Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001497.1 Hibiscus syriacus cultivar Beakdansim tig00002919_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1780709
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:926140 original size:2 final size:2
Alignment explanation
Indices: 926129--926163 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
926119 TTTTAATAAA
926129 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
926164 GCGCGCGCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:929213 original size:24 final size:24
Alignment explanation
Indices: 929167--929214 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
929157 GTTCACGAAC
* *
929167 AAACTCATTTGAAAGTTCGTTTAT
1 AAACTCATTTGAAAGCTCCTTTAT
929191 AAACTCATTT-ATAAGCTCCTTTAT
1 AAACTCATTTGA-AAGCTCCTTTAT
929215 TTGATTCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (24 bp):
AAACTCATTTGAAAGCTCCTTTAT
Found at i:936333 original size:20 final size:20
Alignment explanation
Indices: 936308--936391 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 20
936298 GAACTTTCTA
*
936308 GAACTAGTTCGAGTCAACCC
1 GAACTAGTACGAGTCAACCC
936328 GAACTAGTACGAGTCAACCC
1 GAACTAGTACGAGTCAACCC
936348 GAA-TCAG-ACTGAGTCAACCC
1 GAACT-AGTAC-GAGTCAACCC
936368 GAA-TCAG-ACTGAGTCAACCC
1 GAACT-AGTAC-GAGTCAACCC
936388 GAAC
1 GAAC
936392 CGATCTAACC
Statistics
Matches: 60, Mismatches: 1, Indels: 5
0.91 0.02 0.08
Matches are distributed among these distances:
19 3 0.05
20 57 0.95
ACGTcount: A:0.35, C:0.30, G:0.20, T:0.15
Consensus pattern (20 bp):
GAACTAGTACGAGTCAACCC
Found at i:943140 original size:20 final size:20
Alignment explanation
Indices: 943100--943140 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
943090 TTTGATCATG
*
943100 ATATTTCAATATGCATGTAT
1 ATATTTCAATATGCATATAT
943120 ATATTTC-ATATGACATATAT
1 ATATTTCAATATG-CATATAT
943140 A
1 A
943141 ACCAAGTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (20 bp):
ATATTTCAATATGCATATAT
Found at i:943616 original size:27 final size:27
Alignment explanation
Indices: 943586--943648 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
943576 AGCTTATCTC
*
943586 ATTTCACATTGTCATGTCTCGTAGCAT
1 ATTTCACATTGTCATGTCTCATAGCAT
943613 ATTTCACATTGTCATGTCTCATAGCAT
1 ATTTCACATTGTCATGTCTCATAGCAT
*
943640 ATATCACAT
1 ATTTCACAT
943649 ATGCATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.40
Consensus pattern (27 bp):
ATTTCACATTGTCATGTCTCATAGCAT
Found at i:945193 original size:10 final size:10
Alignment explanation
Indices: 945178--945203 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
945168 TGTCACATTT
945178 TATATATATG
1 TATATATATG
945188 TATATATATG
1 TATATATATG
945198 TATATA
1 TATATA
945204 CTGAGTCTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:945608 original size:28 final size:28
Alignment explanation
Indices: 945576--945632 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
945566 GATTCTCATG
945576 TTAATGATTGTCGACAATTTATTCCTTC
1 TTAATGATTGTCGACAATTTATTCCTTC
945604 TTAATGATTGTCGACAATTTATTCCTTC
1 TTAATGATTGTCGACAATTTATTCCTTC
945632 T
1 T
945633 CATTTGGTCG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.11, T:0.47
Consensus pattern (28 bp):
TTAATGATTGTCGACAATTTATTCCTTC
Found at i:959843 original size:21 final size:22
Alignment explanation
Indices: 959792--959850 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
959782 ATATACAAAT
*
959792 AATATTTTGAATT-ATAAGTCA
1 AATATTTTAAATTAATAAGTCA
* * *
959813 AAAATATTAAATTAATAA-TGA
1 AATATTTTAAATTAATAAGTCA
959834 AATATTTTAAAATTAAT
1 AATATTTT-AAATTAAT
959851 CCAGACTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.41
Consensus pattern (22 bp):
AATATTTTAAATTAATAAGTCA
Found at i:974868 original size:44 final size:43
Alignment explanation
Indices: 974806--974891 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 43
974796 TCGCCATCGT
*
974806 GGTGAAGTTGCACAAATCAGAAAGTGCCTAACCAGTATTACAC
1 GGTGAAGATGCACAAATCAGAAAGTGCCTAACCAGTATTACAC
974849 GGTGAAGGATGCACAAATCAGAAAGTGCCTAACCAGTATTACA
1 GGTGAA-GATGCACAAATCAGAAAGTGCCTAACCAGTATTACA
974892 TGCTGTAATA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
43 6 0.15
44 35 0.85
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (43 bp):
GGTGAAGATGCACAAATCAGAAAGTGCCTAACCAGTATTACAC
Found at i:986438 original size:2 final size:2
Alignment explanation
Indices: 986431--986459 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
986421 CTGAACTGCG
986431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
986460 AAAAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:988103 original size:62 final size:62
Alignment explanation
Indices: 988006--988130 Score: 232
Period size: 62 Copynumber: 2.0 Consensus size: 62
987996 ATAGATTGAA
988006 TTATTATTGTGCGTGTAGCTTCATAGGATCAGGTCGCATGTACTAGTCTTACAACATAGTTG
1 TTATTATTGTGCGTGTAGCTTCATAGGATCAGGTCGCATGTACTAGTCTTACAACATAGTTG
* *
988068 TTATTATTGTGCGTGTAGTTTCATAGGATCAGGTCGTATGTACTAGTCTTACAACATAGTTG
1 TTATTATTGTGCGTGTAGCTTCATAGGATCAGGTCGCATGTACTAGTCTTACAACATAGTTG
988130 T
1 T
988131 CAAACTATGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.39
Consensus pattern (62 bp):
TTATTATTGTGCGTGTAGCTTCATAGGATCAGGTCGCATGTACTAGTCTTACAACATAGTTG
Found at i:989626 original size:12 final size:12
Alignment explanation
Indices: 989609--989634 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
989599 ACGTCAATAA
989609 CACCTCTATGAT
1 CACCTCTATGAT
989621 CACCTCTATGAT
1 CACCTCTATGAT
989633 CA
1 CA
989635 AGTAAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.08, T:0.31
Consensus pattern (12 bp):
CACCTCTATGAT
Found at i:994975 original size:20 final size:20
Alignment explanation
Indices: 994936--994981 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
994926 TTTAATGATT
* *
994936 ATTTTATAATTATTTGATAA
1 ATTTTATAATTATCTAATAA
994956 ATTTTATAATTATCTAATAA
1 ATTTTATAATTATCTAATAA
*
994976 TTTTTA
1 ATTTTA
994982 AACGTTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTATAATTATCTAATAA
Found at i:998682 original size:25 final size:25
Alignment explanation
Indices: 998651--998720 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
998641 TGTTAAAATT
*
998651 TAAAAATCCAATGATATAATTA-AAG
1 TAAAAAT-CAATGATATAATTAGAAC
* *
998676 TCAAAATCAAAGATTATAATTAGAAC
1 TAAAAATCAATGA-TATAATTAGAAC
*
998702 TAAAAATTTAATGATATAA
1 TAAAAA-TCAATGATATAA
998721 ATGATACATC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
24 5 0.14
25 14 0.39
26 12 0.33
27 5 0.14
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (25 bp):
TAAAAATCAATGATATAATTAGAAC
Found at i:1005511 original size:19 final size:20
Alignment explanation
Indices: 1005487--1005530 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1005477 ATTTGGAATT
1005487 TTATTAAAAT-AAAATAAAA
1 TTATTAAAATAAAAATAAAA
* * *
1005506 TTATTATATTAAAAATAGAA
1 TTATTAAAATAAAAATAAAA
1005526 TTATT
1 TTATT
1005531 TTATAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
TTATTAAAATAAAAATAAAA
Found at i:1005519 original size:24 final size:24
Alignment explanation
Indices: 1005484--1005590 Score: 93
Period size: 24 Copynumber: 4.7 Consensus size: 24
1005474 TAAATTTGGA
1005484 ATTTTATTAAAATAAAATAAAATT
1 ATTTTATTAAAATAAAATAAAATT
* *
1005508 ATTATATT---A-AAAATAGAATT
1 ATTTTATTAAAATAAAATAAAATT
* * *
1005528 ATTTTA-T-AAATGAAACAAAGTT
1 ATTTTATTAAAATAAAATAAAATT
* *
1005550 GTTTTATTAAAATAAAATAAGAA-A
1 ATTTTATTAAAATAAAATAA-AATT
1005574 ATTTTATTAAAATAAAA
1 ATTTTATTAAAATAAAA
1005591 CAAGAAGATT
Statistics
Matches: 64, Mismatches: 13, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
19 1 0.02
20 15 0.23
21 2 0.03
22 12 0.19
23 1 0.02
24 32 0.50
25 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (24 bp):
ATTTTATTAAAATAAAATAAAATT
Found at i:1005595 original size:24 final size:24
Alignment explanation
Indices: 1005551--1005596 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1005541 AACAAAGTTG
*
1005551 TTTTATTAAAATAAAATAAGAAAA
1 TTTTATTAAAATAAAACAAGAAAA
1005575 TTTTATTAAAATAAAACAAGAA
1 TTTTATTAAAATAAAACAAGAA
1005597 GATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (24 bp):
TTTTATTAAAATAAAACAAGAAAA
Found at i:1011581 original size:22 final size:22
Alignment explanation
Indices: 1011555--1011603 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
1011545 TTAATCGCTC
* *
1011555 TAAACTATTAAAAATTTTAATT
1 TAAACTAATAAAAATTTAAATT
1011577 TAAAC-AATAAAAATTTAAATT
1 TAAACTAATAAAAATTTAAATT
1011598 TAAACT
1 TAAACT
1011604 GTTTGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAACTAATAAAAATTTAAATT
