position in query- -position in repeat-
% % % query C matching repeat (left) end begin linkage
+ score div. del. ins. sequence begin end (left) + repeat class/fami begin end (left) id/graphic
+ 572 16.7 6.8 0.0 CM000409.1 1 132 (1618) + MIR1_Amn SINE/MIR 13 153 (77) 1
ANNOTATION EVIDENCE: 572 16.67 6.82 0.00 CM000409.1 1 132 1618 + MIR1_Amn SINE/MIR 13 153 77 572 16.67 6.82 0.00 CM000409.1 1 132 (1618) MIR1_Amn#SINE/MIR 13 153 (77) m_b1s601i0 CM000409.1 1 GTGGCCTAGTGTAAAGAGCACAGCCCTGGGAGTCAGAGGTCGTGGGTCCG 50 i v v v vv v i ii v v i ? MIR1_Amn#SINE 13 GTGGTCTAGTGGATAGAGCACTGGACTGGGACTCGGGAGACCTGGGTTCN 62 CM000409.1 51 AATTCCAGCTCTGCCACTTGACTGCTGCGTGACCTTGGACAAGTCACTTC 100 ? i i ? v ? ? i ? MIR1_Amn#SINE 63 ANTCCCGGCTCTGCCACTNGCCNGCTGNGTGACCTTGGGCAAGTCACTTN 112 CM000409.1 101 CCTTCTCCGAG---------CCTCATCTGGAAAGTGGGGAT 132 v i i ? --------- v i MIR1_Amn#SINE 113 ACCTCTCTGNGCCTCAGTTTCCTCATCTGTAAAATGGGGAT 153 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 18.25 Transitions / transversions = 1.00 (11/11) Gap_init rate = 0.01 (1 / 131), avg. gap size = 9.00 (9 / 1)
+ 252 24.1 3.5 4.7 CM000409.1 154 240 (1510) + L2a LINE/L2 3323 3408 (18) 2
ANNOTATION EVIDENCE: 252 24.11 3.45 4.65 CM000409.1 154 240 1510 + L2a_3end LINE/L2 414 499 18 252 24.11 3.45 4.65 CM000409.1 154 240 (1510) L2a_3end#LINE/L2 414 499 (18) m_b1s601i1 CM000409.1 154 GGGCGGGGACTGT-GCCCACCCCGATTTGCTG--GTATCCACCCCGGCGC 200 i v - i iiiiii - ii -- --- i L2a_3end#LINE 414 GGGCAGGGACTTTTGTCTGTTTTG-TTCACTGCTGTATCC---CCAGCGC 459 CM000409.1 201 TTAGGACAGTGCCCGGCACGTAGGAAGCGCTTAACAAATA 240 i i i i v i i i L2a_3end#LINE 460 CTAGAACAGTGCCTGGCACATAGTAGGCGCTCAATAAATA 499 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.84 Transitions / transversions = 9.00 (18/2) Gap_init rate = 0.07 (6 / 86), avg. gap size = 1.17 (7 / 6)
+ 243 15.7 5.6 5.6 CM000409.1 560 613 (1137) C L2b LINE/L2 (18) 3357 3304 3
ANNOTATION EVIDENCE: 243 15.68 5.56 5.56 CM000409.1 560 613 1137 C L2b_3end LINE/L2 395 448 18 243 15.68 5.56 5.56 CM000409.1 560 613 (1137) C L2b_3end#LINE/L2 (18) 448 395 m_b1s601i2 CM000409.1 560 TATTTA---AGTGCTTACTACGTGCCAGGCGCTGCACTGAGCGCTGGGAT 606 --- i i ii ? ii ii -- C L2b_3end#LINE 448 TATTTACTGAGCGCCTACTGTGTGCCAGGCNCTGTGCTAGGCGCTGGG-- 401 CM000409.1 607 AGATACA 613 - C L2b_3end#LINE 400 -GATACA 395 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 16.70 Transitions / transversions = 1.00 (8/0) Gap_init rate = 0.08 (4 / 53), avg. gap size = 1.50 (6 / 4)
+ 336 19.2 13.5 1.6 CM000409.1 619 729 (1021) C L2b LINE/L2 (0) 3375 3252 4 *
ANNOTATION EVIDENCE: 336 19.23 13.51 1.61 CM000409.1 619 729 1021 C L2b_3end LINE/L2 343 466 0 336 19.23 13.51 1.61 CM000409.1 619 729 (1021) C L2b_3end#LINE/L2 (0) 466 343 m_b1s601i3 CM000409.1 619 ATTCATTCATTCGATCG-TATTTATTGAGCGCTTACAGTGTGCAGAGCAC 667 i ivi- i i v vii ? C L2b_3end#LINE 466 ATTCATTCATTCAACAAATATTTACTGAGCGCCTACTGTGTGCCAGGCNC 417 CM000409.1 668 TGTACTAAGCGCT-----TACCA-GGTG--------GGACACGGTCCCTG 703 i i ----- vi- --------i ? C L2b_3end#LINE 416 TGTGCTAGGCGCTGGGGATACAGCGGTGAACAAGACAGACNCGGTCCCTG 367 CM000409.1 704 TCCCACAAGGGGCCCCCGGTCGTAGT 729 - v v i i v i - C L2b_3end#LINE 366 -CCCTCACGGAGCTCACAGTC-TAGT 343 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 23.31 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.05 (6 / 110), avg. gap size = 2.83 (17 / 6)
