Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold167
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: 4199719
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.33
Warning! 197959 characters in sequence are not A, C, G, or T
File 17 of 22
Found at i:2742081 original size:18 final size:20
Alignment explanation
Indices: 2742041--2742081 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
2742031 CAAACGCATA
*
2742041 AAAAAAACTTTTAAAAATAT
1 AAAAAAACTTTAAAAAATAT
2742061 AAAAAAA-TTTAAAAAAT-T
1 AAAAAAACTTTAAAAAATAT
2742079 AAA
1 AAA
2742082 TTACACTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 9 0.45
20 7 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAAAAACTTTAAAAAATAT
Found at i:2746443 original size:24 final size:26
Alignment explanation
Indices: 2746411--2746495 Score: 70
Period size: 24 Copynumber: 3.3 Consensus size: 26
2746401 ATTTTTATAT
2746411 TATATATATATTTAAAAT-TAT-AAAA
1 TATA-ATATATTTAAAATATATAAAAA
*
2746436 TATAATAT-TTT-GAATATATAAAAA
1 TATAATATATTTAAAATATATAAAAA
* * * * *
2746460 TTTAATATATTTATATTAAATATAAA
1 TATAATATATTTAAAATATATAAAAA
2746486 TATAAATATA
1 TAT-AATATA
2746496 AATTTAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.06
23 6 0.12
24 15 0.31
25 7 0.15
26 11 0.23
27 6 0.12
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
TATAATATATTTAAAATATATAAAAA
Found at i:2746485 original size:6 final size:6
Alignment explanation
Indices: 2746476--2746505 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2746466 ATATTTATAT
*
2746476 TAAATA TAAATA TAAATA TAAATT TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA
2746506 ATATATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
TAAATA
Found at i:2746488 original size:19 final size:19
Alignment explanation
Indices: 2746466--2746515 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
2746456 AAAATTTAAT
*
2746466 ATATTTATATTAAATATAA
1 ATATATATATTAAATATAA
* *
2746485 ATATAAATA-TAAATTTAA
1 ATATATATATTAAATATAA
2746503 ATAATATATATTA
1 AT-ATATATATTA
2746516 TTAATATACG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 10 0.40
19 13 0.52
20 2 0.08
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATATATTAAATATAA
Found at i:2746604 original size:59 final size:59
Alignment explanation
Indices: 2746507--2746683 Score: 284
Period size: 59 Copynumber: 3.0 Consensus size: 59
2746497 ATTTAAATAA
* * *
2746507 TATATATTATTAATATACGGAGATGCCTTACCAGTGTACACAACTGCAGGGCAATGGAG
1 TATAAATTATTAATGTACGGAGATGCCTTACCAGTGTACACAACTGCAGGGCCATGGAG
*
2746566 TATAAATTATTAATGTACGGAGATGCCTTACCAGTGTACACAACTGCGGGGCCATGGAG
1 TATAAATTATTAATGTACGGAGATGCCTTACCAGTGTACACAACTGCAGGGCCATGGAG
* * *
2746625 TATAAATTATTAATGTACGGAGATGCCTTA-GAGTGTACACAGCTGCTGGGCCATGGAG
1 TATAAATTATTAATGTACGGAGATGCCTTACCAGTGTACACAACTGCAGGGCCATGGAG
2746683 T
1 T
2746684 GCGAAGAAGA
Statistics
Matches: 111, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 26 0.23
59 85 0.77
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (59 bp):
TATAAATTATTAATGTACGGAGATGCCTTACCAGTGTACACAACTGCAGGGCCATGGAG
Found at i:2747509 original size:2 final size:2
Alignment explanation
Indices: 2747502--2747538 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2747492 GGTTTTGAAG
2747502 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2747539 ACTTTGATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:2747660 original size:2 final size:2
Alignment explanation
Indices: 2747653--2747683 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2747643 GAGCAAAAGG
2747653 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2747684 ACATATGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2752620 original size:17 final size:17
Alignment explanation
Indices: 2752594--2752630 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
2752584 AGCGTTGTTG
2752594 CTTTTGGTTGGTTATTA
1 CTTTTGGTTGGTTATTA
*
2752611 CTTTTTGTTGGTTATTA
1 CTTTTGGTTGGTTATTA
2752628 CTT
1 CTT
2752631 ATTGATATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.62
Consensus pattern (17 bp):
CTTTTGGTTGGTTATTA
Found at i:2754547 original size:26 final size:26
Alignment explanation
Indices: 2754504--2754555 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
2754494 AATAAAAAAT
*
2754504 AAATTCAATTTTTATATTTGATTTTA
1 AAATTCAATTTTTATATTTGAATTTA
*
2754530 AAATT-AATTATTTGTATTTGAATTTA
1 AAATTCAATT-TTTATATTTGAATTTA
2754556 TATTAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 19 0.83
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (26 bp):
AAATTCAATTTTTATATTTGAATTTA
Found at i:2754560 original size:25 final size:26
Alignment explanation
Indices: 2754504--2754586 Score: 75
Period size: 25 Copynumber: 3.3 Consensus size: 26
2754494 AATAAAAAAT
*
2754504 AAATTCAATT-TTTATATTTGATTTTA
1 AAATT-AATTATTTATATTTGAATTTA
*
2754530 AAATTAATTATTTGTATTTGAATTT-
1 AAATTAATTATTTATATTTGAATTTA
* * * *
2754555 ATATTAAATATTTAAAATT-AA-TTA
1 AAATTAATTATTTATATTTGAATTTA
2754579 AAATTAAT
1 AAATTAAT
2754587 AAAAATATAT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 2 0.04
24 8 0.17
25 18 0.39
26 18 0.39
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (26 bp):
AAATTAATTATTTATATTTGAATTTA
Found at i:2756542 original size:2 final size:2
Alignment explanation
Indices: 2756535--2756565 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2756525 CCTGCAAAGC
2756535 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2756566 TGAATGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2760584 original size:14 final size:15
Alignment explanation
Indices: 2760552--2760584 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2760542 ATCCAATCCT
2760552 AATTTGACAAAAAAC
1 AATTTGACAAAAAAC
2760567 AATTTGACAAAAAA-
1 AATTTGACAAAAAAC
2760581 AATT
1 AATT
2760585 AATAATCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (15 bp):
AATTTGACAAAAAAC
Found at i:2760618 original size:16 final size:16
Alignment explanation
Indices: 2760597--2760723 Score: 84
