+ 522 16.2 1.0 0.0 chr11_24931982_24932155 22 120 (0) C L1PBa LINE/L1 (5181) 1682 1583 1
ANNOTATION EVIDENCE:
522 16.16 1.01 0.00 chr11_24931982_24932155 22 120 0 C L1PBa_5end LINE/L1 1583 1682 1289
522 16.16 1.01 0.00 chr11_24931982_24932155 22 120 (0) C L1PBa_5end#LINE/L1 (1289) 1682 1583 m_b1s551i0
chr11_2493198 22 TTGTTTTTGTTTTTTCTT-TCATTTGGTTATACTATATCAGAGGGAAGAT 70
? v vv i - v v i
C L1PBa_5end#LI 1682 TTGNTTTTCTGGTTCCTTCTCATTTGGGTAGACTATGTCAGAGGGAAGAT 1633
chr11_2493198 71 CTGGGGTTCAGGGGTTACTGTTCAGATGATTTTATCCCATGGGGTTCTCC 120
i i i i vv i i v
C L1PBa_5end#LI 1632 CTGGGGCTCAAGGGCTGCTGTTCAGATTCTTTTGTCCCACGGGGTGCTCC 1583
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.30
Transitions / transversions = 1.00 (8/8)
Gap_init rate = 0.01 (1 / 98), avg. gap size = 1.00 (1 / 1)
+ 14 14.6 0.0 3.2 chr11_40140801_40140853 46 77 (43) + (GTG)n Simple_repeat 1 31 (0) 2
ANNOTATION EVIDENCE:
14 14.64 0.00 3.23 chr11_40140801_40140853 46 77 43 + (GTG)n Simple_repeat 1 31 0
14 14.64 0.00 3.23 chr11_40140801_40140853 46 77 (43) (GTG)n#Simple_repeat 1 31 (0) m_b1s252i8
chr11_4014080 46 GTGGTGTCTGTGGTTGGTGGTTGTGGTGGTGG 77
viv - v
(GTG)n#Simple 1 GTGGTGGTGGTGG-TGGTGGTGGTGGTGGTGG 31
Matrix = Unknown
Transitions / transversions = 0.33 (1/3)
Gap_init rate = 0.03 (1 / 31), avg. gap size = 1.00 (1 / 1)
+ 16 7.0 6.7 0.0 chr12_123271564_123271627 84 113 (7) + (CCG)n Simple_repeat 1 32 (0) 3
ANNOTATION EVIDENCE:
16 6.99 6.67 0.00 chr12_123271564_123271627 84 113 7 + (CCG)n Simple_repeat 1 32 0
16 6.99 6.67 0.00 chr12_123271564_123271627 84 113 (7) (CCG)n#Simple_repeat 1 32 (0) m_b1s252i7
chr12_1232715 84 CCGCC-CGGCC-TCGCCGCCGCCGCCGCCGCC 113
- v -i
(CCG)n#Simple 1 CCGCCGCCGCCGCCGCCGCCGCCGCCGCCGCC 32
Matrix = Unknown
Transitions / transversions = 1.00 (1/1)
Gap_init rate = 0.07 (2 / 29), avg. gap size = 1.00 (2 / 2)
+ 355 21.3 18.5 0.0 chr13_43870564_43870591 13 120 (0) + MIR SINE/MIR 107 234 (28) 4
ANNOTATION EVIDENCE:
355 21.30 18.52 0.00 chr13_43870564_43870591 13 120 0 + MIR SINE/MIR 107 234 28
355 21.30 18.52 0.00 chr13_43870564_43870591 13 120 (0) MIR#SINE/MIR 107 234 (28) m_b1s601i0
chr13_4387056 13 ACCTCCCTGTACTT---TTT-----TTTGTAAAATGAACATTGTAATAAT 54
i i i --- ----- i iiv vi i
MIR#SINE/MIR 107 ACCTCTCTGTGCCTCAGTTTCCTCATCTGTAAAATGGGGATAATAATAGT 156
chr13_4387056 55 ATCTACCTTATAGGGTT------------AAATGAGTTACTATTTGTAAA 92
i i ------------ v iv
MIR#SINE/MIR 157 ACCTACCTCATAGGGTTGTTGTGAGGATTAAATGAGTTAATACATGTAAA 206
chr13_4387056 93 GTTCTTAGAACACCATCTGGCACAGAAT 120
iv viii v i
MIR#SINE/MIR 207 GCGCTTAGAACAGTGCCTGGCACATAGT 234
Matrix = 25p43g.matrix
Kimura (with divCpGMod) = 24.58
Transitions / transversions = 2.29 (16/7)
Gap_init rate = 0.03 (3 / 107), avg. gap size = 6.67 (20 / 3)
+ 17 5.0 0.0 0.0 chr13_77292258_77292342 67 87 (33) + (TG)n Simple_repeat 1 21 (0) 5
ANNOTATION EVIDENCE:
17 5.00 0.00 0.00 chr13_77292258_77292342 67 87 33 + (TG)n Simple_repeat 1 21 0
17 5.00 0.00 0.00 chr13_77292258_77292342 67 87 (33) (TG)n#Simple_repeat 1 21 (0) m_b1s252i6
chr13_7729225 67 TGTGTGTGTATGTGTGTGTGT 87
i
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGT 21
Matrix = Unknown
Transitions / transversions = 1.00 (1/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 277 9.8 7.7 1.8 chr14_22905606_22905659 2 53 (67) + 7SLRNA srpRNA 256 310 (10) 6
ANNOTATION EVIDENCE:
277 9.80 7.69 1.82 chr14_22905606_22905659 2 53 67 + 7SLRNA SINE/Alu 256 310 10
277 9.80 7.69 1.82 chr14_22905606_22905659 2 53 (67) 7SLRNA#SINE/Alu 256 310 (10) m_b1s502i0
chr14_2290560 2 GCCACTGCACTCCAGCCTGGGTGAC--AGCGGAAACCCTG--TCTTAAAA 47
ii -- - i i --
7SLRNA#SINE/A 256 GCCACTGCACTCCAGCCTGGGCAACATAGC-GAGACCCCGTCTCTTAAAA 304
chr14_2290560 48 AAACAA 53
v
7SLRNA#SINE/A 305 AAAAAA 310
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 8.61
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.06 (3 / 51), avg. gap size = 1.67 (5 / 3)
+ 243 17.4 0.5 0.5 chr14_23959902_23960003 2 55 (65) + SVA_F Retroposon/SVA 383 421 (954) 7
ANNOTATION EVIDENCE:
225 22.64 1.85 1.85 chr14_23959902_23960003 2 55 65 + SVA_A Retroposon/SVA 135 188 1199
225 22.64 1.85 1.85 chr14_23959902_23960003 2 55 (65) SVA_A#Retroposon/SVA 135 188 (1199) m_b1s502i1
chr14_2395990 2 AGTGAGCCTCCCACCTTGGCCTCCCAAAGTGCC-ATGATTACAGGCATGA 50
v ii i -i -iv i ii v
SVA_A#Retropo 135 AGTGATCCTCCTGCCTCGGCCTCCC-GAGTGCCTGGGATTGCAGGCGCGC 183
chr14_2395990 51 GCCAC 55
i
SVA_A#Retropo 184 GCCGC 188
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 15.84
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.04 (2 / 53), avg. gap size = 1.00 (2 / 2)
243 15.38 0.00 0.00 chr14_23959902_23960003 6 44 76 + SVA_F Retroposon/SVA 383 421 954
243 15.38 0.00 0.00 chr14_23959902_23960003 6 44 (76) SVA_F#Retroposon/SVA 383 421 (954) m_b1s502i2
chr14_2395990 6 AGCCTCCCACCTTGGCCTCCCAAAGTGCCATGATTACAG 44
v ii iv i
SVA_F#Retropo 383 AGCCGCCTGCCTTGGCCTCCCAAAGTGCCGAGATTGCAG 421
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 14.51
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 55 0.0 0.0 0.0 chr14_61037059_61037141 52 98 (22) + (TG)n Simple_repeat 1 47 (0) 8
ANNOTATION EVIDENCE:
55 0.00 0.00 0.00 chr14_61037059_61037141 52 98 22 + (TG)n Simple_repeat 1 47 0
55 0.00 0.00 0.00 chr14_61037059_61037141 52 98 (22) (TG)n#Simple_repeat 1 47 (0) c_b1s251i0
chr14_6103705 52 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 98
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 47
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 46), avg. gap size = 0.0 (0 / 0)
+ 374 17.5 0.0 3.8 chr15_70895849_70895936 1 83 (37) C L1MB5 LINE/L1 (282) 5892 5813 9
ANNOTATION EVIDENCE:
374 17.53 0.00 3.75 chr15_70895849_70895936 1 83 37 C L1MB5_3end LINE/L1 560 639 282