Found at i:1017407 original size:31 final size:33
Alignment explanation
Indices: 1017359--1017437 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
1017349 TTTAAATAGT
* *
1017359 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
1017391 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
1017425 TATTATTTATTTA
1 TATTATTTTTTTA
1017438 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:1017429 original size:34 final size:31
Alignment explanation
Indices: 1017349--1017437 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1017339 TTAGTATTTT
* * *
1017349 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
1017381 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
1017415 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
1017438 GAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:1017601 original size:17 final size:17
Alignment explanation
Indices: 1017579--1017632 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1017569 AATGTTAAAA
1017579 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1017596 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1017613 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1017630 TTT
1 TTT
1017633 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1021863 original size:2 final size:2
Alignment explanation
Indices: 1021856--1021885 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1021846 ATTTTTAATC
1021856 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1021886 CAATGCATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1022050 original size:21 final size:20
Alignment explanation
Indices: 1022016--1022072 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 20
1022006 ATTGTTTTCT
* * *
1022016 ATAATAATAAATTAATTAGA
1 ATAATTATAAATTAATAAAA
1022036 ATAATTATAAAATTAATAAAA
1 ATAATTAT-AAATTAATAAAA
1022057 ATAACTTATTAAATTA
1 ATAA-TTA-TAAATTA
1022073 GGTCTGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 14 0.45
22 9 0.29
23 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
ATAATTATAAATTAATAAAA
Found at i:1024552 original size:16 final size:17
Alignment explanation
Indices: 1024531--1024563 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1024521 AATTTATTTC
1024531 ATATATGTTTT-TTTAT
1 ATATATGTTTTCTTTAT
*
1024547 ATATATTTTTTCTTTAT
1 ATATATGTTTTCTTTAT
1024564 GTCTATGTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
ATATATGTTTTCTTTAT
Found at i:1028667 original size:26 final size:27
Alignment explanation
Indices: 1028615--1028669 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
1028605 TTAAAAGACA
*
1028615 ATAATTTTTCAAAAATATATGAAATTT
1 ATAATTTTTCAAAAATATATAAAATTT
*
1028642 ATAATTTTT-AAAATTATA-AAATATTT
1 ATAATTTTTCAAAAATATATAAA-ATTT
1028668 AT
1 AT
1028670 TATTATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 14 0.56
27 9 0.36
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (27 bp):
ATAATTTTTCAAAAATATATAAAATTT
Found at i:1028915 original size:14 final size:14
Alignment explanation
Indices: 1028896--1028928 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1028886 CGTGGCGTAA
1028896 AGCGCGGTGTAGGG
1 AGCGCGGTGTAGGG
1028910 AGCGCGGTGTAGGG
1 AGCGCGGTGTAGGG
*
1028924 GGCGC
1 AGCGC
1028929 CTTCCTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.58, T:0.12
Consensus pattern (14 bp):
AGCGCGGTGTAGGG
Found at i:1031632 original size:19 final size:20
Alignment explanation
Indices: 1031584--1031632 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1031574 AACTATTAAA
* *
1031584 TTTAATAATATTTTGTTAATT
1 TTTAAT-ATATTTTGTAAAAT
1031605 TTTAA-ATATTTT-TAAAAT
1 TTTAATATATTTTGTAAAAT
1031623 TTTAATATAT
1 TTTAATATAT
1031633 ATTATTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
19 11 0.44
21 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTAATATATTTTGTAAAAT
Found at i:1039441 original size:26 final size:27
Alignment explanation
Indices: 1039390--1039441 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1039380 CTAACTGCTT
* *
1039390 AATACATGTGCATATTTCTTTAACAGC
1 AATACACGTGCATAGTTCTTTAACAGC
1039417 AATACACGTGCAT-GTTCTTTAACAG
1 AATACACGTGCATAGTTCTTTAACAG
1039442 TCTAACACTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (27 bp):
AATACACGTGCATAGTTCTTTAACAGC
Found at i:1039751 original size:24 final size:25
Alignment explanation
Indices: 1039722--1039777 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
1039712 TGATTATATA
*
1039722 TATATATATATAATATTTTATATTTT
1 TATATATA-ATAATATATTATATTTT
* *
1039748 TATAT-TAATTATATATAATA-TTT
1 TATATATAATAATATATTATATTTT
1039771 TATATAT
1 TATATAT
1039778 TTTATATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 8 0.31
24 11 0.42
25 2 0.08
26 5 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
TATATATAATAATATATTATATTTT
Found at i:1039845 original size:25 final size:26
Alignment explanation
Indices: 1039795--1039846 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
1039785 TAATTATATA
*
1039795 TATAATATTTTCGGGTTCGGGTTCGGG
1 TATAATATTTTC-GGATCGGGTTCGGG
1039822 TATAATATTTT-GGATCGGGTTCGGG
1 TATAATATTTTCGGATCGGGTTCGGG
1039847 GCAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.54
27 11 0.46
ACGTcount: A:0.17, C:0.10, G:0.33, T:0.40
Consensus pattern (26 bp):
TATAATATTTTCGGATCGGGTTCGGG
Found at i:1051489 original size:28 final size:28
Alignment explanation
Indices: 1051392--1051478 Score: 165
Period size: 28 Copynumber: 3.1 Consensus size: 28
1051382 TAAATTTGTG
1051392 TATATACTACTATATCCCCTCAATAAAC
1 TATATACTACTATATCCCCTCAATAAAC
*
1051420 TATATACTATTATATCCCCTCAATAAAC
1 TATATACTACTATATCCCCTCAATAAAC
1051448 TATATACTACTATATCCCCTCAATAAAC
1 TATATACTACTATATCCCCTCAATAAAC
1051476 TAT
1 TAT
1051479 TACAGACTAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 57 1.00
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.34
Consensus pattern (28 bp):
TATATACTACTATATCCCCTCAATAAAC
Found at i:1054017 original size:20 final size:20
Alignment explanation
Indices: 1053992--1054047 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
1053982 CGAATTTGGA
*
1053992 AAATCGCAATGCGATTACGT
1 AAATCGCAATGCGAATACGT
1054012 AAATCGCAATGCGAATACGT
1 AAATCGCAATGCGAATACGT
*
1054032 AAATCGCAACGCGAAT
1 AAATCGCAATGCGAAT
1054048 CTGACTATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAATGCGAATACGT
Found at i:1054057 original size:20 final size:20
Alignment explanation
Indices: 1054034--1054100 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
1054024 GAATACGTAA
* *
1054034 ATCGCAACGCGAATCTGACT
1 ATCGCAACGAGATTCTGACT
1054054 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
1054074 ATTGCAACGAGATTCTGACT
1 ATCGCAACGAGATTCTGACT
1054094 ATCGCAA
1 ATCGCAA
1054101 TACTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:1054969 original size:24 final size:24
Alignment explanation
Indices: 1054940--1054992 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1054930 TATTCGAAAC
*
1054940 TTGATCTTGGTTAATACCCGGACT
1 TTGATCTTGGTCAATACCCGGACT
* *
1054964 TTGATCTTGGTCAATACTCGGATT
1 TTGATCTTGGTCAATACCCGGACT
1054988 TTGAT
1 TTGAT
1054993 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.42
Consensus pattern (24 bp):
TTGATCTTGGTCAATACCCGGACT
Found at i:1057429 original size:14 final size:14
Alignment explanation
Indices: 1057410--1057436 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1057400 TCATTTGACT
1057410 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
1057424 ATCGCAACGCGAA
1 ATCGCAACGCGAA
1057437 TATGACTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.30, G:0.22, T:0.07
Consensus pattern (14 bp):
ATCGCAACGCGAAA
Found at i:1057449 original size:20 final size:20
Alignment explanation
Indices: 1057424--1057472 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1057414 CAACGCGAAA
1057424 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
1057444 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
1057464 ATCGCAACG
1 ATCGCAACG
1057473 AGAGAATCGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 23 0.88
21 3 0.12
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:1057505 original size:33 final size:34
Alignment explanation
Indices: 1057468--1057539 Score: 119
Period size: 33 Copynumber: 2.1 Consensus size: 34
1057458 ATGACTATCG
1057468 CAACGAGAGAATCGTAATGCG-AAATGAAAATCA
1 CAACGAGAGAATCGTAATGCGAAAATGAAAATCA
* *
1057501 CAACGAGTGAATCGTAATGCGAAAATGAAAATCG
1 CAACGAGAGAATCGTAATGCGAAAATGAAAATCA
1057535 CAACG
1 CAACG
1057540 CGAATTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 20 0.56