Period size: 16 Copynumber: 8.0 Consensus size: 16
2760587 TAATCTGAAT
*
2760597 CCGAATTGACTCGAAC
1 CCGAAATGACTCGAAC
*
2760613 CCG-AATGA-TCCGAAT
1 CCGAAATGACT-CGAAC
2760628 CC-AGAATGA-TCCGAAC
1 CCGA-AATGACT-CGAAC
* * *
2760644 TCGAAATGACTCAAAT
1 CCGAAATGACTCGAAC
* * *
2760660 CCAAAATAATTCGAAC
1 CCGAAATGACTCGAAC
* *
2760676 CCGAAAT-AATCCGAAT
1 CCGAAATGACT-CGAAC
*
2760692 CCGAAATGACCCGAAC
1 CCGAAATGACTCGAAC
2760708 CCGAAATGACTCGAAC
1 CCGAAATGACTCGAAC
2760724 TTAAATTAAG
Statistics
Matches: 85, Mismatches: 19, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
14 1 0.01
15 12 0.14
16 69 0.81
17 3 0.04
ACGTcount: A:0.39, C:0.28, G:0.16, T:0.17
Consensus pattern (16 bp):
CCGAAATGACTCGAAC
Found at i:2760661 original size:32 final size:32
Alignment explanation
Indices: 2760608--2760719 Score: 97
Period size: 32 Copynumber: 3.5 Consensus size: 32
2760598 CGAATTGACT
*
2760608 CGAACCCG-AATGA-TCCGAATCCAGAATGATC
1 CGAACCCGAAATGACT-CAAATCCAGAATGATC
* * * *
2760639 CGAACTCGAAATGACTCAAATCCAAAATAATT
1 CGAACCCGAAATGACTCAAATCCAGAATGATC
* * *
2760671 CGAACCCGAAAT-AATCCGAATCC-GAAATGACC
1 CGAACCCGAAATGACT-CAAATCCAG-AATGATC
2760703 CGAACCCGAAATGACTC
1 CGAACCCGAAATGACTC
2760720 GAACTTAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 9
0.74 0.15 0.11
Matches are distributed among these distances:
31 9 0.14
32 51 0.81
33 3 0.05
ACGTcount: A:0.40, C:0.29, G:0.15, T:0.16
Consensus pattern (32 bp):
CGAACCCGAAATGACTCAAATCCAGAATGATC
Found at i:2760722 original size:48 final size:47
Alignment explanation
Indices: 2760585--2760723 Score: 131
Period size: 48 Copynumber: 2.9 Consensus size: 47
2760575 AAAAAAAATT
* * *
2760585 AATAATCTGAATCCGAATTGACTCGAACCCG-AATGATCCGAATCCAG
1 AATAATCCGAATCCGAAATGACTCGAACCCGAAATGAT-CGAACCCAG
* * * * *
2760632 AATGATCCGAA-CTCGAAATGACTCAAATCCAAAATAATTCGAACCC-G
1 AATAATCCGAATC-CGAAATGACTCGAACCCGAAATGA-TCGAACCCAG
*
2760679 AAATAATCCGAATCCGAAATGACCCGAACCCGAAATGACTCGAAC
1 -AATAATCCGAATCCGAAATGACTCGAACCCGAAATGA-TCGAAC
2760724 TTAAATTAAG
Statistics
Matches: 72, Mismatches: 15, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
46 1 0.01
47 24 0.33
48 45 0.62
49 2 0.03
ACGTcount: A:0.40, C:0.27, G:0.15, T:0.18
Consensus pattern (47 bp):
AATAATCCGAATCCGAAATGACTCGAACCCGAAATGATCGAACCCAG
Found at i:2761822 original size:32 final size:33
Alignment explanation
Indices: 2761786--2761857 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 33
2761776 TAACTCGAAT
* * *
2761786 CCAAAGTGACCTGAATCCG-AAATGACCCAAAC
1 CCAAAATGACCCGAACCCGAAAATGACCCAAAC
*
2761818 CCAAAATGACCCGAACCCGAAAATGACGCAAAC
1 CCAAAATGACCCGAACCCGAAAATGACCCAAAC
2761851 CCGAAAA
1 CC-AAAA
2761858 CAATCTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 16 0.47
33 14 0.41
34 4 0.12
ACGTcount: A:0.44, C:0.32, G:0.15, T:0.08
Consensus pattern (33 bp):
CCAAAATGACCCGAACCCGAAAATGACCCAAAC
Found at i:2761842 original size:17 final size:17
Alignment explanation
Indices: 2761757--2761857 Score: 75
Period size: 16 Copynumber: 6.2 Consensus size: 17
2761747 CCTAAACTCG
* *
2761757 AAATGACTCGAACCTG-
1 AAATGACCCGAACCCGA
* * *
2761773 AAATAACTCGAATCC-A
1 AAATGACCCGAACCCGA
* * *
2761789 AAGTGACCTGAATCCG-
1 AAATGACCCGAACCCGA
*
2761805 AAATGACCCAAACCC-A
1 AAATGACCCGAACCCGA
2761821 AAATGACCCGAACCCGA
1 AAATGACCCGAACCCGA
* *
2761838 AAATGACGCAAACCCGA
1 AAATGACCCGAACCCGA
2761855 AAA
1 AAA
2761858 CAATCTAAAA
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
16 48 0.72
17 19 0.28
ACGTcount: A:0.45, C:0.29, G:0.15, T:0.12
Consensus pattern (17 bp):
AAATGACCCGAACCCGA
Found at i:2763180 original size:14 final size:14
Alignment explanation
Indices: 2763151--2763183 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
2763141 ATTCTAACAA
2763151 TTTTTTAACCATTT
1 TTTTTTAACCATTT
2763165 TTTTTCTAACCATTT
1 TTTTT-TAACCATTT
2763180 TTTT
1 TTTT
2763184 AATAACAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.15, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTTTAACCATTT
Found at i:2763189 original size:15 final size:15
Alignment explanation
Indices: 2763156--2763189 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2763146 AACAATTTTT
**
2763156 TAACCATTTTTTTTC
1 TAACCATTTTTTTAA
2763171 TAACCATTTTTTTAA
1 TAACCATTTTTTTAA
2763186 TAAC
1 TAAC
2763190 AGGAACGTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (15 bp):
TAACCATTTTTTTAA
Found at i:2766471 original size:18 final size:18
Alignment explanation
Indices: 2766448--2766498 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
2766438 TTTTTTATGT
2766448 TTTTTTGCATCAGTTTAA
1 TTTTTTGCATCAGTTTAA
*
2766466 TTTTTTGCATCAATTTAA
1 TTTTTTGCATCAGTTTAA
*
2766484 -TTTTTGCATTAGTTT
1 TTTTTTGCATCAGTTT
2766499 TGATTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.22, C:0.10, G:0.10, T:0.59
Consensus pattern (18 bp):
TTTTTTGCATCAGTTTAA
Found at i:2777967 original size:4 final size:4
Alignment explanation
Indices: 2777953--2777988 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
2777943 TTTAAACACG
2777953 AAAT GAAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
2777989 CATAAAGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:2778752 original size:14 final size:15
Alignment explanation
Indices: 2778733--2778761 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2778723 TTAAATTGTA
2778733 ATTTAAATTT-TTTT
1 ATTTAAATTTATTTT
2778747 ATTTAAATTTATTTT
1 ATTTAAATTTATTTT
2778762 GAATTAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTAAATTTATTTT
Found at i:2779233 original size:34 final size:34
Alignment explanation
Indices: 2779190--2779255 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
2779180 AATGCCAAGT
* * *
2779190 TGATATCAAATCGACATTTACGCTATGTTTGAAG
1 TGATATCAAATCAACACTTACGCCATGTTTGAAG
2779224 TGATATCAAATCAACACTTACGCCATGTTTGA
1 TGATATCAAATCAACACTTACGCCATGTTTGA
2779256 GAGTTCTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (34 bp):
TGATATCAAATCAACACTTACGCCATGTTTGAAG
Found at i:2780745 original size:4 final size:4
Alignment explanation