374 17.53 0.00 3.75 chr15_70895849_70895936 1 83 (37) C L1MB5_3end#LINE/L1 (282) 639 560 m_b1s551i1
chr15_7089584 1 TGTCAGTTTTCTTTCACTTGGCATGATGTTTTCAAGGTTCATCCACATTG 50
v vi i i i i
C L1MB5_3end#LI 639 TGTCTGGCTTCTTTCACTTAGCATAATGTTTTCGAGGTTCATCCACGTTG 590
chr15_7089584 51 TACCATGTGTATCAGTTATTATATGTTTTTTTA 83
v -- - i vi vii
C L1MB5_3end#LI 589 TAGCA--TGTATCAG-TACTTCATTCCTTTTTA 560
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 17.22
Transitions / transversions = 1.80 (9/5)
Gap_init rate = 0.04 (3 / 82), avg. gap size = 1.00 (3 / 3)
+ 652 14.6 0.0 0.0 chr17_29519354_29519574 25 120 (0) + AluSx SINE/Alu 1 96 (216) 10
ANNOTATION EVIDENCE:
652 14.58 0.00 0.00 chr17_29519354_29519574 25 120 0 + AluSx SINE/Alu 1 96 216
652 14.58 0.00 0.00 chr17_29519354_29519574 25 120 (0) AluSx#SINE/Alu 1 96 (216) m_b1s357i0
chr17_2951935 25 GGCTGGGTGTGATGGTTCATGGCTGTGATCCTAGCACTTTGGGAGGCCAA 74
i i i i i i v i i i
AluSx#SINE/Al 1 GGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGA 50
chr17_2951935 75 GGCAGGTGGATCACTTGAGGTCAGGAGTTTGAGACCAGCCTGGCCA 120
i i i i
AluSx#SINE/Al 51 GGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCA 96
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.56
Transitions / transversions = 13.00 (13/1)
Gap_init rate = 0.00 (0 / 95), avg. gap size = 0.0 (0 / 0)
+ 293 27.6 6.0 0.8 chr19_44288483_44289196 1 117 (3) C L1MB4 LINE/L1 (6483) 124 2 11
ANNOTATION EVIDENCE:
293 27.57 5.98 0.81 chr19_44288483_44289196 1 117 3 C L1MB4_5end LINE/L1 2 124 1671
293 27.57 5.98 0.81 chr19_44288483_44289196 1 117 (3) C L1MB4_5end#LINE/L1 (1671) 124 2 m_b1s551i2
chr19_4428848 1 CTGCTTTTCAGAGTTCCTATAAATTTATTTCAGCCAG--TCTAGTTGTTT 48
i i iv i v iv v v -- iv v
C L1MB4_5end#LI 124 CTGTTTTCCAGAGTTCTGACAAAGTTGGTTCTGACAGTTTCTGCTTTTTT 75
chr19_4428848 49 TTTT-GACGTTTCCATGGGGAAAATGAGAGCTTAGATCTTAATTCTCTAC 97
- i ii i -ii i i i v ?vv v ii
C L1MB4_5end#LI 74 TTTTCGATGTTTCTGTGGAG-GGACGGGAGCTTGGAGCTNCCTACTCCGC 26
chr19_4428848 98 ----TTTGCTAATGTCAGTCTCTT 117
---- i i v ?i
C L1MB4_5end#LI 25 CATTTTTGCTGACGTCACTNCCTT 2
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 32.04
Transitions / transversions = 1.67 (20/12)
Gap_init rate = 0.03 (4 / 116), avg. gap size = 2.00 (8 / 4)
+ 296 33.9 8.5 2.4 chr19_44303390_44303452 2 119 (1) + MER91A DNA/hAT-Tip100 71 195 (1) 12
ANNOTATION EVIDENCE:
296 33.86 8.47 2.40 chr19_44303390_44303452 2 119 1 + MER91A DNA/hAT-Tip100 71 195 1
296 33.86 8.47 2.40 chr19_44303390_44303452 2 119 (1) MER91A#DNA/hAT-Tip100 71 195 (1) m_b1s502i3
chr19_4430339 2 GCTGGGAGCTAGCTCCCGTTCTCCTCACTAAGCCGTGTGC---------- 41
ii v i i v i iv i i i ----------
MER91A#DNA/hA 71 GCTGAAATCCAGCCCGCGCTCCGCTCGCCAAGCCGTGCGCCCTGGCGCGG 120
chr19_4430339 42 AACTGTGTCTGCCTAGAGACAGGGGGACCTTTCTCTGAAGTGTCACATAA 91
ii i i ii iv vi i i ---v i i
MER91A#DNA/hA 121 GGCTGCGTCCGCCCGGAGGAAGGGGCGCCTTTTTCTAA---TTCGCACAA 167