34 16 0.44
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (34 bp):
CAACGAGAGAATCGTAATGCGAAAATGAAAATCA
Found at i:1057637 original size:33 final size:33
Alignment explanation
Indices: 1057569--1057638 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1057559 CAATTTTAAT
***
1057569 TTTCGCATTGCGATTCTCTCATTGCGATTTTCA
1 TTTCGCATTGCGATTCTCTCATTGCGATAGCCA
*
1057602 TTTCGCATTGCGATTCTCTCGTTGCGATAGCCA
1 TTTCGCATTGCGATTCTCTCATTGCGATAGCCA
1057635 TTTC
1 TTTC
1057639 CGCGATGCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (33 bp):
TTTCGCATTGCGATTCTCTCATTGCGATAGCCA
Found at i:1057774 original size:14 final size:14
Alignment explanation
Indices: 1057755--1057791 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1057745 CATCAATTAA
1057755 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1057769 ACAAATCATCTTTT
1 ACAAATCAACATTT
1057783 ACAAATCAA
1 ACAAATCAA
1057792 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1059278 original size:42 final size:41
Alignment explanation
Indices: 1059171--1059280 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 41
1059161 TCTAAAATGT
* *
1059171 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGG-CCTCTTGAACGATGACAGTGGCCTCTTGAACGA
* ** *
1059213 TGGGAGGGGACTCTTGAGGGATGATAG-GGACCTCTTGAACGA
1 TGGGA-GGGCCTCTTGAACGATGACAGTGG-CCTCTTGAACGA
1059255 TAAGGGA-GGCCTCTTGAACGATGACA
1 T--GGGAGGGCCTCTTGAACGATGACA
1059281 AGTGAGTTGG
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
41 2 0.04
42 45 0.83
43 3 0.06
44 4 0.07
ACGTcount: A:0.25, C:0.19, G:0.35, T:0.21
Consensus pattern (41 bp):
TGGGAGGGCCTCTTGAACGATGACAGTGGCCTCTTGAACGA
Found at i:1059788 original size:20 final size:20
Alignment explanation
Indices: 1059762--1059830 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 20
1059752 GAAACTTAAA
**
1059762 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAATTTGACT
* * *
1059782 ATTGCAATGCTAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
1059802 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1059822 ATCGCAACG
1 ATCGCAACG
1059831 AGAGAATCGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:1059900 original size:20 final size:20
Alignment explanation
Indices: 1059875--1060017 Score: 192
Period size: 20 Copynumber: 7.5 Consensus size: 20
1059865 GATTCTTTCG
*
1059875 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
1059895 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1059915 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
**
1059935 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1059954 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
1059968 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1059988 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
1060008 TTGCGATAGT
1 TTGCGATAGT
1060018 AAACTATTCT
Statistics
Matches: 111, Mismatches: 6, Indels: 12
0.86 0.05 0.09
Matches are distributed among these distances:
14 7 0.06
16 6 0.05
17 2 0.02
18 4 0.04
19 14 0.13
20 78 0.70
ACGTcount: A:0.17, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1059901 original size:34 final size:36
Alignment explanation
Indices: 1059854--1060014 Score: 140
Period size: 40 Copynumber: 4.4 Consensus size: 36
1059844 GCGATTTTCA
1059854 TTTCGCATTGCGATTC-TTTCG-TTGCGATAGTCAT
1 TTTCGCATTGCGATTCATTTCGATTGCGATAGTCAT
*
1059888 TTTTGCATTGCGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTGCGAT--TCA-TTTCG-ATTGCGATAGTCAT
1059928 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT--TC--
1 TTTCGCATTGCGA--TTCATTTCG-ATTGCGATAGTCAT
* *
1059963 TCTCG--TTGCGATAGTCATTTTCGCGTTGCGATAGTCAT
1 TTTCGCATTGCGAT--TCA-TTTCG-ATTGCGATAGTCAT
1060001 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1060015 AGTAAACTAT
Statistics
Matches: 105, Mismatches: 5, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
31 1 0.01
33 9 0.09
34 26 0.25
35 4 0.04
36 4 0.04
37 2 0.02
38 9 0.09
39 14 0.13
40 35 0.33
42 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.43
Consensus pattern (36 bp):
TTTCGCATTGCGATTCATTTCGATTGCGATAGTCAT
Found at i:1059950 original size:93 final size:93
Alignment explanation
Indices: 1059837--1060017 Score: 326
Period size: 93 Copynumber: 1.9 Consensus size: 93
1059827 AACGAGAGAA
* *
1059837 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATAGTCATTTTTGCATTGCGAT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGAT
1059902 AGTCATTTTCGCATTGCGATAGTCATTT
66 AGTCATTTTCGCATTGCGATAGTCATTT
* *
1059930 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGAT
1059995 AGTCATTTTCGCATTGCGATAGT
66 AGTCATTTTCGCATTGCGATAGT
1060018 AAACTATTCT
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.17, C:0.20, G:0.20, T:0.42
Consensus pattern (93 bp):
TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTCGCATTGCGAT
AGTCATTTTCGCATTGCGATAGTCATTT
Found at i:1061917 original size:20 final size:20
Alignment explanation
Indices: 1061894--1061983 Score: 92
Period size: 20 Copynumber: 4.5 Consensus size: 20
1061884 TCTGAAACTT
1061894 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1061914 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * **
1061934 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
1061954 ACTATCGCAAC-GGGAAATG
1 AAAATCGCAACACGAAAATG
1061973 AAAATCGCAAC
1 AAAATCGCAAC
1061984 GACAGAATCG
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
19 13 0.22
20 46 0.78
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1062354 original size:22 final size:22
Alignment explanation
Indices: 1062320--1062381 Score: 106
Period size: 22 Copynumber: 2.8 Consensus size: 22
1062310 TGACCGTGAA
*
1062320 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
*
1062342 TGATATCGTCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGAGAC
1062364 TGATTTCGTCGGAGATGG
1 TGATTTCGTCGGAGATGG
1062382 GGACGGATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.26
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGAGAC
Found at i:1062606 original size:20 final size:20
Alignment explanation
Indices: 1062583--1062656 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
1062573 CGATAGTCAG
*
1062583 ATTCGCGTTGCTATTTACGT
1 ATTCGCGTTGCGATTTACGT
* * **
1062603 ATTCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGA-TTTACGT
1062624 ATTCGCGTTGCGATTTACGT
1 ATTCGCGTTGCGATTTACGT
* *
1062644 ATTTGCATTGCGA
1 ATTCGCGTTGCGA
1062657 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.62
21 16 0.38
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACGT
Found at i:1062679 original size:21 final size:21
Alignment explanation
Indices: 1062653--1062698 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
1062643 TATTTGCATT
1062653 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1062674 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1062695 GCGA
1 GCGA
1062699 TAGTTAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1069524 original size:20 final size:20
Alignment explanation
Indices: 1069499--1069540 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1069489 TCATTTCATT
1069499 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
1069519 TAAAGGTCTTAACCTTTCAA
1 TAAAGGTCTTAACCTTTCAA
1069539 TA
1 TA
1069541 CTCTCCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.36
Consensus pattern (20 bp):
TAAAGGTCTTAACCTTTCAA
Found at i:1077112 original size:9 final size:9
Alignment explanation
Indices: 1077098--1077131 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1077088 TAAAAGGGAA
1077098 AAATAAAAT
1 AAATAAAAT
1077107 AAATAAAAT
1 AAATAAAAT
1077116 AAAT-AAAT
1 AAATAAAAT
1077124 AAGATAAA
1 AA-ATAAA
1077132 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1077119 original size:13 final size:13
Alignment explanation
Indices: 1077097--1077131 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1077087 ATAAAAGGGA
1077097 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1077111 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1077124 AAGATAAA
1 AAAATAAA
1077132 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1077141 original size:18 final size:18
Alignment explanation
Indices: 1077066--1077142 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 18
1077056 TTAGATAAAC
1077066 AAGATAAA-GAAAACAAAT
1 AAGATAAAGGAAAA-AAAT
1077084 AAGATAAAAGGGAAAAATAAAAT
1 AAGAT-AAA-GG--AAA-AAAAT
** *
1077107 AA-ATAAAATAAATAAAT
1 AAGATAAAGGAAAAAAAT
1077124 AAGATAAAGGAAAAAAAT
1 AAGATAAAGGAAAAAAAT
1077142 A
1 A
1077143 GTAAAATAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.13