Indices: 2780736--2780766 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
2780726 CGTTCCAACT
2780736 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2780767 TTAAGTTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:2784329 original size:11 final size:11
Alignment explanation
Indices: 2784313--2784337 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
2784303 ATTGAACTAA
2784313 ATAGTTAAATT
1 ATAGTTAAATT
2784324 ATAGTTAAATT
1 ATAGTTAAATT
2784335 ATA
1 ATA
2784338 TCACTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
ATAGTTAAATT
Found at i:2785005 original size:20 final size:20
Alignment explanation
Indices: 2784981--2785031 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2784971 AATAATTTTT
2784981 ATAAAAAATAAAATAT-TAA
1 ATAAAAAATAAAATATGTAA
* *
2785000 ATTAAATAATAAACTATGTAA
1 A-TAAAAAATAAAATATGTAA
*
2785021 ATAAAACATAA
1 ATAAAAAATAA
2785032 GTAAAGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.81
21 4 0.15
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (20 bp):
ATAAAAAATAAAATATGTAA
Found at i:2786743 original size:19 final size:18
Alignment explanation
Indices: 2786688--2786743 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
2786678 TTAATTTAAA
*
2786688 ATTTTATTTATTATTTATT
1 ATTTTATTTAATATTT-TT
* *
2786707 ATATTATTTAA-A-TATT
1 ATTTTATTTAATATTTTT
2786723 ATTTTATATTAATATTTTT
1 ATTTTAT-TTAATATTTTT
2786742 AT
1 AT
2786744 AAATTTATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
16 8 0.28
17 5 0.17
18 2 0.07
19 14 0.48
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTTATTTAATATTTTT
Found at i:2786793 original size:19 final size:19
Alignment explanation
Indices: 2786765--2786808 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 19
2786755 TAAATATAAA
2786765 TAAA-AATATTTTTA-TTAT
1 TAAATAATA-TTTTACTTAT
2786783 TAAATAATATTTTACTTAT
1 TAAATAATATTTTACTTAT
2786802 TCAAATA
1 T-AAATA
2786809 TTCTAAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.39
19 9 0.39
20 5 0.22
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAATAATATTTTACTTAT
Found at i:2791009 original size:8 final size:8
Alignment explanation
Indices: 2790996--2791028 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
2790986 AATTATTTTT
2790996 TATTTTAA
1 TATTTTAA
2791004 TATTTTAA
1 TATTTTAA
2791012 TATTTTAA
1 TATTTTAA
2791020 TATTTTAA
1 TATTTTAA
2791028 T
1 T
2791029 GCTTAAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTTTAA
Found at i:2791180 original size:12 final size:12
Alignment explanation
Indices: 2791160--2791195 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2791150 AATATAAAAA
2791160 ATATATATATTT
1 ATATATATATTT
*
2791172 ATGTATATATTT
1 ATATATATATTT
*
2791184 ATATATTTATTT
1 ATATATATATTT
2791196 TTCATAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
ATATATATATTT
Found at i:2791188 original size:8 final size:8
Alignment explanation
Indices: 2791160--2791231 Score: 57
Period size: 8 Copynumber: 9.6 Consensus size: 8
2791150 AATATAAAAA
*
2791160 ATATATAT
1 ATATATTT
* *
2791168 ATTTATGT
1 ATATATTT
2791176 ATATATTT
1 ATATATTT
2791184 ATATATTT
1 ATATATTT
2791192 AT-T-TTT
1 ATATATTT
2791198 CATA-ATTT
1 -ATATATTT
2791206 -TAT-TTT
1 ATATATTT
*
2791212 AAATA-TT
1 ATATATTT
2791219 ATATATTT
1 ATATATTT
2791227 ATATA
1 ATATA
2791232 AAATTTAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
6 8 0.16
7 11 0.22
8 32 0.63
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (8 bp):
ATATATTT
Found at i:2791227 original size:20 final size:18
Alignment explanation
Indices: 2791200--2791249 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
2791190 TTATTTTTCA
2791200 TAAT-TTTATTTTAAATAT
1 TAATATTTATTTTAAAT-T
* *
2791218 TATATATTTATATAAAATT
1 TA-ATATTTATTTTAAATT
2791237 TAATATTTATTTT
1 TAATATTTATTTT
2791250 TTTATATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 11 0.42
19 5 0.19
20 10 0.38
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TAATATTTATTTTAAATT
Found at i:2809849 original size:14 final size:13
Alignment explanation
Indices: 2809821--2809861 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2809811 TGATTTGAAT
*
2809821 TTTTTTTTATTGG
1 TTTTTGTTATTGG
2809834 TTTTTGTTATTGG
1 TTTTTGTTATTGG
*
2809847 -GTTTGTT-TTGG
1 TTTTTGTTATTGG
2809858 TTTT
1 TTTT
2809862 AGAGTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.05, C:0.00, G:0.22, T:0.73
Consensus pattern (13 bp):
TTTTTGTTATTGG
Found at i:2814189 original size:16 final size:16
Alignment explanation
Indices: 2814156--2814211 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
2814146 ATTAATGTAT
2814156 TAAAAT-TTATAAAAA
1 TAAAATATTATAAAAA
* *
2814171 TAAAATATTTTAAATA
1 TAAAATATTATAAAAA
*
2814187 TAATAATAATATAAAAA
1 TAA-AATATTATAAAAA
*
2814204 TATAATAT
1 TAAAATAT
2814212 AAATATTCGA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
15 6 0.19
16 14 0.44
17 12 0.38
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TAAAATATTATAAAAA
Found at i:2814258 original size:32 final size:32
Alignment explanation
Indices: 2814217--2814281 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2814207 AATATAAATA
* *
2814217 TTCGAATTATTCGATTTTCTTTATTAGAACTC
1 TTCGAATTATTAGATTTCCTTTATTAGAACTC
2814249 TTCGAATTATTAGATTTCCTTTATTAGAACTC
1 TTCGAATTATTAGATTTCCTTTATTAGAACTC
2814281 T
1 T
2814282 CAGATGGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.49
Consensus pattern (32 bp):
TTCGAATTATTAGATTTCCTTTATTAGAACTC
Found at i:2816766 original size:2 final size:2
Alignment explanation
Indices: 2816759--2816784 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2816749 TTTTTACTTC
2816759 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
2816785 GTGGATGGAA
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):
AT
Found at i:2822332 original size:32 final size:31
Alignment explanation
Indices: 2822287--2822362 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 31
2822277 CCCATTCTAA
*
2822287 ATTATATTTATATAAATATTAATATATTAAT
