2902) + (AACA)n Simple_repeat 1 26 (0) 116
ANNOTATION EVIDENCE:
16 4.12 0.00 3.85 UnnamedSequence 47636 47662 2810 + (AACA)n Simple_repeat 1 26 0
16 4.12 0.00 3.85 UnnamedSequence 47636 47662 (2810) (AACA)n#Simple_repeat 1 26 (0) m_b1s252i24
UnnamedSequen 47636 AACAACAAAAACAAACAAACAAACAAA 47662
- v
(AACA)n#Simpl 1 AACAA-ACAAACAAACAAACAAACAAA 26
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.04 (1 / 26), avg. gap size = 1.00 (1 / 1)
+ 240 19.2 0.0 16.9 UnnamedSequence 48898 48911 (1653) C B1_Mur3 SINE/Alu (73) 76 18 117
ANNOTATION EVIDENCE:
240 19.19 0.00 16.95 UnnamedSequence 48898 48966 1506 C B1_Mur3 SINE/Alu 18 76 73
240 19.19 0.00 16.95 UnnamedSequence 48898 48966 (1506) C B1_Mur3#SINE/Alu (73) 76 18 m_b1s501i46
UnnamedSequen 48898 CCTGGAACTCAGCATAAACTCAGAACTCTGTCTCCCTTCTGCCTCCTGGG 48947
v --------- iv i i v - i i
C B1_Mur3#SINE/ 76 CCTCGAACTCA---------CAGAGATCCGCCTGCCT-CTGCCTCCCGAG 37
UnnamedSequen 48948 TGCCAGGATTAAAGGCCTG 48966
ii v
C B1_Mur3#SINE/ 36 TGCTGGGATTAAAGGCGTG 18
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 17.63
Transitions / transversions = 1.75 (7/4)
Gap_init rate = 0.15 (10 / 68), avg. gap size = 1.00 (10 / 10)
+ 293 18.5 0.0 1.9 UnnamedSequence 48912 48966 (1598) C ORR1B1-int LTR/ERVL-MaLR (791) 718 665 118
ANNOTATION EVIDENCE:
293 18.52 0.00 1.85 UnnamedSequence 48912 48966 1506 C ORR1B1-int LTR/ERVL-MaLR 665 718 791
293 18.52 0.00 1.85 UnnamedSequence 48912 48966 (1506) C ORR1B1-int#LTR/ERVL-MaLR (791) 718 665 m_b1s501i47
UnnamedSequen 48912 TAAACTCAGAACTCTGTCTCCCTTCTGCCTCCTGGGTGCCAGGATTAAAG 48961
i iv i i v - i ii
C ORR1B1-int#LT 718 TGAACTCAGAGATCCGCCTGCCT-CTGCCTCCTGAGTGCTGGGATTAAAG 670
UnnamedSequen 48962 GCCTG 48966
v
C ORR1B1-int#LT 669 GCGTG 665
Matrix = 25p41g.matrix
Kimura (with divCpGMod) = 19.47
Transitions / transversions = 2.33 (7/3)
Gap_init rate = 0.02 (1 / 54), avg. gap size = 1.00 (1 / 1)
+ 26 10.7 5.8 0.0 UnnamedSequence 49143 49194 (1370) + G-rich Low_complexity 1 55 (0) 119
ANNOTATION EVIDENCE:
26 10.68 5.77 0.00 UnnamedSequence 49143 49194 1278 + (GGGA)n Simple_repeat 1 55 0
26 10.68 5.77 0.00 UnnamedSequence 49143 49194 (1278) (GGGA)n#Simple_repeat 1 55 (0) m_b1s252i25
UnnamedSequen 49143 GGGGGGGGGGGAGGGA--GAGGGAGGGAGAGA-GGAGGGGGAGAGGGAGG 49189
i i -- i - i i
(GGGA)n#Simpl 1 GGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGGGAGG 50
UnnamedSequen 49190 GAGGG 49194
(GGGA)n#Simpl 51 GAGGG 55
Matrix = Unknown