chr19_4430339 92 AAGTGCCATGGTGACTAATGCCATCCCT 119
i i i ivv i ii v iv
MER91A#DNA/hA 168 AGGCGCCGTATGGGCTAGCGGCGGCCCT 195
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.46
Transitions / transversions = 2.90 (29/10)
Gap_init rate = 0.03 (4 / 117), avg. gap size = 3.25 (13 / 4)
+ 466 9.7 0.0 0.0 chr1_58522827_58522912 1 62 (58) + Tigger2 DNA/TcMar-Tigger 2090 2151 (567) 13
ANNOTATION EVIDENCE:
466 9.68 0.00 0.00 chr1_58522827_58522912 1 62 58 + Tigger2 DNA/TcMar-Tigger 2090 2151 567
466 9.68 0.00 0.00 chr1_58522827_58522912 1 62 (58) Tigger2#DNA/TcMar-Tigger 2090 2151 (567) m_b1s502i4
chr1_58522827 1 ATTAGACAATCTAGCAGAAGGATTCTGATTATTCAAGACTACTTTTGACT 50
i i i i
Tigger2#DNA/T 2090 ATTAGACAATCTGGCAGAAGGGTTCCGATTATTCAAGACTGCTTTTGACT 2139
chr1_58522827 51 TATTTTACAACA 62
v i
Tigger2#DNA/T 2140 TCTTTTACGACA 2151
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.17
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.00 (0 / 61), avg. gap size = 0.0 (0 / 0)
+ 384 14.8 0.0 0.0 chr1_58522827_58522912 60 120 (0) + Tigger2 DNA/TcMar-Tigger 2256 2316 (402) 14 *
ANNOTATION EVIDENCE:
384 14.75 0.00 0.00 chr1_58522827_58522912 60 120 0 + Tigger2 DNA/TcMar-Tigger 2256 2316 402
384 14.75 0.00 0.00 chr1_58522827_58522912 60 120 (0) Tigger2#DNA/TcMar-Tigger 2256 2316 (402) m_b1s502i5
chr1_58522827 60 ACAGAAATTACAAAGTATCTCCATTAAGTTACACTGATTATGCCTGCCTT 109
i v i ? v i v i i
Tigger2#DNA/T 2256 ACAGAAATTACGATGTATTTCNATAAAGTTACACCGAGTGTGCCTGCCTC 2305
chr1_58522827 110 TCCTGTCTCCC 120
i
Tigger2#DNA/T 2306 TCCTGCCTCCC 2316
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 13.17
Transitions / transversions = 2.00 (6/3)
Gap_init rate = 0.00 (0 / 60), avg. gap size = 0.0 (0 / 0)
+ 371 8.3 0.0 0.0 chr1_77172334_77172560 72 119 (1) C MER57-int LTR/ERV1 (7152) 385 338 15
ANNOTATION EVIDENCE:
371 8.33 0.00 0.00 chr1_77172334_77172560 72 119 1 C MER57-int LTR/ERV1 338 385 7152
371 8.33 0.00 0.00 chr1_77172334_77172560 72 119 (1) C MER57-int#LTR/ERV1 (7152) 385 338 m_b1s701i0
chr1_77172334 72 CCCTGCGAATTTTTAAAAGCCAAATTTTATAGCCCCTGCAATATTACC 119
i i i i
C MER57-int#LTR 385 CCCTGTGAATTTTCAAAAGCCAAATTTTACAACCCCTGCAATATTACC 338
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 9.12
Transitions / transversions = 1.00 (4/0)
Gap_init rate = 0.00 (0 / 47), avg. gap size = 0.0 (0 / 0)
+ 932 10.0 0.0 0.0 chr1_77172664_77172754 1 120 (0) C AluY SINE/Alu (48) 263 144 16
ANNOTATION EVIDENCE:
932 10.00 0.00 0.00 chr1_77172664_77172754 1 120 0 C AluY SINE/Alu 144 263 48
932 10.00 0.00 0.00 chr1_77172664_77172754 1 120 (0) C AluY#SINE/Alu (48) 263 144 m_b1s356i0
chr1_77172664 1 GTCGCCCAGGCTGGAGTGCAGTGGCGTGATCTCGGCTCATTGCAATCTCC 50
i i v
C AluY#SINE/Alu 263 GTCGCCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCAAGCTCC 214
chr1_77172664 51 ACCTCCCAGGTTCATGCCATTCTCTTTCCTCAGCCTCCCGAGTAGCTGGG 100