18 21 0.46
19 3 0.07
21 4 0.09
22 2 0.04
23 9 0.20
24 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (18 bp):
AAGATAAAGGAAAAAAAT
Found at i:1077678 original size:18 final size:17
Alignment explanation
Indices: 1077655--1077697 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1077645 ATATATACAT
1077655 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1077673 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1077690 ATAA-AATA
1 ATAATAATA
1077698 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1078136 original size:35 final size:36
Alignment explanation
Indices: 1078066--1078165 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
1078056 GTGCTTGTGG
* * *
1078066 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
1078103 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
1078138 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
1078166 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:1079388 original size:204 final size:204
Alignment explanation
Indices: 1078654--1079999 Score: 1426
Period size: 210 Copynumber: 6.4 Consensus size: 204
1078644 CTGTGAAGTT
** * * * * *
1078654 GAAATTGTTTGTTGACAGTCAGTCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCT
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
* * * *
1078719 AATATCCTTCGCTGTGAAGATGAAATTGACTCTGAACGAAA-T-CTTATTGACAATCAGCCGTCC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTC----CGAAATTGCTTGTTGACAGTCAGCCGTCC
* * * **
1078782 ATTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTACGAAGTTGAAATTG
127 CTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTG
*
1078847 GCTCTGAAATTTG
192 GCTCTGAAATTGG
* * *
1078860 AAAAATGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGG
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--
* * * * * * **
1078925 CACGATATCCTCCG-TCGTGGAGTTGAAATCGCGGATGAAACTGAAAAGTTG-TTCGTTGACAAC
64 C-CAATATCCTTCGCT-GTGAAGTTGAAAT--TGGCT----CCG-AAA-TTGCTT-GTTGACAGT
* * *
1078988 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCG-TCGT
118 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGGGT--C-CAATATCCTTCGCT-GT
* * *
1079052 GGAGTTGAAATCGGCTCTGGAATTGG
179 GAAGTTGAAATTGGCTCTGAAATTGG
*
1079078 GAAATTGTTTGTTGACAACCAGCCATCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
* * *
1079143 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGCTTGTTGACAGTCAGCCGTCCCTTC
* * *
1079208 GTTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCC
131 GTTGTGAAGTTGAACTTGTGTTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
1079273 TGAAACTGG
196 TGAAATTGG
* *
1079282 GAAATTGTTTGTTGACAACCAGTCGTCCCTTCACTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
* * *
1079347 AATATCCTTCGCTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGCTTGTTGACAGTCAGCCGTCCCTTC
* * * *
1079412 GCTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCCC
131 GTTGTGAAGTTGAACTTGTGTTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
*
1079477 TGAAACTGG
196 TGAAATTGG
* * * *
1079486 GAAATT-ATTGTTGACAACCAGCCGTACCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
*
1079550 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG-CAGC
66 AATATCCTTCGCTGTGAAGTTGAAATTGGCTC--CGA-----AA-TTGCTTGTTGAC-AGTCAGC
* * ** *
1079613 GGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTTG
122 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTTG
* * *
1079677 AAATTGGCTATGAGATTGA
186 AAATTGGCTCTGAAATTGG
* * * *
1079696 GAAGTTG-TTGTTGACAAGCAGCGGTCCCTTCG-TCGTGAAGTTGAACTTGCGTTGTCT-GAAGT
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCT-GTGAAGTTGAACTTGTGTTGTCTCG-AGT
* * *
1079758 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG-CAG
64 CCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATT-----G--CTTGTTGAC-AGTCAG
* * * *
1079822 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGTTGTGAAGTT
121 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTTGG-GTCCAATATCCTTCGCTGTGAAGTT
*
1079886 GAAATTGGCTCTGAAATTGA
185 GAAATTGGCTCTGAAATTGG
* * **
1079906 GAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTCTCGAGTGC
1 GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGT--
* *
1079971 CACAATATCCTCCG-TCGTGGAGTTGAAAT
64 C-CAATATCCTTCGCT-GTGAAGTTGAAAT
1080000 CGCGGATGGC
Statistics
Matches: 992, Mismatches: 98, Indels: 92
0.84 0.08 0.08
Matches are distributed among these distances:
202 2 0.00
203 85 0.09
204 239 0.24
205 4 0.00
206 54 0.05
207 50 0.05
208 9 0.01
209 27 0.03
210 264 0.27
211 56 0.06
212 5 0.01
213 5 0.01
214 26 0.03
215 71 0.07
216 2 0.00
217 2 0.00
218 91 0.09
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (204 bp):
GAAATTGTTTGTTGACAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCTCGAGTCC
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGCTTGTTGACAGTCAGCCGTCCCTTC
GTTGTGAAGTTGAACTTGTGTTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
TGAAATTGG
Found at i:1079542 original size:105 final size:104
Alignment explanation
Indices: 1079406--1079999 Score: 803
Period size: 105 Copynumber: 5.6 Consensus size: 104
1079396 AGTCAGCCGC
* * * *
1079406 CCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 CCCTTCGTC-GTGAAGTTGAACTTGCGTTGTC-TGGGTCCAATATCCTTCGTTGTGAAGTTGAAA
* * * * * * *
1079470 TTGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCGT
64 TTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
* * * * * *
1079511 ACCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGCTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-GGGTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
1079576 TGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGT
65 TGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
*
1079616 CCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG-GTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
1079681 TGGCTATGAGATTGAGAAGTTGTTGTTGACAAGCAGCGGT
65 TGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
*
1079721 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG-GGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1079786 TGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
65 TGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
1079826 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG-GTCCAATATCCTTCGTTGTGAAGTTGAAAT
* *
1079891 TGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGT
65 TGGCTCTGAAATTGAGAAGTTG-TTGTTGACAAGCAGCGGT
* * * * * *
1079932 CCCTTCGTTGTGAAGTTGAACTTGCATTGTCTCGAGTGCCACAATATCCTCCGTCGTGGAGTTGA
1 CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G-G-GTC-CAATATCCTTCGTTGTGAAGTTGA
1079997 AAT
62 AAT
1080000 CGCGGATGGC
Statistics
Matches: 444, Mismatches: 36, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
104 2 0.00
105 368 0.83
106 46 0.10
107 1 0.00
108 3 0.01
109 24 0.05
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (104 bp):
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGAGAAGTTGTTGTTGACAAGCAGCGGT
Found at i:1080717 original size:36 final size:36
Alignment explanation
Indices: 1080672--1081054 Score: 307
Period size: 36 Copynumber: 10.9 Consensus size: 36
1080662 GAAGATTTTG
* *
1080672 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1080708 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
1080745 AGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * *
1080781 TGTTTCAA-AGAAAACATAT-T-----TA-A-ATATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
1080810 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1080846 TATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
1080882 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * *
1080919 TGTTTCAAGGGAAATTATCTCAAGAGAGAAGAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAG-ACAAAATT
* * * * *
1080956 TATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAATT
*
1080984 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 -TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
1081021 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1081055 CTCTTCTAGT
Statistics
Matches: 279, Mismatches: 43, Indels: 50
0.75 0.12 0.13
Matches are distributed among these distances:
28 4 0.01
29 31 0.11
30 5 0.02
32 1 0.00
34 2 0.01
35 4 0.01
36 149 0.53
37 78 0.28
38 5 0.02
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1080825 original size:102 final size:101
Alignment explanation
Indices: 1080706--1080889 Score: 260
Period size: 102 Copynumber: 1.8 Consensus size: 101
1080696 GGAGACAAAA
* * *