Transitions / transversions = 1.00 (5/0)
Gap_init rate = 0.04 (2 / 51), avg. gap size = 1.50 (3 / 2)
+ 50 2.0 2.0 0.0 UnnamedSequence 49200 49250 (1314) + (GA)n Simple_repeat 1 52 (0) 120
ANNOTATION EVIDENCE:
50 1.99 1.96 0.00 UnnamedSequence 49200 49250 1314 + (GA)n Simple_repeat 1 52 0
50 1.99 1.96 0.00 UnnamedSequence 49200 49250 (1314) (GA)n#Simple_repeat 1 52 (0) c_b1s251i15
UnnamedSequen 49200 GAGAGAGAGACAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAG-GA 49248
v -
(GA)n#Simple_ 1 GAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGA 50
UnnamedSequen 49249 GA 49250
(GA)n#Simple_ 51 GA 52
Matrix = Unknown
Transitions / transversions = 0.00 (0/1)
Gap_init rate = 0.02 (1 / 50), avg. gap size = 1.00 (1 / 1)
+ 34 13.3 0.0 0.0 UnnamedSequence 49251 49318 (1246) + (CACA)n Simple_repeat 1 68 (0) 121
ANNOTATION EVIDENCE:
34 13.34 0.00 0.00 UnnamedSequence 49251 49308 1214 + (CACA)n Simple_repeat 1 58 0
34 13.34 0.00 0.00 UnnamedSequence 49251 49308 (1214) (CACA)n#Simple_repeat 1 58 (0) m_b1s252i28
UnnamedSequen 49251 CACACACACACACACACACACACACACACACACACAGAGACAGAGACAGA 49300
v v v v v
(CACA)n#Simpl 1 CACACACACACACACACACACACACACACACACACACACACACACACACA 50
UnnamedSequen 49301 CAGAGACA 49308
v v
(CACA)n#Simpl 51 CACACACA 58
Matrix = Unknown
Transitions / transversions = 0.00 (0/7)
Gap_init rate = 0.00 (0 / 57), avg. gap size = 0.0 (0 / 0)
33 18.92 0.00 0.00 UnnamedSequence 49252 49318 1204 + (ACACAG)n Simple_repeat 1 67 0
33 18.92 0.00 0.00 UnnamedSequence 49252 49318 (1204) (ACACAG)n#Simple_repeat 1 67 (0) m_b1s252i30
UnnamedSequen 49252 ACACACACACACACACACACACACACACACACACAGAGACAGAGACAGAC 49301
v v v v v v v
(ACACAG)n#Sim 1 ACACAGACACAGACACAGACACAGACACAGACACAGACACAGACACAGAC 50
UnnamedSequen 49302 AGAGACAGAGAGAAAGA 49318
v v v v
(ACACAG)n#Sim 51 ACAGACACAGACACAGA 67
Matrix = Unknown
Transitions / transversions = 0.00 (0/11)
Gap_init rate = 0.00 (0 / 66), avg. gap size = 0.0 (0 / 0)
+ 46 0.0 2.3 0.0 UnnamedSequence 50220 50262 (302) + (AC)n Simple_repeat 1 44 (0) 122
ANNOTATION EVIDENCE:
46 0.00 2.33 0.00 UnnamedSequence 50220 50262 302 + (AC)n Simple_repeat 1 44 0
46 0.00 2.33 0.00 UnnamedSequence 50220 50262 (302) (AC)n#Simple_repeat 1 44 (0) c_b1s251i16
UnnamedSequen 50220 ACAC-CACACACACACACACACACACACACACACACACACACAC 50262
-
(AC)n#Simple_ 1 ACACACACACACACACACACACACACACACACACACACACACAC 44
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.02 (1 / 42), avg. gap size = 1.00 (1 / 1)