i i i i v
C AluY#SINE/Alu 213 GCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGG 164
chr1_77172664 101 AGTACAGGCACCTGCCATCA 120
v i i i
C AluY#SINE/Alu 163 ACTACAGGCGCCCGCCACCA 144
Matrix = 14p43g.matrix
Kimura (with divCpGMod) = 5.72
Transitions / transversions = 3.00 (9/3)
Gap_init rate = 0.00 (0 / 119), avg. gap size = 0.0 (0 / 0)
+ 24 14.1 0.0 0.0 chr22_31100885_31101049 8 46 (74) + (TG)n Simple_repeat 1 39 (0) 17
ANNOTATION EVIDENCE:
24 14.09 0.00 0.00 chr22_31100885_31101049 8 46 74 + (TG)n Simple_repeat 1 39 0
24 14.09 0.00 0.00 chr22_31100885_31101049 8 46 (74) (TG)n#Simple_repeat 1 39 (0) m_b1s252i4
chr22_3110088 8 TGTCTCTGTGTGTGTGTGTGTATGTGTGTGTGTCTCTGT 46
v v i v v
(TG)n#Simple_ 1 TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT 39
Matrix = Unknown
Transitions / transversions = 0.25 (1/4)
Gap_init rate = 0.00 (0 / 38), avg. gap size = 0.0 (0 / 0)
+ 16 15.7 9.3 0.0 chr22_31100885_31101049 40 82 (38) + (TC)n Simple_repeat 1 47 (0) 18 *
ANNOTATION EVIDENCE:
16 15.68 9.30 0.00 chr22_31100885_31101049 40 82 38 + (TC)n Simple_repeat 1 47 0
16 15.68 9.30 0.00 chr22_31100885_31101049 40 82 (38) (TC)n#Simple_repeat 1 47 (0) m_b1s252i5
chr22_3110088 40 TCTCTGTTTC-CTC-CCCTCTCTCT-TCTCTGCCTCT-TCCCTCTCT 82
v i - - i - vi - i
(TC)n#Simple_ 1 TCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCT 47
Matrix = Unknown
Transitions / transversions = 2.00 (4/2)
Gap_init rate = 0.10 (4 / 42), avg. gap size = 1.00 (4 / 4)
+ 353 8.4 22.5 0.0 chr2_182756314_182756469 3 73 (47) + Tigger4b DNA/TcMar-Tigger 275 361 (0) 19
ANNOTATION EVIDENCE:
353 8.45 22.54 0.00 chr2_182756314_182756469 3 73 47 + Tigger4b DNA/TcMar-Tigger 275 361 0
353 8.45 22.54 0.00 chr2_182756314_182756469 3 73 (47) Tigger4b#DNA/TcMar-Tigger 275 361 (0) m_b1s502i6
chr2_18275631 3 TATATGCAAATATTCCAAAATTC---AAAATTC----TC---AATACTTC 42
i --- i ---- --- i
Tigger4b#DNA/ 275 TATATGCAAATATTCCAAAATCCGAAAAAATCCGAAATCCGAAACACTTC 324
chr2_18275631 43 ------CAAGTATTTTGGATAAGAGATACTCAACCTG 73
------ i i i
Tigger4b#DNA/ 325 TGGTCCCAAGCATTTCGGATAAGGGATACTCAACCTG 361
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 7.75
Transitions / transversions = 1.00 (6/0)
Gap_init rate = 0.06 (4 / 70), avg. gap size = 4.00 (16 / 4)
+ 412 13.6 32.0 0.0 chr2_189463694_189463753 1 103 (17) C MER30 DNA/hAT-Charlie (93) 137 2 20
ANNOTATION EVIDENCE:
412 13.59 32.04 0.00 chr2_189463694_189463753 1 103 17 C MER30 DNA/hAT-Charlie 2 137 93
412 13.59 32.04 0.00 chr2_189463694_189463753 1 103 (17) C MER30#DNA/hAT-Charlie (93) 137 2 m_b1s502i7
chr2_18946369 1 CTGATGAGCTAAAAATAATAATAA---------------TAATAATGTTT 35
? v v v --------------- v
C MER30#DNA/hAT 137 CTGATGAGCTNAAAAAAAAAAAAAAATCGCAAAAAAATCTCATAATGTTT 88
chr2_18946369 36 TCAGAAAGTTTATGAATTTGTGTTAGGCTGCATAAAAAGCCACCCTGAGC 85
v i i i vv ii i
C MER30#DNA/hAT 87 TAAGAAAGTTTACGAATTTGTGTTGGGCCGCATTCAAAGCCGTCCTGGGC 38