1 ATTATATTTATATAAATATTAAAATATTAAT
* *
2822318 AATT-TATATTATATAAATTTTAAAATATTTAT
1 -ATTATAT-TTATATAAATATTAAAATATTAAT
2822350 ATTATATTTATAT
1 ATTATATTTATAT
2822363 TTTTTATTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 12 0.31
32 27 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTATATTTATATAAATATTAAAATATTAAT
Found at i:2822557 original size:23 final size:23
Alignment explanation
Indices: 2822498--2822575 Score: 65
Period size: 23 Copynumber: 3.3 Consensus size: 23
2822488 AAGTTCAAAT
2822498 TATTATTTAATTAATAAAATATTAA
1 TATT-TTT-ATTAATAAAATATTAA
*
2822523 -ATTTAATT-TTAATAATATATTAA
1 TATTT--TTATTAATAAAATATTAA
2822546 TATTTTTATTAA-AAAA-ATTAA
1 TATTTTTATTAATAAAATATTAA
*
2822567 AATATTTTA
1 TAT-TTTTA
2822576 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
21 7 0.16
22 10 0.22
23 19 0.42
24 7 0.16
25 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTTTTATTAATAAAATATTAA
Found at i:2824275 original size:53 final size:53
Alignment explanation
Indices: 2824204--2824332 Score: 145
Period size: 53 Copynumber: 2.4 Consensus size: 53
2824194 TTTAATTTCG
* * *
2824204 TTACAAACATATTATCATAAATTTTTAT-TCCATTTAAATTTCGTCAGTATAATA
1 TTACAAA-ATACTATCATAAATTTTTATAT-CATTTAAATTTCATCACTATAATA
* * **
2824258 TTAC-AAATAACTATCATAAATTTTTGTATCATTTAAATTTTATCACTATTCTA
1 TTACAAAAT-ACTATCATAAATTTTTATATCATTTAAATTTCATCACTATAATA
*
2824311 TTACAAAATTCTATCATAAATT
1 TTACAAAATACTATCATAAATT
2824333 AAAATTGTGT
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
52 2 0.03
53 53 0.83
54 9 0.14
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (53 bp):
TTACAAAATACTATCATAAATTTTTATATCATTTAAATTTCATCACTATAATA
Found at i:2824336 original size:18 final size:18
Alignment explanation
Indices: 2824315--2824349 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2824305 ATTCTATTAC
2824315 AAAATTCTATCATAAATT
1 AAAATTCTATCATAAATT
* *
2824333 AAAATTGTGTCATAAAT
1 AAAATTCTATCATAAAT
2824350 AACTATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.09, G:0.06, T:0.37
Consensus pattern (18 bp):
AAAATTCTATCATAAATT
Found at i:2824560 original size:20 final size:20
Alignment explanation
Indices: 2824518--2824580 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 20
2824508 ATTAAATCCG
* * *
2824518 TCACAACTTATGATATTTTA
1 TCACAACTTATAAAATTTCA
*
2824538 TCACAACTTATAAAATTCCA
1 TCACAACTTATAAAATTTCA
* * *
2824558 TCAAAACTTGTAACATTTCA
1 TCACAACTTATAAAATTTCA
2824578 TCA
1 TCA
2824581 TAATTTTCAT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.21, G:0.03, T:0.37
Consensus pattern (20 bp):
TCACAACTTATAAAATTTCA
Found at i:2826069 original size:18 final size:17
Alignment explanation
Indices: 2826031--2826072 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
2826021 TTTCGAATTG
*
2826031 AATTATAATTTATAATC
1 AATTATAATTTATAATA
2826048 AATTCATAATTT-TAAATA
1 AATT-ATAATTTAT-AATA
2826066 AATTATA
1 AATTATA
2826073 CAATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATAATTTATAATA
Found at i:2827049 original size:2 final size:2
Alignment explanation
Indices: 2827042--2827068 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2827032 TTAGTCTATG
2827042 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 A
2827069 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2827196 original size:39 final size:39
Alignment explanation
Indices: 2827153--2827239 Score: 104
Period size: 39 Copynumber: 2.2 Consensus size: 39
2827143 TTTTTAAAAT
* *
2827153 TAATATATTGAGTTAAT-TAATAATTAAAATATAAACATA
1 TAATATATTGAGTTAATGAAAT-ATTAAAAGATAAACATA
* * * *
2827192 TAATATATTTATTTGATGAAATATTAAAAGATAAATATA
1 TAATATATTGAGTTAATGAAATATTAAAAGATAAACATA
2827231 TAATATATT
1 TAATATATT
2827240 AAAATTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 38 0.93
40 3 0.07
ACGTcount: A:0.52, C:0.01, G:0.06, T:0.41
Consensus pattern (39 bp):
TAATATATTGAGTTAATGAAATATTAAAAGATAAACATA
Found at i:2827340 original size:18 final size:18
Alignment explanation
Indices: 2827317--2827352 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
2827307 ACATAAAATT
2827317 AAATTATAA-AAATATAAA
1 AAATTA-AATAAATATAAA
2827335 AAATTAAATAAATATAAA
1 AAATTAAATAAATATAAA
2827353 TTTAATTTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (18 bp):
AAATTAAATAAATATAAA
Found at i:2827812 original size:21 final size:20
Alignment explanation
Indices: 2827755--2827816 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
2827745 GATAATATTT
2827755 AATTATAATAATAT-TTTTTA
1 AATT-TAATAATATATTTTTA
** * *
2827775 AAAATAATATTAAATTTATTA
1 AATTTAATAATATATTT-TTA
2827796 AATTTAATAATATATTTTTA
1 AATTTAATAATATATTTTTA
2827816 A
1 A
2827817 TATTATTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
19 7 0.22
20 9 0.28
21 16 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAATAATATATTTTTA
Found at i:2828474 original size:2 final size:2
Alignment explanation
Indices: 2828427--2828462 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2828417 GCTTAGTGTG
* *
2828427 TA TA TA TG TA TG 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 TA TA TA TA TA
2828463 AGAAAATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2829157 original size:29 final size:29
Alignment explanation
Indices: 2829124--2829198 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
2829114 TATATTTTAT
*
2829124 TATAAATATAATTTTATA-AATTCTTCTAA
1 TATAAATATAATTTTATATAATTATTC-AA
*
2829153 TATAAATATAACTTTTA-ATTATTATTCAA
1 TATAAATATAA-TTTTATATAATTATTCAA
*
2829182 CATAAATATAATTTTAT
1 TATAAATATAATTTTAT
2829199 TTATATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.12
29 24 0.60
30 11 0.28
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (29 bp):
TATAAATATAATTTTATATAATTATTCAA
Found at i:2829223 original size:35 final size:33
Alignment explanation
Indices: 2829184--2829266 Score: 87
Period size: 35 Copynumber: 2.4 Consensus size: 33
2829174 TTATTCAACA
* *
2829184 TAAATATAATTTTATTTATATT-TTATTACATAATT
1 TAAATATAAATTTAATTAT-TTATTA-TACAT-ATT
2829219 TAAATATAAAATTTAATTATTTATTATACATATT