1080706 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAAATGTCTCAAGAG
* * *
1080771 GGACGAAATTTGTTTCAAAGAAAACATATTTAAATAT
65 AGACAAAATTTATTTCAAAGAAAACATATTTAAATAT
* * * **
1080808 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
1080873 GACAAAATTTATTTCAA
66 GACAAAATTTATTTCAA
1080890 GGGAAACTGT
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
101 34 0.48
102 37 0.52
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (101 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAAATGTCTCAAGAGA
GACAAAATTTATTTCAAAGAAAACATATTTAAATAT
Found at i:1080839 original size:138 final size:138
Alignment explanation
Indices: 1080672--1080926 Score: 368
Period size: 138 Copynumber: 1.8 Consensus size: 138
1080662 GAAGATTTTG
* * * *
1080672 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
* * * *
1080737 TAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAA-TTTGTTTCAAAGAAAACATATT
66 CAAAACTTA-TTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAACATATT
1080801 TAAATATTT
130 TAAATATTT
* *
1080810 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAAATGTCTCAAGAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
* * **
1080875 CAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
66 CAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAA
1080927 GGGAAATTAT
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
137 26 0.25
138 76 0.75
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (138 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAAATGTCTCAAGAGAGA
CAAAACTTATTCCAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAAGAAAACATATTT
AAATATTT
Found at i:1080890 original size:21 final size:21
Alignment explanation
Indices: 1080829--1080890 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1080819 GGAAACTGTC
1080829 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
* *
1080850 TCAAG-G-G--AAAA--TGTC
1 TCAAGAGAGACAAAATTTATT
1080865 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTATT
1080886 TCAAG
1 TCAAG
1080891 GGAAACTGTC
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 5 0.16
19 5 0.16
20 1 0.03
21 12 0.39
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTATT
Found at i:1081042 original size:175 final size:174
Alignment explanation
Indices: 1080672--1081054 Score: 498
Period size: 174 Copynumber: 2.2 Consensus size: 174
1080662 GAAGATTTTG
* * * *
1080672 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
* * * * * *
1080737 TAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGGGACGAAATTTGTTTCAAAGAAAACATATTT
66 CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGAAGAAATTTATTTCAAAGAAAACATATTT
*
1080802 AAATATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
131 AAATATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
1080846 TATTTCAAGGGAAAATGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
* * * ** * * * **
1080911 CAAAATTTTGTTTCAAGGGAAATTATCTCAAGAGAGAAGAAAATTTATTTCAAGGGAAATGT-TT
66 CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGAAG-AAATTTATTTCAAAGAAAACATATT
* * *
1080975 TCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
130 TAAATATTT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1081021 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1081055 CTCTTCTAGT
Statistics
Matches: 178, Mismatches: 29, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
174 95 0.53
175 83 0.47
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (174 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGA
CAAAACTTAGTTCCAAAAGAAACTATCTCAAGAGAGAAGAAATTTATTTCAAAGAAAACATATTT
AAATATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:1081104 original size:35 final size:35
Alignment explanation
Indices: 1080809--1081104 Score: 120
Period size: 36 Copynumber: 8.4 Consensus size: 35
1080799 TTTAAATATT
*
1080809 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
*
1080845 TTATTTCAAGGGAAAA-TGTCTCAAGAGAGACAAAAT-
1 TTGTTTCAA--GAAAACTGTCTCAAGAGAGAC-AAATC
* * *
1080881 TTATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGAC-AAATC
* * * *
1080918 TTGTTTCAAGGGAAATTATCTCAAGAGAGAAGAAAAT-
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAG-A-CAAATC
* * * * *
1080955 TTATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TT
1 TTGTTTCAA-GAAAACTG-TCTCAAGAGAGACAAATC
*
1080983 TATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAAT-
1 T-TGTTTCAAGA-AAACTGTCTCAAGAGAGAC-AAATC
* *
1081020 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAA-GAAAACTGTCTCAAGAGAGACAAATC
* * * *
1081056 -T-CTTCTAGTGAAAACGGTCTCAAGCGAGACAAATC
1 TTGTTTC-A-AGAAAACTGTCTCAAGAGAGACAAATC
*
1081091 TTGTTTTAAGAAAA
1 TTGTTTCAAGAAAA
1081105 ACAATCATGA
Statistics
Matches: 207, Mismatches: 28, Indels: 51
0.72 0.10 0.18
Matches are distributed among these distances:
27 1 0.00
28 2 0.01
29 13 0.06
30 3 0.01
32 1 0.00
34 4 0.02
35 38 0.18
36 87 0.42
37 52 0.25
38 6 0.03
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (35 bp):
TTGTTTCAAGAAAACTGTCTCAAGAGAGACAAATC
Found at i:1081563 original size:18 final size:18
Alignment explanation
Indices: 1081536--1081571 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1081526 TGTTGAATCC
*
1081536 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1081554 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
1081572 TTGATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:1082031 original size:22 final size:22
Alignment explanation
Indices: 1082006--1082048 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
1081996 CATTTTTGTT
1082006 CATTTGATGCT-AAATGGTTTGA
1 CATTTGATGCTCAAA-GGTTTGA
1082028 CATTTGATGCTCAAAGGTTTG
1 CATTTGATGCTCAAAGGTTTG
1082049 GTGGGGTAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.40
Consensus pattern (22 bp):
CATTTGATGCTCAAAGGTTTGA
Found at i:1082663 original size:23 final size:24
Alignment explanation
Indices: 1082637--1082689 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
1082627 TTTGCATGTG
*
1082637 CTTTTTGTCCCTTTTT-CTTTTTT
1 CTTTTTGTCCCTTTTTGCTTTTGT
* *
1082660 CTTTTTGTTCTTTTTTGCTTTTGT
1 CTTTTTGTCCCTTTTTGCTTTTGT
1082684 -TTTTTG
1 CTTTTTG
1082690 CTTCTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.00, C:0.15, G:0.09, T:0.75
Consensus pattern (24 bp):
CTTTTTGTCCCTTTTTGCTTTTGT
Found at i:1082670 original size:16 final size:16
Alignment explanation
Indices: 1082651--1082698 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
1082641 TTGTCCCTTT
1082651 TTCTTTTTTCTTTTTG
1 TTCTTTTTTCTTTTTG
1082667 TTCTTTTTTGC-TTTTG
1 TTCTTTTTT-CTTTTTG
1082683 TT-TTTTGCTTCTTTTT
1 TTCTTTT--TTCTTTTT
1082699 TTTTGCCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.14
16 17 0.61
17 7 0.25
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.79
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTG
Found at i:1082675 original size:24 final size:24
Alignment explanation
Indices: 1082648--1082700 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1082638 TTTTTGTCCC
*
1082648 TTTTTCTTTTTTCTTTTTG-TTCTT
1 TTTTTCTTTTGT-TTTTTGCTTCTT
*
1082672 TTTTGCTTTTGTTTTTTGCTTCTT
1 TTTTTCTTTTGTTTTTTGCTTCTT
1082696 TTTTT
1 TTTTT
1082701 TTGCCTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.00, C:0.11, G:0.08, T:0.81
Consensus pattern (24 bp):
TTTTTCTTTTGTTTTTTGCTTCTT
Found at i:1082688 original size:13 final size:13
Alignment explanation
Indices: 1082670--1082709 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
1082660 CTTTTTGTTC
1082670 TTTTTTGCTTTTG
1 TTTTTTGCTTTTG
*
1082683 TTTTTTGCTTCTTT
1 TTTTTTGCTT-TTG
1082697 TTTTTTGCCTTTT
1 TTTTTTG-CTTTT
1082710 TTATTCTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 10 0.42
14 11 0.46
15 3 0.12
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (13 bp):
TTTTTTGCTTTTG
Found at i:1082710 original size:13 final size:13
Alignment explanation
Indices: 1082670--1082711 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
1082660 CTTTTTGTTC
1082670 TTTTTTG-CTTTT
1 TTTTTTGCCTTTT
*
1082682 GTTTTTTGCTTCTTT
1 -TTTTTTGCCT-TTT
1082697 TTTTTTGCCTTTT
1 TTTTTTGCCTTTT
1082710 TT
1 TT
1082712 ATTCTGATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 12 0.48
14 10 0.40
15 3 0.12
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.79
Consensus pattern (13 bp):
TTTTTTGCCTTTT
Found at i:1085708 original size:9 final size:9
Alignment explanation
Indices: 1085694--1085727 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
1085684 TAAAAGGGAA
1085694 AAATAAAAT
1 AAATAAAAT
1085703 AAATAAAAT
1 AAATAAAAT