chr2_18946369 86 CACA------------------GGTTGGACAAGCTT 103
i ------------------
C MER30#DNA/hAT 37 CGCATGCGGCCCGCGGGCCGCGGGTTGGACAAGCTT 2
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 10.96
Transitions / transversions = 1.00 (7/7)
Gap_init rate = 0.02 (2 / 102), avg. gap size = 16.50 (33 / 2)
+ 349 18.9 4.3 2.1 chr3_41802498_41802606 29 120 (0) C L1MEc LINE/L1 (4347) 2053 1960 21
ANNOTATION EVIDENCE:
349 18.88 4.35 2.13 chr3_41802498_41802606 29 120 0 C L1MEc_5end LINE/L1 1960 2053 474
349 18.88 4.35 2.13 chr3_41802498_41802606 29 120 (0) C L1MEc_5end#LINE/L1 (474) 2053 1960 m_b1s551i3
chr3_41802498 29 TAAGAACCTTACACCAGAATAAT-CTAGTATTCTCCTTCTAGCCTTC--- 74
v v v - i v vi i i ii? i---
C L1MEc_5end#LI 2053 TAAGAACCTTACAACAGTATACTTCCATTTCTCCCCTCCCGNCCTTTGTG 2004
chr3_41802498 75 CTACTATTGTCATACATTTTATGTCTACATATGTTATAAAGCTCAC 120
i i ? --i v i
C L1MEc_5end#LI 2003 CTATTGTTGTCATACATTTTNT--TTACATATGTTATAAACCCCAC 1960
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 21.18
Transitions / transversions = 1.83 (11/6)
Gap_init rate = 0.04 (4 / 91), avg. gap size = 1.50 (6 / 4)
+ 421 21.2 7.6 0.8 chr3_52609313_52609955 2 120 (0) C L1MC5 LINE/L1 (1629) 6318 6192 22
ANNOTATION EVIDENCE:
421 21.18 7.56 0.79 chr3_52609313_52609955 2 120 0 C L1MC5_3end LINE/L1 939 1065 1629
421 21.18 7.56 0.79 chr3_52609313_52609955 2 120 (0) C L1MC5_3end#LINE/L1 (1629) 1065 939 m_b1s551i4
chr3_52609313 2 TTTTTGTCTGCAGGTTATATTTCACTATAGACATGC--T--AATTGCTAG 47
ivi v ii vi ii i -- -- i iv
C L1MC5_3end#LI 1065 TTTTTGTCCTTAGGGTATATCCCACTAGGGATGTACAGTCAAATTACTGT 1016
chr3_52609313 48 ATTTTACAAATTACTTGGAATCGTCCCT-----TGTGGTTATGCTACCAT 92
i - i i v i ----- i v
C L1MC5_3end#LI 1015 GTTTTA-AAGTCACTTGGAATAGTTCCTCTCTGTGTGGTTATGCCACCAA 967
chr3_52609313 93 CTGTATACAAATTTAGGTTCATTTATTT 120
?v v v i
C L1MC5_3end#LI 966 CTNGATACACAGTTAGGTTCATTTGTTT 939
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 25.75
Transitions / transversions = 1.78 (16/9)
Gap_init rate = 0.03 (4 / 118), avg. gap size = 2.50 (10 / 4)
+ 326 28.2 0.0 1.2 chr5_128156298_128156415 6 91 (29) C HAL1 LINE/L1 (2194) 313 229 23
ANNOTATION EVIDENCE:
326 28.24 0.00 1.18 chr5_128156298_128156415 6 91 29 C HAL1 LINE/L1 229 313 2194
326 28.24 0.00 1.18 chr5_128156298_128156415 6 91 (29) C HAL1#LINE/L1 (2194) 313 229 m_b1s551i5
chr5_12815629 6 CCACTTCCAGAGGGACCTACTGTTCCTAACTCCTAGGCATTTTGGTGATT 55
v iv iiv i i ii v v
C HAL1#LINE/L1 313 CCACTTCCAGAGGTACCTGGTGCCGCCAATTCCTGAGCCTTTTGGGGATT 264
chr5_12815629 56 TTTAGATGTAAAATCAGGTAGTTTCATAGCTTCCTC 91
i vv i - i v i vii i i
C HAL1#LINE/L1 263 CTGCGGTGT-AAATCGGGTTGCTTCTCGGCTTTCCC 229
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 30.91
Transitions / transversions = 1.67 (15/9)
Gap_init rate = 0.01 (1 / 85), avg. gap size = 1.00 (1 / 1)