1 TAAATAT-AAATTTAATTATTTATTATACATATT
*
2829253 TTAATATAACATTT
1 TAAATATAA-ATTT
2829267 TTAATAGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 2 0.05
34 13 0.31
35 14 0.33
36 13 0.31
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (33 bp):
TAAATATAAATTTAATTATTTATTATACATATT
Found at i:2831746 original size:16 final size:17
Alignment explanation
Indices: 2831717--2831749 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2831707 ATTTTTATAA
*
2831717 ATTTTTATATAATTAAT
1 ATTTTAATATAATTAAT
2831734 ATTTTAATA-AATTAAT
1 ATTTTAATATAATTAAT
2831750 TAATTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATATAATTAAT
Found at i:2832008 original size:21 final size:24
Alignment explanation
Indices: 2831982--2832056 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 24
2831972 ATGATATAAA
2831982 ATATATAAAAT-TAA-TTTA-ATT
1 ATATATAAAATATAATTTTATATT
2832003 ATATAT-AAATATAATTTTATATT
1 ATATATAAAATATAATTTTATATT
2832026 A-ATAT-AAATAT-ATTTATATATAT
1 ATATATAAAATATAATTT-TATAT-T
2832049 ATATATAA
1 ATATATAA
2832057 TACTTTGGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.09
21 13 0.28
22 19 0.40
23 6 0.13
24 4 0.09
25 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
ATATATAAAATATAATTTTATATT
Found at i:2832023 original size:16 final size:16
Alignment explanation
Indices: 2831998--2832056 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
2831988 AAAATTAATT
2831998 TAATTATATATAAATA
1 TAATTATATATAAATA
* *
2832014 TAATTTTATATTAATA
1 TAATTATATATAAATA
* * *
2832030 TAAATATATTTATATA
1 TAATTATATATAAATA
2832046 T-A-TATATATAA
1 TAATTATATATAA
2832057 TACTTTGGTT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 26 0.76
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TAATTATATATAAATA
Found at i:2832534 original size:11 final size:12
Alignment explanation
Indices: 2832520--2832563 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
2832510 AAAATATTAA
2832520 ATAAT-TAAAAT
1 ATAATATAAAAT
2832531 ATAATATAAAA-
1 ATAATATAAAAT
2832542 ATAATATAAATAT
1 ATAATATAAA-AT
2832555 ATAAATATA
1 AT-AATATA
2832564 TTAAAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 15 0.52
12 6 0.21
13 2 0.07
14 6 0.21
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:2832545 original size:22 final size:25
Alignment explanation
Indices: 2832518--2832653 Score: 73
Period size: 28 Copynumber: 5.2 Consensus size: 25
2832508 AAAAAATATT
2832518 AAATAAT-TAAA-ATAT-AATATAA
1 AAATAATATAAATATATAAATATAA
2832540 AAATAATATAAATATATAAATATATTA
1 AAATAATATAAATATATAAATATA--A
* * * *
2832567 AAATTTATATAAAAATAAAAATAT-T
1 AAA-TAATATAAATATATAAATATAA
* * * *
2832592 TAATATTTTAAATATGATCATAATAAAA
1 AAATAATATAAATAT-AT-A-AATATAA
*
2832620 AAATAAATATAAAATAATATGAATATATA
1 AAAT-AATAT-AAAT-ATATAAATATA-A
2832649 AAATA
1 AAATA
2832654 TATTTTTTAA
Statistics
Matches: 83, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
22 7 0.08
23 4 0.05
24 12 0.14
25 9 0.11
26 1 0.01
27 8 0.10
28 26 0.31
29 8 0.10
30 6 0.07
31 2 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (25 bp):
AAATAATATAAATATATAAATATAA
Found at i:2832555 original size:17 final size:16
Alignment explanation
Indices: 2832528--2832653 Score: 54
Period size: 16 Copynumber: 8.1 Consensus size: 16
2832518 AAATAATTAA
2832528 AATATAATATAAAAAT
1 AATATAATATAAAAAT
* *
2832544 AATATAA-ATATATA-
1 AATATAATATAAAAAT
*
2832558 AATAT-AT-TAAAATT
1 AATATAATATAAAAAT
* *
2832572 TATATAAAAATAAAAAT
1 AATAT-AATATAAAAAT
* **
2832589 -ATTTAATATTTTAAAT
1 AATATAATA-TAAAAAT
*
2832605 -ATGATCATAATAAAAA-
1 AAT-ATAAT-ATAAAAAT
2832621 AATA-AATAT-AAAAT
1 AATATAATATAAAAAT
2832635 AATATGAATATATAAAAT
1 AATAT-AATATA-AAAAT
2832653 A
1 A
2832654 TATTTTTTAA
Statistics
Matches: 79, Mismatches: 17, Indels: 26
0.65 0.14 0.21
Matches are distributed among these distances:
13 8 0.10
14 15 0.19
15 10 0.13
16 24 0.30
17 15 0.19
18 7 0.09
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.35
Consensus pattern (16 bp):
AATATAATATAAAAAT
Found at i:2832561 original size:39 final size:37
Alignment explanation
Indices: 2832506--2832637 Score: 126
Period size: 39 Copynumber: 3.5 Consensus size: 37
2832496 TTAACTTTTT
*
2832506 TAAAAAAATATTAAATAATTAAAATATAATATAAAAA
1 TAAATAAATATTAAATAATTAAAATATAATATAAAAA
*
2832543 TAATATAAATATATAAATATATTAAAAT-TTATATAAAAA
1 TAA-ATAAATAT-TAAATA-ATTAAAATATAATATAAAAA
* * * *
2832582 T-AA-AAATATTTAATATTTTAAATATGATCATAATAAA
1 TAAATAAATATTAAATAATTAAAATATAAT-ATAA-AAA
* *
2832619 AAAATAAATATAAAATAAT
1 TAAATAAATATTAAATAAT
2832638 ATGAATATAT
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
34 6 0.08
35 8 0.10
36 10 0.13
37 7 0.09
38 10 0.13
39 28 0.36
40 8 0.10
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.35
Consensus pattern (37 bp):
TAAATAAATATTAAATAATTAAAATATAATATAAAAA
Found at i:2832912 original size:18 final size:17
Alignment explanation
Indices: 2832889--2832975 Score: 56
Period size: 17 Copynumber: 5.1 Consensus size: 17
2832879 ATTATTTAAA
2832889 ATATTAAAATATTATTTT
1 ATATTAAAATA-TATTTT
*
2832907 ATATTAATATATATTTT
1 ATATTAAAATATATTTT
* *
2832924 A-AGTAAAAAATAATTTT
1 ATATTAAAATAT-ATTTT
*
2832941 TTATTGAATAATA-A-TTT
1 ATATT-AA-AATATATTTT
* *
2832958 AAATTAAATTA-ATTTT
1 ATATTAAAATATATTTT
2832974 AT
1 AT
2832976 CTAAAATTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
15 4 0.08
16 13 0.25
17 18 0.34
18 13 0.25
19 2 0.04
20 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATATTAAAATATATTTT
Found at i:2832940 original size:34 final size:34
Alignment explanation
Indices: 2832893--2832959 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
2832883 TTTAAAATAT
* * *
2832893 TAAAATATTATTTTATATT-AATATATATTTTAAG
1 TAAAAAATAATTTTATATTGAATA-ATAATTTAAG
*
2832927 TAAAAAATAATTTTTTATTGAATAATAATTTAA
1 TAAAAAATAATTTTATATTGAATAATAATTTAA
2832960 ATTAAATTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (34 bp):
TAAAAAATAATTTTATATTGAATAATAATTTAAG
Found at i:2833172 original size:11 final size:11
Alignment explanation