1085712 AAAT-AAAT
1 AAATAAAAT
1085720 AAGATAAA
1 AA-ATAAA
1085728 GGAAAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 6 0.26
9 15 0.65
10 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1085715 original size:13 final size:13
Alignment explanation
Indices: 1085693--1085727 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1085683 ATAAAAGGGA
1085693 AAAATAAAATAAAT
1 AAAAT-AAATAAAT
1085707 AAAATAAATAAAT
1 AAAATAAATAAAT
*
1085720 AAGATAAA
1 AAAATAAA
1085728 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1085737 original size:18 final size:18
Alignment explanation
Indices: 1085662--1085738 Score: 59
Period size: 18 Copynumber: 4.1 Consensus size: 18
1085652 TTAGATAAAC
1085662 AAGATAAA-GAAAACAAAT
1 AAGATAAAGGAAAA-AAAT
1085680 AAGATAAAAGGGAAAAATAAAAT
1 AAGAT-AAA-GG--AAA-AAAAT
** *
1085703 AA-ATAAAATAAATAAAT
1 AAGATAAAGGAAAAAAAT
1085720 AAGATAAAGGAAAAAAAT
1 AAGATAAAGGAAAAAAAT
1085738 A
1 A
1085739 GTAAAGTAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.13
18 21 0.46
19 3 0.07
21 4 0.09
22 2 0.04
23 9 0.20
24 1 0.02
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.14
Consensus pattern (18 bp):
AAGATAAAGGAAAAAAAT
Found at i:1086030 original size:2 final size:2
Alignment explanation
Indices: 1085990--1086014 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1085980 AACGAAAATA
1085990 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1086015 AAGTTATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1086286 original size:18 final size:17
Alignment explanation
Indices: 1086263--1086305 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1086253 ATATATACAT
1086263 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1086281 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1086298 ATAA-AATA
1 ATAATAATA
1086306 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1086743 original size:35 final size:37
Alignment explanation
Indices: 1086681--1086772 Score: 109
Period size: 35 Copynumber: 2.6 Consensus size: 37
1086671 GGATCCTATC
* * *
1086681 TTTAG-GAGTTTAAAACATAGCAAAATTCTATCATAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
* *
1086717 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
*
1086752 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
1086773 TAGGACGAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
35 26 0.54
36 11 0.23
37 11 0.23
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTCTATCATAT
Found at i:1087506 original size:2 final size:2
Alignment explanation
Indices: 1087499--1087527 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1087489 GATAAAATTA
1087499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1087528 AACTAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1087621 original size:18 final size:16
Alignment explanation
Indices: 1087598--1087637 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
1087588 ATTTAAATTC
1087598 AAAATTAAATTAAATTTT
1 AAAATTAAA--AAATTTT
*
1087616 AAAATTAAAATATTTT
1 AAAATTAAAAAATTTT
1087632 AAAATT
1 AAAATT
1087638 TATTGATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.57
18 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAAATTAAAAAATTTT
Found at i:1098875 original size:6 final size:7
Alignment explanation
Indices: 1098858--1098884 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1098848 AAGAAGTGAT
1098858 TTTTTTC
1 TTTTTTC
1098865 TTTTTTC
1 TTTTTTC
1098872 TTTTTTC
1 TTTTTTC
1098879 TTTTTT
1 TTTTTT
1098885 AAGAGCGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTTTTC
Found at i:1099181 original size:16 final size:16
Alignment explanation
Indices: 1099156--1099187 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1099146 TAGTTATATA
1099156 TATATAATGGATTATT
1 TATATAATGGATTATT
*
1099172 TATATCATGGATTATT
1 TATATAATGGATTATT
1099188 AAATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (16 bp):
TATATAATGGATTATT
Found at i:1101472 original size:20 final size:20
Alignment explanation
Indices: 1101429--1101473 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1101419 CAGGCCGTTT
* *
1101429 AAAATGTATTATTTAAATAT
1 AAAAAGTATTATTTAAATAA
1101449 AAAAAGTATTATATT-AATAA
1 AAAAAGTATTAT-TTAAATAA
1101469 AAAAA
1 AAAAA
1101474 TATAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
AAAAAGTATTATTTAAATAA
Found at i:1109580 original size:13 final size:14
Alignment explanation
Indices: 1109550--1109578 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1109540 AAATCACCCA
1109550 TTCCATCTTTATTT
1 TTCCATCTTTATTT
1109564 TTCCATCTTTATTT
1 TTCCATCTTTATTT
1109578 T
1 T
1109579 CCTATCAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCCATCTTTATTT
Found at i:1113129 original size:17 final size:18
Alignment explanation
Indices: 1113097--1113130 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1113087 TAATTAAATA
1113097 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
1113115 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
1113131 ACTTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:1113388 original size:40 final size:40
Alignment explanation
Indices: 1113312--1113390 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
1113302 GAATTTCAGG
* *
1113312 AAGGAGCGACCCATGCACTACGCCTTACCCTACGTGGCAA
1 AAGGAGCGACCCATGCACCACGCCTTACCCGACGTGGCAA
* *
1113352 AAGGCGCGACCCATGCACCGCGCCTTA-CCGAGCGTGGCA
1 AAGGAGCGACCCATGCACCACGCCTTACCCGA-CGTGGCA
1113391 CCATGTCATC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.09
40 31 0.91
ACGTcount: A:0.24, C:0.37, G:0.27, T:0.13
Consensus pattern (40 bp):
AAGGAGCGACCCATGCACCACGCCTTACCCGACGTGGCAA
Found at i:1123188 original size:20 final size:22
Alignment explanation
Indices: 1123165--1123269 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 22
1123155 AAATTTGGAA
1123165 AATTATAAAATTA-T-TTAAAT
1 AATTATAAAATTATTATTAAAT
*
1123185 AATTATAAAATAATTATTAAAT
1 AATTATAAAATTATTATTAAAT
*
1123207 --TTATTAAATTATTATTAAAT
1 AATTATAAAATTATTATTAAAT
* *
1123227 TATTATTAAAA-T-TTATCAAA-
1 AATTA-TAAAATTATTATTAAAT
* *
1123247 ATATCATAAAATGATTATTAAAT
1 A-ATTATAAAATTATTATTAAAT
1123270 TGAGTGAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
20 35 0.52
21 11 0.16
22 17 0.25
23 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (22 bp):
AATTATAAAATTATTATTAAAT
Found at i:1123197 original size:11 final size:10
Alignment explanation
Indices: 1123166--1123269 Score: 63
Period size: 11 Copynumber: 10.0 Consensus size: 10
1123156 AATTTGGAAA
1123166 ATTATAAAATT
1 ATTATAAAA-T
1123177 ATT-T-AAAT
1 ATTATAAAAT
1123185 AATTATAAAAT
1 -ATTATAAAAT
*
1123196 AATTATTAAAT
1 -ATTATAAAAT
*
1123207 -TTATTAAATT
1 ATTA-TAAAAT
*
1123217 ATTATTAAATT
1 ATTA-TAAAAT
1123228 ATTATTAAAAT
1 ATTA-TAAAAT
1123239 -TTATCAAAAT
1 ATTAT-AAAAT
*
1123249 ATCATAAAAT
1 ATTATAAAAT
*
1123259 GATTATTAAAT
1 -ATTATAAAAT
1123270 TGAGTGAACT
Statistics
Matches: 78, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
8 1 0.01
9 10 0.13
10 19 0.24
11 48 0.62
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (10 bp):
ATTATAAAAT
Found at i:1123201 original size:31 final size:30
Alignment explanation
Indices: 1123165--1123270 Score: 88
Period size: 31 Copynumber: 3.4 Consensus size: 30
1123155 AAATTTGGAA
1123165 AATTATAAAATTATTTAAATAATTATAAAAT
1 AATTATAAAATTATTTAAAT-ATTATAAAAT
* *
1123196 AATTATTAAATT-TATTAAATTATTATTAAAT
1 AATTATAAAATTAT-TTAAA-TATTATAAAAT
* ** *
1123227 TATTATTAAAATTTATCAAAATATCATAAAAT
1 AATTA-TAAAA-TTATTTAAATATTATAAAAT
* *
1123259 GATTATTAAATT
1 AATTATAAAATT
1123271 GAGTGAACTC
Statistics
Matches: 60, Mismatches: 10, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
30 3 0.05
31 33 0.55
32 18 0.30
33 5 0.08
34 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (30 bp):
AATTATAAAATTATTTAAATATTATAAAAT
Found at i:1123239 original size:32 final size:32
Alignment explanation
Indices: 1123165--1123268 Score: 115
Period size: 32 Copynumber: 3.3 Consensus size: 32
1123155 AAATTTGGAA
*
1123165 AATTA-TAAAA-TTATTTAAATAATTATAAAAT
1 AATTATTAAAATTTA-TTAAATTATTATAAAAT
*
1123196 AATTATT-AAATTTATTAAATTATTATTAAAT
1 AATTATTAAAATTTATTAAATTATTATAAAAT
* * * *
1123227 TATTATTAAAATTTATCAAAATATCATAAAAT
1 AATTATTAAAATTTATTAAATTATTATAAAAT
*
1123259 GATTATTAAA
1 AATTATTAAA
1123269 TTGAGTGAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
31 29 0.47
32 33 0.53
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (32 bp):
AATTATTAAAATTTATTAAATTATTATAAAAT
Found at i:1126841 original size:135 final size:135
Alignment explanation