+ 16 0.0 0.0 0.0 chr5_71545039_71545219 1 17 (103) + (A)n Simple_repeat 1 17 (0) 24
ANNOTATION EVIDENCE:
16 0.00 0.00 0.00 chr5_71545039_71545219 1 17 103 + (A)n Simple_repeat 1 17 0
16 0.00 0.00 0.00 chr5_71545039_71545219 1 17 (103) (A)n#Simple_repeat 1 17 (0) m_b1s252i3
chr5_71545039 1 AAAAAAAAAAAAAAAAA 17
(A)n#Simple_r 1 AAAAAAAAAAAAAAAAA 17
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 16), avg. gap size = 0.0 (0 / 0)
+ 749 5.9 2.0 0.0 chr5_71562274_71562520 1 101 (19) + AluSx SINE/Alu 210 312 (0) 25
ANNOTATION EVIDENCE:
749 5.94 1.98 0.00 chr5_71562274_71562520 1 101 19 + AluSx SINE/Alu 210 312 0
749 5.94 1.98 0.00 chr5_71562274_71562520 1 101 (19) AluSx#SINE/Alu 210 312 (0) m_b1s357i1
chr5_71562274 1 GAGGTGGAGGTTGCAGTGAGCCGAGATTGCGCCACTGCACTCCAGCCTGG 50
i i
AluSx#SINE/Al 210 GAGGCGGAGGTTGCAGTGAGCCGAGATCGCGCCACTGCACTCCAGCCTGG 259
chr5_71562274 51 GTG--AGAGTGAGACTGCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 98
i -- i v
AluSx#SINE/Al 260 GCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAA 309
chr5_71562274 99 AGA 101
i
AluSx#SINE/Al 310 AAA 312
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 2.42
Transitions / transversions = 5.00 (5/1)
Gap_init rate = 0.01 (1 / 100), avg. gap size = 2.00 (2 / 1)
+ 390 4.5 0.0 0.0 chr6_111382273_111382390 66 109 (11) C L1M1 LINE/L1 (7212) 353 310 26
ANNOTATION EVIDENCE:
390 4.55 0.00 0.00 chr6_111382273_111382390 66 109 11 C L1M1_5end LINE/L1 310 353 3322
390 4.55 0.00 0.00 chr6_111382273_111382390 66 109 (11) C L1M1_5end#LINE/L1 (3322) 353 310 m_b1s551i6
chr6_11138227 66 TTGCTTTCCACTGTGACAGGGTAGCACTGAGTTCCAATGCAAAG 109
i i
C L1M1_5end#LIN 353 TTGCTTTCCGCTGTGACAGGGCAGCACTGAGTTCCAATGCAAAG 310
Matrix = 20p43g.matrix
Kimura (with divCpGMod) = 2.56
Transitions / transversions = 1.00 (2/0)
Gap_init rate = 0.00 (0 / 43), avg. gap size = 0.0 (0 / 0)
+ 12 20.4 0.0 0.0 chr6_142753389_142753931 53 81 (39) + (TGAA)n Simple_repeat 1 29 (0) 27
ANNOTATION EVIDENCE:
12 20.36 0.00 0.00 chr6_142753389_142753931 53 81 39 + (TGAA)n Simple_repeat 1 29 0
12 20.36 0.00 0.00 chr6_142753389_142753931 53 81 (39) (TGAA)n#Simple_repeat 1 29 (0) m_b1s252i2
chr6_14275338 53 TGAATGTGTGAATGGGTGAGTGAATGAAT 81
vi ii i
(TGAA)n#Simpl 1 TGAATGAATGAATGAATGAATGAATGAAT 29
Matrix = Unknown
Transitions / transversions = 4.00 (4/1)
Gap_init rate = 0.00 (0 / 28), avg. gap size = 0.0 (0 / 0)
+ 721 12.2 0.0 0.0 chr8_140674298_140674404 1 98 (22) C AluSx SINE/Alu (214) 98 1 28
ANNOTATION EVIDENCE:
721 12.24 0.00 0.00 chr8_140674298_140674404 1 98 22 C AluSx SINE/Alu 1 98 214
721 12.24 0.00 0.00 chr8_140674298_140674404 1 98 (22) C AluSx#SINE/Alu (214) 98 1 m_b1s357i2
chr8_14067429 1 GTTGGTCAGGCTGATCTCGAATTCCTGACCTCAGGTGATCTGCCCGCTTC 50
i i i i i
C AluSx#SINE/Al 98 GTTGGCCAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCCGCCCGCCTC 49
chr8_14067429 51 AGCCTCCCAAAGTGCTGAGATTATAGGCATGAGCCACTGCCCCCAGCC 98