Indices: 2833141--2833181 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
2833131 AAAATTAAGT
*
2833141 AATT-TATTGA
1 AATTATATTTA
*
2833151 AATCATA-TTA
1 AATTATATTTA
2833161 AATTATATTTA
1 AATTATATTTA
2833172 AATTATATTT
1 AATTATATTT
2833182 TGTATGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 11 0.42
11 15 0.58
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (11 bp):
AATTATATTTA
Found at i:2833174 original size:21 final size:20
Alignment explanation
Indices: 2833141--2833180 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2833131 AAAATTAAGT
2833141 AATTTATTGAAATCATATTA
1 AATTTATTGAAATCATATTA
* *
2833161 AATTATATTTAAATTATATT
1 AATT-TATTGAAATCATATT
2833181 TTGTATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATTTATTGAAATCATATTA
Found at i:2833224 original size:20 final size:21
Alignment explanation
Indices: 2833199--2833238 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
2833189 ATTAAAATAA
2833199 TTTAAAAAT-TATTTTTATAT
1 TTTAAAAATATATTTTTATAT
2833219 TTTAAAAATAATATTTTTAT
1 TTTAAAAAT-ATATTTTTAT
2833239 TTAAATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTAAAAATATATTTTTATAT
Found at i:2836383 original size:17 final size:17
Alignment explanation
Indices: 2836361--2836405 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
2836351 CAAGCATGAA
2836361 ACAAAACAAAT-CATAAC
1 ACAAAACAAATACA-AAC
*
2836378 ACAAAAAAAATACAAAC
1 ACAAAACAAATACAAAC
2836395 ACAAATACAAA
1 ACAAA-ACAAA
2836406 AATATATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.71, C:0.20, G:0.00, T:0.09
Consensus pattern (17 bp):
ACAAAACAAATACAAAC
Found at i:2837172 original size:19 final size:17
Alignment explanation
Indices: 2837148--2837186 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
2837138 TTTCGTATCA
*
2837148 TTATTTTATTTATAATATT
1 TTATTTT-TATATAA-ATT
2837167 TTATTTTTATATAAATT
1 TTATTTTTATATAAATT
2837184 TTA
1 TTA
2837187 ATATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 6 0.32
19 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTTTTATATAAATT
Found at i:2837255 original size:19 final size:19
Alignment explanation
Indices: 2837223--2837278 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
2837213 ATTTAAGATA
2837223 TTTTTATTAT-ATTTATAT
1 TTTTTATTATAATTTATAT
2837241 TTTTTATTATAATTTA-AT
1 TTTTTATTATAATTTATAT
2837259 TATTTT-TT-TAATATTATAT
1 T-TTTTATTATAAT-TTATAT
2837278 T
1 T
2837279 CTTATCAAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.12
18 18 0.53
19 12 0.35
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTATTATAATTTATAT
Found at i:2844805 original size:15 final size:16
Alignment explanation
Indices: 2844785--2844828 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
2844775 ATCAATCAAA
2844785 AATATTATTTTTAAT-
1 AATATTATTTTTAATG
*
2844800 AATATTATATTTAATG
1 AATATTATTTTTAATG
* *
2844816 ATTATTTTTTTTA
1 AATATTATTTTTA
2844829 CCTTGAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
AATATTATTTTTAATG
Found at i:2844936 original size:22 final size:22
Alignment explanation
Indices: 2844889--2844940 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
2844879 ATATCAACGC
* *
2844889 AAATAAAATATAAAATATAATT
1 AAATTAAATATAAAATATAATA
*
2844911 AAATTAAATATAAATTAT-ATGA
1 AAATTAAATATAAAATATAAT-A
2844933 AAATTAAA
1 AAATTAAA
2844941 AAATATATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 2 0.08
22 24 0.92
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATTAAATATAAAATATAATA
Found at i:2845453 original size:22 final size:23
Alignment explanation
Indices: 2845397--2845453 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
2845387 AATTTATATA
2845397 AAAATA-AATTAT-TAATATTTT
1 AAAATATAATTATATAATATTTT
*
2845418 AAAATATAAATATATAATATTTT
1 AAAATATAATTATATAATATTTT
*
2845441 -AAATATGATTATA
1 AAAATATAATTATA
2845454 ATAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 16 0.52
23 9 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
AAAATATAATTATATAATATTTT
Found at i:2847072 original size:17 final size:17
Alignment explanation
Indices: 2847047--2847095 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
2847037 TATTATTAAA
2847047 AATAT-TATTTTATATT
1 AATATATATTTTATATT
*
2847063 AATATATATTTTA-AAT
1 AATATATATTTTATATT
*
2847079 AA-AGATATTTT-TATT
1 AATATATATTTTATATT
2847094 AA
1 AA
2847096 ATAATAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 12 0.43
16 9 0.32
17 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATATATATTTTATATT
Found at i:2847077 original size:31 final size:31
Alignment explanation
Indices: 2847013--2847077 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
2847003 AATCGACAAA
*
2847013 AAAAATTTATTTTATTATTTATTATATTATT
1 AAAAATTTATTTTATTATTAATTATATTATT
2847044 AAAAATATTATTTTA-TATTAATATATATT-TT
1 AAAAAT-TTATTTTATTATTAAT-TATATTATT
2847075 AAA
1 AAA
2847078 TAAAGATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 17 0.55
32 14 0.45
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (31 bp):
AAAAATTTATTTTATTATTAATTATATTATT
Found at i:2851042 original size:3 final size:3
Alignment explanation
Indices: 2851034--2851069 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2851024 AGTCTCAGCT
2851034 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
2851070 CTCCTCCCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2852182 original size:19 final size:20
Alignment explanation
Indices: 2852144--2852186 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2852134 ATATCATATA
* *
2852144 ATATTTATTATTTTATTTTT
1 ATATTTATTATATAATTTTT
2852164 ATATTTATTA-ATAATTTTT
1 ATATTTATTATATAATTTTT
2852183 ATAT
1 ATAT
2852187 CATATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATATTTATTATATAATTTTT
Found at i:2859619 original size:21 final size:19
Alignment explanation
Indices: 2859595--2859642 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
2859585 TATTATTTAA
2859595 TAATAATTAAAGATATTAATT
1 TAATAATTAAA-ATA-TAATT
*
2859616 TAATAA-TATAATATAATT
1 TAATAATTAAAATATAATT