Indices: 1126599--1126873 Score: 505
Period size: 135 Copynumber: 2.0 Consensus size: 135
1126589 TGATGAACTA
* *
1126599 ACATTTCCTTTTGCAGAGCTGCAACCTTCTCGTGATTTAGCCAAGAAGAATTCGTTTGCTTTAGA
1 ACATTTCCTTTTGCAGAGCTGCAACCTTCTCGTGATTTAGCCAAGAAGAATTCGTCTACTTTAGA
1126664 CATAATTATGCAGCCACAACGGTTGCGTGTATCTATGGCTTCTTCGCATGGAAATACCTCTCCTC
66 CATAATTATGCAGCCACAACGGTTGCGTGTATCTATGGCTTCTTCGCATGGAAATACCTCTCCTC
1126729 GGCTT
131 GGCTT
*
1126734 ACATTTCCTTTTGCAGAGCTGTAACCTTCTCGTGATTTAGCCAAGAAGAATTCGTCTACTTTAGA
1 ACATTTCCTTTTGCAGAGCTGCAACCTTCTCGTGATTTAGCCAAGAAGAATTCGTCTACTTTAGA
* *
1126799 CATAATTATGCAGCCACAACGGTTGCGTGTATCTATGGCTTCTTCGCATGGAAATACTTCTCCTG
66 CATAATTATGCAGCCACAACGGTTGCGTGTATCTATGGCTTCTTCGCATGGAAATACCTCTCCTC
1126864 GGCTT
131 GGCTT
1126869 ACATT
1 ACATT
1126874 GACCCCCCAC
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (135 bp):
ACATTTCCTTTTGCAGAGCTGCAACCTTCTCGTGATTTAGCCAAGAAGAATTCGTCTACTTTAGA
CATAATTATGCAGCCACAACGGTTGCGTGTATCTATGGCTTCTTCGCATGGAAATACCTCTCCTC
GGCTT
Found at i:1127058 original size:33 final size:33
Alignment explanation
Indices: 1127021--1127086 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1127011 GAGTCTCACA
*
1127021 CACCTGAACAGTCTGTAGCTGAGCCGGTTGTGG
1 CACCTGAACAATCTGTAGCTGAGCCGGTTGTGG
*
1127054 CACCTGAACAATCTGTAGCTGATCCGGTTGTGG
1 CACCTGAACAATCTGTAGCTGAGCCGGTTGTGG
1127087 TGTCACAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.20, C:0.24, G:0.30, T:0.26
Consensus pattern (33 bp):
CACCTGAACAATCTGTAGCTGAGCCGGTTGTGG
Found at i:1129185 original size:2 final size:2
Alignment explanation
Indices: 1129178--1129233 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1129168 TTATATTGTA
1129178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1129220 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1129234 TCCATATTGG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1133677 original size:2 final size:2
Alignment explanation
Indices: 1133670--1133709 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1133660 CTATAATCCC
1133670 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1133710 TGAATAGTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1141427 original size:21 final size:22
Alignment explanation
Indices: 1141387--1141427 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1141377 TTAAAAACAA
*
1141387 TAATATATAAATCTATTTGAAC
1 TAATATATAAATCGATTTGAAC
*
1141409 TAATATATAAGT-GATTTGA
1 TAATATATAAATCGATTTGA
1141428 GTTTAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (22 bp):
TAATATATAAATCGATTTGAAC
Found at i:1155299 original size:6 final size:6
Alignment explanation
Indices: 1155288--1155313 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1155278 GTCTCAAGCT
1155288 TTATTG TTATTG TTATTG TTATTG TT
1 TTATTG TTATTG TTATTG TTATTG TT
1155314 TTAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTATTG
Found at i:1159409 original size:2 final size:2
Alignment explanation
Indices: 1159402--1159427 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1159392 TTAAAAGAAT
1159402 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1159428 ATAATTTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1161162 original size:21 final size:21
Alignment explanation
Indices: 1161138--1161180 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1161128 GGGTTTAGGG
1161138 TTTAGTGGATCCACCACTGGC
1 TTTAGTGGATCCACCACTGGC
1161159 TTTAGTGGATCCACCACTGGC
1 TTTAGTGGATCCACCACTGGC
1161180 T
1 T
1161181 GTAACCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.23, T:0.30
Consensus pattern (21 bp):
TTTAGTGGATCCACCACTGGC
Found at i:1166575 original size:10 final size:10
Alignment explanation
Indices: 1166560--1166587 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1166550 CTACTAACAT
1166560 TATTGTTGGA
1 TATTGTTGGA
1166570 TATTGTTGGA
1 TATTGTTGGA
1166580 TATTGTTG
1 TATTGTTG
1166588 CACTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.54
Consensus pattern (10 bp):
TATTGTTGGA
Found at i:1166882 original size:2 final size:2
Alignment explanation
Indices: 1166875--1166942 Score: 54
Period size: 2 Copynumber: 34.0 Consensus size: 2
1166865 CCATCATACT
*
1166875 TA TA TA TA TA TA TA TA TA TA TA TA -A GTA GA CT- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA -TA TA TA TA TA TA
*
1166917 TA TA -A GTA GA CT- TA TA TA TA TA TA TA
1 TA TA TA -TA TA -TA TA TA TA TA TA TA TA
1166943 ATTTTCTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
1 4 0.07
2 48 0.89
3 2 0.04
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (2 bp):
TA
Found at i:1166913 original size:22 final size:22
Alignment explanation
Indices: 1166885--1166943 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
1166875 TATATATATA
1166885 TATATATATATATAAGTAGACT
1 TATATATATATATAAGTAGACT
1166907 TATATATATATATAAGTAGACT
1 TATATATATATATAAGTAGACT
1166929 TATATATATATATAA
1 TATATATATATATAA
1166944 TTTTCTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (22 bp):
TATATATATATATAAGTAGACT
Found at i:1167281 original size:20 final size:20
Alignment explanation
Indices: 1167256--1167349 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1167246 AATTGGAAAA
1167256 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
1167276 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* * *
1167296 ATCGCAATACGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1167317 ATCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1167337 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1167350 TTACATAGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.74
21 12 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1167880 original size:19 final size:20
Alignment explanation
Indices: 1167831--1167882 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1167821 TAGTTTCGAG
1167831 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
*
1167851 AAT-AACTATCGCAACGC-GA
1 AATGAA-AATCGCAACGCGGA
1167870 AATGAAAATCGCA
1 AATGAAAATCGCA
1167883 TTGCGATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.46, C:0.21, G:0.19, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:1167936 original size:33 final size:33
Alignment explanation
Indices: 1167894--1167976 Score: 121
Period size: 33 Copynumber: 2.5 Consensus size: 33
1167884 TGCGATTTTT
1167894 ATTTCGCGTTGCGATTATCTCGTCCCGATAGTC
1 ATTTCGCGTTGCGATTATCTCGTCCCGATAGTC
* ** *
1167927 ATTTCGCGTTGCGATTCTCTCGTTGCGATATTC
1 ATTTCGCGTTGCGATTATCTCGTCCCGATAGTC
1167960 ATTTCCGCGTTGCGATT
1 ATTT-CGCGTTGCGATT
1167977 CTCATTATCT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.73
34 12 0.27
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (33 bp):
ATTTCGCGTTGCGATTATCTCGTCCCGATAGTC
Found at i:1167972 original size:20 final size:19
Alignment explanation
Indices: 1167947--1168004 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 19
1167937 GCGATTCTCT
1167947 CGTTGCGATATTCATTTCCG
1 CGTTGCGAT-TTCATTTCCG
*
1167967 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATT-TCATT-TCCG
1167987 CGTTGCGATTTTCATTTC
1 CGTTGCGA-TTTCATTTC
1168005 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
19 2 0.06
20 28 0.85
21 3 0.09
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTCATTTCCG
Found at i:1170153 original size:42 final size:42
Alignment explanation
Indices: 1170093--1170215 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 42
1170083 GCCCGACTCG
* * * *
1170093 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCGCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
1170135 CCTATCATTCCGCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCGCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** *
1170177 ACTGTCATCGTTG-AAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATC-CCGCAAGA-GTCCACTCCCACCGTTCAAGAG
1170216 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
42 60 0.92
43 5 0.08
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CCTATCATCCCGCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:1170173 original size:21 final size:21
Alignment explanation
Indices: 1170149--1170215 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1170139 TCATTCCGCG
1170149 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
1170170 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
1170191 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
1170212 AGAG
1 AGAG
1170216 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:1171587 original size:14 final size:14
Alignment explanation