+ 508 17.9 1.7 0.8 CM000409.1 729 846 (904) C MIR1_Amn SINE/MIR (78) 152 34 5
ANNOTATION EVIDENCE: 508 17.95 1.69 0.84 CM000409.1 729 846 904 C MIR1_Amn SINE/MIR 34 152 78 508 17.95 1.69 0.84 CM000409.1 729 846 (904) C MIR1_Amn#SINE/MIR (78) 152 34 m_b1s601i4 CM000409.1 729 TCCCCGTTTTACAGATGCGGTAACTGAGGCACGGAGAAGTGAAATGACTC 778 i v v ? i i ? i i C MIR1_Amn#SINE 152 TCCCCATTTTACAGATGAGGAAACTGAGGCNCAGAGAGGTNAAGTGACTT 103 CM000409.1 779 TCCCAAGGTCACACAGCAGACGGGTGGCAGAACTGGAATTAGGAACCCCG 828 v ? ? i ?i i i i ? -? v C MIR1_Amn#SINE 102 GCCCAAGGTCACNCAGCNGGCNAGTGGCAGAGCCGGGANT-NGAACCCAG 54 CM000409.1 829 --CTCCAAGGCCTGAGGCCA 846 -- vii i iv v C MIR1_Amn#SINE 53 GTCTCCCGAGTCCCAGTCCA 34 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 20.21 Transitions / transversions = 2.00 (14/7) Gap_init rate = 0.02 (2 / 117), avg. gap size = 1.50 (3 / 2)
+ 212 26.5 3.0 0.0 CM000409.1 1393 1452 (298) C L2d2 LINE/L2 (17) 3447 3364 6
ANNOTATION EVIDENCE: 190 26.98 7.94 0.00 CM000409.1 1393 1455 295 C L2a_3end LINE/L2 450 517 0 190 26.98 7.94 0.00 CM000409.1 1393 1455 (295) C L2a_3end#LINE/L2 (0) 517 450 m_b1s601i5 CM000409.1 1393 ATTCATTCCGTCA-----TATTGATCGAGCAGTTACTGGGTGCGGAGCAC 1437 vv ----- v i ivi iv vii C L2a_3end#LINE 517 ATTCATTCATTCAACAAATATTTATTGAGCGCCTACTATGTGCCAGGCAC 468 CM000409.1 1438 TGTACTGAGCGCTTGGAA 1455 v ii v i C L2a_3end#LINE 467 TGTTCTAGGCGCTGGGGA 450 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.56 Transitions / transversions = 1.12 (9/8) Gap_init rate = 0.02 (1 / 62), avg. gap size = 5.00 (5 / 1) 212 26.42 1.89 0.00 CM000409.1 1405 1457 293 C L2d2_3end LINE/L2 485 538 17 212 26.42 1.89 0.00 CM000409.1 1405 1457 (293) C L2d2_3end#LINE/L2 (17) 538 485 m_b1s601i6 CM000409.1 1405 ATATTGATCGAGCAGTTACTGGGTGCGGAGCACTGTACTGAGCGCT-TGG 1453 v i ivi v iii i ii - C L2d2_3end#LIN 538 ATATTTATTGAGCGCCTACTGTGTGCAAGGCACTGTGCTAGGCGCTGTGG 489 CM000409.1 1454 AAGA 1457 ii C L2d2_3end#LIN 488 GGGA 485 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 31.79 Transitions / transversions = 3.67 (11/3) Gap_init rate = 0.02 (1 / 52), avg. gap size = 1.00 (1 / 1)
+ 569 18.8 0.6 4.7 CM000409.1 1453 1608 (142) + MIRb SINE/MIR 3 152 (116) 7
ANNOTATION EVIDENCE: 569 18.83 0.64 4.67 CM000409.1 1453 1608 142 + MIRb SINE/MIR 3 152 116 569 18.83 0.64 4.67 CM000409.1 1453 1608 (142) MIRb#SINE/MIR 3 152 (116) m_b1s601i7 CM000409.1 1453 GAAGAGTAGCGTGGCTTAGGTGGAAAGAGCCCGGGGTTTGGGGAGTCAGA 1502 i i i ivi - v v -- MIRb#SINE/MIR 3 GAGGGGCAGCGTGGTGCAG-TGGAAAGAGCACGGGCTTTGG--AGTCAGA 49 CM000409.1 1503 -GGTCGTGGGAGCTGATGCCGCCTCCGCCACTGCTCAGCTGTGTGACTTT 1551 -i v v vv vi v v i vvii i MIRb#SINE/MIR 50 CAGACCTGGGTTCGAATCCCGGCTCTGCCACTTACTAGCTGTGTGACCTT 99 CM000409.1 1552 CGGGCAAGTCACTTTCCACTTCTCTGGGGCCTCAGTTCCCTCATCTGTAA 1601 - i --v i i - i MIRb#SINE/MIR 100 -GGGCAAGTTACTT--AACCTCTCTGAG-CCTCAGTTTCCTCATCTGTAA 145 CM000409.1 1602 AATGGGG 1608 MIRb#SINE/MIR 146 AATGGGG 152 Matrix = 25p43g.matrix Kimura (with divCpGMod) = 21.82 Transitions / transversions = 1.15 (15/13) Gap_init rate = 0.05 (8 / 155), avg. gap size = 1.00 (8 / 8)