2859634 TAA-AATTAA
1 TAATAATTAA
2859643 TTAAGGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 2 0.08
18 10 0.42
19 3 0.12
20 3 0.12
21 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TAATAATTAAAATATAATT
Found at i:2859810 original size:16 final size:16
Alignment explanation
Indices: 2859789--2859819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2859779 GATCTCAAGA
2859789 TAAAATGAAATTTAAT
1 TAAAATGAAATTTAAT
*
2859805 TAAAATTAAATTTAA
1 TAAAATGAAATTTAA
2859820 AATAATCAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TAAAATGAAATTTAAT
Found at i:2860243 original size:17 final size:18
Alignment explanation
Indices: 2860209--2860259 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
2860199 AAATCATATT
2860209 ATATATTTATATATTTTTA
1 ATATATTT-TATATTTTTA
*
2860228 TTATATTTTA-ATTTTTA
1 ATATATTTTATATTTTTA
2860245 ATATTATTTTATATT
1 ATA-TATTTTATATT
2860260 ATATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 9 0.32
18 9 0.32
19 10 0.36
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATATTTTATATTTTTA
Found at i:2860252 original size:18 final size:17
Alignment explanation
Indices: 2860209--2860255 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
2860199 AAATCATATT
2860209 ATATATTTATATATTTTTA
1 ATATATTT-TA-ATTTTTA
*
2860228 TTATATTTTAATTTTTA
1 ATATATTTTAATTTTTA
2860245 ATATTATTTTA
1 ATA-TATTTTA
2860256 TATTATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 9 0.36
18 9 0.36
19 7 0.28
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATATATTTTAATTTTTA
Found at i:2860278 original size:10 final size:9
Alignment explanation
Indices: 2860207--2860278 Score: 55
Period size: 10 Copynumber: 8.1 Consensus size: 9
2860197 TGAAATCATA
2860207 TTATATA-T
1 TTATATATT
2860215 TTATATATTT
1 TTATATA-TT
2860225 TTATTATATT
1 TTA-TATATT
2860235 TTA-AT-TT
1 TTATATATT
2860242 TTA-ATATT
1 TTATATATT
*
2860250 ATTTTATATT
1 -TTATATATT
*
2860260 ATATA-ATT
1 TTATATATT
2860268 TTATTATATT
1 TTA-TATATT
2860278 T
1 T
2860279 AAAATTATCT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
7 7 0.13
8 16 0.31
9 7 0.13
10 18 0.35
11 4 0.08
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TTATATATT
Found at i:2860486 original size:2 final size:2
Alignment explanation
Indices: 2860479--2860511 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2860469 GACAGTGACC
2860479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2860512 CATTCCTCCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2861598 original size:38 final size:39
Alignment explanation
Indices: 2861508--2861594 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 39
2861498 AAAAAATAAT
* * *
2861508 TAAAAATAATATAATATATTTATTATAAATTATTAATATA
1 TAAAAATATTA-AATATATTAAATATAAATTATTAATATA
2861548 TAAAAATATTAAATATATTAAATA-AAATTA-TAATATA
1 TAAAAATATTAAATATATTAAATATAAATTATTAATATA
2861585 -ATAAAATATT
1 TA-AAAATATT
2861595 TAAAAATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
36 1 0.02
37 15 0.35
38 6 0.14
39 11 0.26
40 10 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (39 bp):
TAAAAATATTAAATATATTAAATATAAATTATTAATATA
Found at i:2861611 original size:37 final size:37
Alignment explanation
Indices: 2861528--2861611 Score: 91
Period size: 37 Copynumber: 2.2 Consensus size: 37
2861518 ATAATATATT
* *
2861528 TATTATAAATTATTAATATATAAAAATATTAAATATAT
1 TATTA-AAATTATTAATATATAAAAATATTAAAAATAA
*
2861566 TAAATAAAATTA-TAATATA-ATAAAATATTTAAAAATAA
1 T-ATTAAAATTATTAATATATA-AAAATA-TTAAAAATAA
2861604 TATTAAAA
1 TATTAAAA
2861612 ATATGAATTC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
36 1 0.03
37 19 0.49
38 16 0.41
39 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (37 bp):
TATTAAAATTATTAATATATAAAAATATTAAAAATAA
Found at i:2861613 original size:38 final size:38
Alignment explanation
Indices: 2861528--2861613 Score: 88
Period size: 38 Copynumber: 2.3 Consensus size: 38
2861518 ATAATATATT
* * *
2861528 TATTATAAATTATTAATATATAAAAATATTAAATATAT
1 TATTAAAAATTATTAATATATAAAAATATTAAAAATAA
*
2861566 TA-AATAAAATTA-TAATATA-ATAAAATATTTAAAAATAA
1 TATTA-AAAATTATTAATATATA-AAAATA-TTAAAAATAA
2861604 TATTAAAAAT
1 TATTAAAAAT
2861614 ATGAATTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
36 1 0.03
37 14 0.36
38 23 0.59
39 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (38 bp):
TATTAAAAATTATTAATATATAAAAATATTAAAAATAA
Found at i:2865555 original size:58 final size:60
Alignment explanation
Indices: 2865445--2865562 Score: 186
Period size: 58 Copynumber: 2.0 Consensus size: 60
2865435 ATCCATCTGC
* *
2865445 TAAGTTCCTAGCTTCATTACCATCATCATCATCTTGATTAGAATACACTGAAATAAAGTTT
1 TAAGTTCCTAGCTTCATTA-CATCATCATCATCTTAATCAGAATACACTGAAATAAAGTTT
*
2865506 TAAGTTCCTAGCTTCA-T-CATCATCATCATCTTAATCAGAATACATTGAAATAAAGTT
1 TAAGTTCCTAGCTTCATTACATCATCATCATCTTAATCAGAATACACTGAAATAAAGTT
2865563 AGACAATGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 37 0.69
60 1 0.02
61 16 0.30
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.36
Consensus pattern (60 bp):
TAAGTTCCTAGCTTCATTACATCATCATCATCTTAATCAGAATACACTGAAATAAAGTTT
Found at i:2867389 original size:4 final size:4
Alignment explanation
Indices: 2867380--2867418 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
2867370 AACACTCGCA
2867380 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
2867419 AACACATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2867584 original size:24 final size:24
Alignment explanation
Indices: 2867557--2867612 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
2867547 TTACATGCAG
*
2867557 ACAGACATACAAATACACATTCAT
1 ACAGACATACAAACACACATTCAT
* * * *
2867581 ACAGAAATATATACACTCATTCAT
1 ACAGACATACAAACACACATTCAT
*
2867605 ACATACAT
1 ACAGACAT
2867613 GCTGAGAGAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (24 bp):
ACAGACATACAAACACACATTCAT
Found at i:2868345 original size:15 final size:16
Alignment explanation
Indices: 2868320--2868349 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2868310 GCAGAAAAAA