i i i i i v i
C AluSx#SINE/Al 48 GGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 8.22
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.00 (0 / 97), avg. gap size = 0.0 (0 / 0)
+ 873 10.1 0.8 0.0 chr8_140746760_140746860 1 119 (1) + AluSx SINE/Alu 180 299 (13) 29
ANNOTATION EVIDENCE:
873 10.08 0.84 0.00 chr8_140746760_140746860 1 119 1 + AluSx SINE/Alu 180 299 13
873 10.08 0.84 0.00 chr8_140746760_140746860 1 119 (1) AluSx#SINE/Alu 180 299 (13) m_b1s357i3
chr8_14074676 1 GGCTGAGGCAGGAGAATCACTTGAACCCAGGAGGTGGAGGTTGCAATGAG 50
i i i i
AluSx#SINE/Al 180 GGCTGAGGCAGGAGAATCGCTTGAACCCGGGAGGCGGAGGTTGCAGTGAG 229
chr8_14074676 51 TCGAGATTGTACCACTGCACTCCAGCCT-GGTGACAGAATGAGACTCCGT 99
i i ii - i ii
AluSx#SINE/Al 230 CCGAGATCGCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGT 279
chr8_14074676 100 CTAAAAAAAAAAAAAAAAAA 119
v
AluSx#SINE/Al 280 CTCAAAAAAAAAAAAAAAAA 299
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 4.90
Transitions / transversions = 11.00 (11/1)
Gap_init rate = 0.01 (1 / 118), avg. gap size = 1.00 (1 / 1)
+ 12 16.3 2.8 2.8 chr9_129923844_129924026 78 113 (7) + (TTGTTTC)n Simple_repeat 1 36 (0) 30
ANNOTATION EVIDENCE:
12 16.31 2.78 2.78 chr9_129923844_129924026 78 113 7 + (TTGTTTC)n Simple_repeat 1 36 0
12 16.31 2.78 2.78 chr9_129923844_129924026 78 113 (7) (TTGTTTC)n#Simple_repeat 1 36 (0) m_b1s252i1
chr9_12992384 78 TTGATGCTTATTT-TTGTTTTGTGTCTTCTTGTTTCT 113
v v i - iv -
(TTGTTTC)n#Si 1 TTGTTTCTTGTTTCTTGTTTCTTGT-TTCTTGTTTCT 36
Matrix = Unknown
Transitions / transversions = 0.67 (2/3)
Gap_init rate = 0.06 (2 / 35), avg. gap size = 1.00 (2 / 2)
+ 19 0.0 0.0 0.0 chr9_68269600_68269722 100 120 (0) + (T)n Simple_repeat 1 21 (0) 31
ANNOTATION EVIDENCE:
19 0.00 0.00 0.00 chr9_68269600_68269722 100 120 0 + (T)n Simple_repeat 1 21 0
19 0.00 0.00 0.00 chr9_68269600_68269722 100 120 (0) (T)n#Simple_repeat 1 21 (0) m_b1s252i0
chr9_68269600 100 TTTTTTTTTTTTTTTTTTTTT 120
(T)n#Simple_r 1 TTTTTTTTTTTTTTTTTTTTT 21
Matrix = Unknown
Transitions / transversions = 1.00 (0/0)
Gap_init rate = 0.00 (0 / 20), avg. gap size = 0.0 (0 / 0)
+ 624 10.3 0.0 0.0 chr9_83682951_83683066 1 87 (33) C AluY SINE/Alu (224) 87 1 32
ANNOTATION EVIDENCE:
624 10.34 0.00 0.00 chr9_83682951_83683066 1 87 33 C AluY SINE/Alu 1 87 224
624 10.34 0.00 0.00 chr9_83682951_83683066 1 87 (33) C AluY#SINE/Alu (224) 87 1 m_b1s357i4
chr9_83682951 1 GATGTTCTCTATCTCTTGACCTCGTGATCAGCCAGCTTCGGCCTCCCAAA 50
v v i v v i
C AluY#SINE/Alu 87 GATGGTCTCGATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAA 38
chr9_83682951 51 GTGCTGGGATTACAGGCGTGAGCCACTGTGCCTGGCC 87
i i i
C AluY#SINE/Alu 37 GTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC 1
Matrix = 18p43g.matrix
Kimura (with divCpGMod) = 7.62
Transitions / transversions = 1.25 (5/4)
Gap_init rate = 0.00 (0 / 86), avg. gap size = 0.0 (0 / 0)