Indices: 1171568--1171603 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1171558 ATTGTTTAAT
1171568 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1171582 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1171596 TGATTTGT
1 TGATTTGT
1171604 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1171770 original size:19 final size:19
Alignment explanation
Indices: 1171748--1171865 Score: 67
Period size: 19 Copynumber: 6.7 Consensus size: 19
1171738 CGAAATTAAA
1171748 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1171767 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1171782 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
1171800 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
1171815 -TCTCGTTGCGATTTTTAT
1 TTCGCGTTGCGATTTTCAT
* ** *
1171833 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
1171852 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
1171866 AGACATTAAG
Statistics
Matches: 72, Mismatches: 16, Indels: 21
0.66 0.15 0.19
Matches are distributed among these distances:
14 17 0.24
16 5 0.07
17 6 0.08
19 34 0.47
20 10 0.14
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:1171794 original size:33 final size:33
Alignment explanation
Indices: 1171752--1171845 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1171742 ATTAAATTCG
1171752 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1171785 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
*
1171818 CGTTGCGATTTTTATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1171846 AGTAATTTCC
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1174153 original size:12 final size:12
Alignment explanation
Indices: 1174136--1174160 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1174126 TCTTCGGGGA
1174136 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1174148 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1174160 C
1 C
1174161 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1174369 original size:24 final size:24
Alignment explanation
Indices: 1174335--1174388 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1174325 CTGAAACATC
*
1174335 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
1174359 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1174383 ATCAAA
1 ATCAAA
1174389 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1175242 original size:20 final size:20
Alignment explanation
Indices: 1175128--1175241 Score: 140
Period size: 20 Copynumber: 5.7 Consensus size: 20
1175118 GATTCTGTAT
*
1175128 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1175148 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
1175168 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
1175188 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
1175209 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
1175229 TATCGCATTGCGA
1 TATCGCGTTGCGA
1175242 TTTTCCCAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
19 3 0.04
20 63 0.77
21 14 0.17
22 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:1175244 original size:41 final size:41
Alignment explanation
Indices: 1175108--1175245 Score: 172
Period size: 41 Copynumber: 3.4 Consensus size: 41
1175098 AACTTTGAAA
* * *
1175108 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** *
1175149 ATCGCGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGT-ATTATCGCGTTGCGAAAGTCAGT
* *
1175189 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
1175230 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1175246 CCCAATTCGC
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
39 2 0.02
40 32 0.39
41 47 0.57
42 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:1175256 original size:41 final size:41
Alignment explanation
Indices: 1175108--1175263 Score: 136
Period size: 41 Copynumber: 3.8 Consensus size: 41
1175098 AACTTTGAAA
* ** * * * *
1175108 ATCGCATTGCGATTCTGTATTATCTCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* *** * *
1175149 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
* ** *
1175189 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
1175230 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
1175264 TTACTTATTC
Statistics
Matches: 95, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
40 33 0.35
41 60 0.63
42 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTCAGT
Found at i:1177191 original size:3 final size:3
Alignment explanation
Indices: 1177185--1177212 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1177175 ATTATTATTA
1177185 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1177213 TACTTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1178481 original size:33 final size:33
Alignment explanation
Indices: 1178433--1178524 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 33
1178423 TCGTCCTCAG
*
1178433 CCCTAGGC-ACTCCCTGGTGTGCGACGGTCACGA
1 CCCTAGGCGAC-CCCTGGTGTGCGACGGCCACGA
* * ** *
1178466 CCCTAGGTGCCCCCTGGTGTGCGGTGGCCTCGA
1 CCCTAGGCGACCCCTGGTGTGCGACGGCCACGA
* *
1178499 CCCTAGGCGACTCTTGGTGTGCGACG
1 CCCTAGGCGACCCCTGGTGTGCGACG
1178525 ACTTCGGCCC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
33 45 0.98
34 1 0.02
ACGTcount: A:0.11, C:0.35, G:0.34, T:0.21
Consensus pattern (33 bp):
CCCTAGGCGACCCCTGGTGTGCGACGGCCACGA
Found at i:1188770 original size:128 final size:126
Alignment explanation
Indices: 1188542--1188788 Score: 370
Period size: 128 Copynumber: 1.9 Consensus size: 126
1188532 TAACATGGCA
*
1188542 ACTTTGCAGAAGTCAAAACCAAAGGGAAACAGGTTAAAGGAAAGGGATAACAAAGGAATTTATTA
1 ACTTTGCAGAAGTCAAAACCAAAGGGAAACAGGTTAAAGGAAAGGGATAACAAAGGAACTTATTA
* *
1188607 CATGAACTTCGGCATCCCCTTATATACCTAAAAAAAATTTGACTTTAGTATGCATGGGTTTGC
66 CATGAACTTCGGCATCCCCGTATATACCT-AAAAAAATCTGA-TTTAGTATGCATGGGTTTGC
* * * **
1188670 ACTTTGCAGAAGTCAAAACTAAAGTGAAATAGGTTAAAGGAAAGGGATAAC-CCGCGAACTTATT
1 ACTTTGCAGAAGTCAAAACCAAAGGGAAACAGGTTAAAGGAAAGGGATAACAAAG-GAACTTATT
* *
1188734 ACATGAATTTTGGCATCCCCGTATATACCTAAAAAAATCTGATTTAGTATGCATG
65 ACATGAACTTCGGCATCCCCGTATATACCTAAAAAAATCTGATTTAGTATGCATG
1188789 TGCAGGTTTT
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
126 13 0.12
127 12 0.11
128 83 0.77
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (126 bp):
ACTTTGCAGAAGTCAAAACCAAAGGGAAACAGGTTAAAGGAAAGGGATAACAAAGGAACTTATTA
CATGAACTTCGGCATCCCCGTATATACCTAAAAAAATCTGATTTAGTATGCATGGGTTTGC
Found at i:1192137 original size:3 final size:3
Alignment explanation
Indices: 1192129--1192194 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
1192119 ATTAATTTAA
1192129 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1192177 AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT
1192195 GGTGCTACTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1193220 original size:20 final size:20
Alignment explanation
Indices: 1193195--1193245 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1193185 ACTTGATATT
*
1193195 CGACTCGAAAAGTTCGTGAG
1 CGACTCGAAAAGCTCGTGAG
1193215 CGACTCGAAAAGCTCGTGAG
1 CGACTCGAAAAGCTCGTGAG
1193235 C-AGCTCGAAAA
1 CGA-CTCGAAAA
1193246 CATAATATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (20 bp):
CGACTCGAAAAGCTCGTGAG
Found at i:1197864 original size:16 final size:18
Alignment explanation
Indices: 1197824--1197870 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
1197814 TAAAAAAATA
*
1197824 ATATAAAAATATATTTAT
1 ATATTAAAATATATTTAT
*
1197842 ATATTAAAATAT-TTTTT
1 ATATTAAAATATATTTAT
1197859 AT-TTAAAA-ATAT
1 ATATTAAAATATAT
1197871 CAGAAAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 2 0.08
16 7 0.27
17 6 0.23
18 11 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATTAAAATATATTTAT
Found at i:1197869 original size:17 final size:19
Alignment explanation
Indices: 1197827--1197870 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
1197817 AAAAATAATA
1197827 TAAAAATATATTTATATAT
1 TAAAAATATATTTATATAT
*
1197846 T-AAAATAT-TTTTTAT-T
1 TAAAAATATATTTATATAT
1197862 TAAAAATAT
1 TAAAAATAT
1197871 CAGAAAATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 2 0.09
17 13 0.57
18 7 0.30
19 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAAATATATTTATATAT
Found at i:1199506 original size:3 final size:3
Alignment explanation
Indices: 1199498--1199554 Score: 80
Period size: 3 Copynumber: 18.7 Consensus size: 3
1199488 ATATTTATTA
*
1199498 AAT AAT AAT AAT -AT ATAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
1199544 AAT AAT AAT AA
1 AAT AAT AAT AA
1199555 AACGAAATGA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Done.