2868320 AAAGAAACAAAGAAAG
1 AAAGAAACAAAGAAAG
2868336 AAAG-AACAAAGAAA
1 AAAGAAACAAAGAAA
2868350 TAAGGGGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.77, C:0.07, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGAAACAAAGAAAG
Found at i:2869605 original size:21 final size:22
Alignment explanation
Indices: 2869571--2869615 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
2869561 AAATAAATAT
*
2869571 ATTTTATTAATTTTATTTATAAA
1 ATTTTATTAATTTTA-CTATAAA
2869594 ATTTT-TT-ATTTTACTATAAA
1 ATTTTATTAATTTTACTATAAA
2869614 AT
1 AT
2869616 AATTATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 6 0.29
22 2 0.10
23 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTATTAATTTTACTATAAA
Found at i:2871714 original size:18 final size:18
Alignment explanation
Indices: 2871677--2871735 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
2871667 TAGATATATT
* *
2871677 TATTT-ATAAATAAAAAA
1 TATTTAATAAATTAAATA
**
2871694 TATTTTTTAAATTAAATA
1 TATTTAATAAATTAAATA
* *
2871712 TATTAAAAAAATTAAATA
1 TATTTAATAAATTAAATA
2871730 TATTTA
1 TATTTA
2871736 TATTGAACAA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATTTAATAAATTAAATA
Found at i:2872634 original size:2 final size:2
Alignment explanation
Indices: 2872611--2872665 Score: 69
Period size: 2 Copynumber: 28.5 Consensus size: 2
2872601 CACTATAATC
* * *
2872611 TA TA TA CA TA TA -A TA TA CA TA TA TA TA CA TA -A 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
2872651 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
2872666 GTAAAGTAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2875471 original size:31 final size:31
Alignment explanation
Indices: 2875436--2875496 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2875426 ATGTACCATT
*
2875436 AATAAATAAAT-ATTATTATATAAAATATTAA
1 AATAAATAAATAATTAATAT-TAAAATATTAA
*
2875467 AATAAATAAATAATTAATATTAAATTATTA
1 AATAAATAAATAATTAATATTAAAATATTA
2875497 TATATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (31 bp):
AATAAATAAATAATTAATATTAAAATATTAA
Found at i:2875496 original size:14 final size:15
Alignment explanation
Indices: 2875473--2875508 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
2875463 TTAAAATAAA
2875473 TAAATAATTA-ATAT
1 TAAATAATTATATAT
*
2875487 TAAATTATTATATAT
1 TAAATAATTATATAT
2875502 TAAATAA
1 TAAATAA
2875509 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAAATAATTATATAT
Found at i:2877137 original size:20 final size:20
Alignment explanation
Indices: 2877087--2877178 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
2877077 AAATTAATTA
* *
2877087 AAATATAATATAAATATTAT
1 AAATATATTATAAATAATAT
2877107 -AA-A-ATTA-AAATAATAT
1 AAATATATTATAAATAATAT
2877123 AAATATATTATAAATAATAT
1 AAATATATTATAAATAATAT
* * *
2877143 ATATAAATATATAAATTTATAT
1 AAATATAT-TATAAA-TAATAT
*
2877165 AAATATAATATAAA
1 AAATATATTATAAA
2877179 CACATAAATT
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
16 8 0.14
17 5 0.09
18 2 0.03
19 6 0.10
20 15 0.26
21 12 0.21
22 10 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATATATTATAAATAATAT
Found at i:2877190 original size:28 final size:30
Alignment explanation
Indices: 2877121--2877194 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 30
2877111 TTAAAATAAT
* *
2877121 ATAAATATATTATAAATAATATATATAAATAT
1 ATAAAT-TA-TATAAATAATATATATAAACAC
2877153 ATAAATTTATATAAAT-ATA-ATATAAACAC
1 ATAAA-TTATATAAATAATATATATAAACAC
2877182 ATAAATTATATAA
1 ATAAATTATATAA
2877195 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 13 0.33
30 3 0.08
31 7 0.18
32 7 0.18
33 1 0.03
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
ATAAATTATATAAATAATATATATAAACAC
Found at i:2878214 original size:7 final size:7
Alignment explanation
Indices: 2878202--2878234 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
2878192 CATATAATAA
2878202 ATTTAAT
1 ATTTAAT
2878209 ATTTAAT
1 ATTTAAT
2878216 ATTTAAT
1 ATTTAAT
2878223 ATTTATAT
1 ATTTA-AT
2878231 ATTT
1 ATTT
2878235 TTTATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.76
8 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTAAT
Found at i:2879777 original size:14 final size:13
Alignment explanation
Indices: 2879715--2879786 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 13
2879705 TATGTTAATA
2879715 ATTTTTATTATAT
1 ATTTTTATTATAT
*
2879728 ATTTTT-TAATAT
1 ATTTTTATTATAT
*
2879740 ATATTTATT-TAT
1 ATTTTTATTATAT
** *
2879752 ATCATAATTATATT
1 ATTTTTATTATA-T
2879766 ATTTTTA-T-TAT
1 ATTTTTATTATAT
2879777 ATTTTTATTA
1 ATTTTTATTA
2879787 CATTTAATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 8 0.18
12 22 0.49
13 10 0.22
14 5 0.11
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.65
Consensus pattern (13 bp):
ATTTTTATTATAT
Found at i:2880291 original size:24 final size:24
Alignment explanation
Indices: 2880262--2880325 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
2880252 TAATTAAAAT
2880262 ATATTATAAAATATGAAAATA-TAA
1 ATATTATAAAATAT-AAAATATTAA
*
2880286 ATATTATAATACTATAAAATATTAA
1 ATATTATAA-AATATAAAATATTAA
*
2880311 ATA-TATTAAATATAA
1 ATATTATAAAATATAA
2880326 TTACAACACA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 6 0.17
24 19 0.54
25 10 0.29
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATTATAAAATATAAAATATTAA
Found at i:2880307 original size:18 final size:16
Alignment explanation
Indices: 2880266--2880323 Score: 66
Period size: 16 Copynumber: 3.6 Consensus size: 16
2880256 TAAAATATAT
*
2880266 TATAAAATATGAAA-A
1 TATAAAATATTAAATA
2880281 TAT-AAATATTATAATA
1 TATAAAATATTA-AATA
2880297 CTATAAAATATTAAATA
1 -TATAAAATATTAAATA
*
2880314 TATTAAATAT
1 TATAAAATAT
2880324 AATTACAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 10 0.27
17 7 0.19
18 8 0.22
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TATAAAATATTAAATA
Found at i:2880325 original size:31 final size:30
Alignment explanation
Indices: 2880254--2880326 Score: 78
Period size: 32 Copynumber: 2.4 Consensus size: 30
2880244 CTAAAAATTA
*
2880254 ATTAAA-AT-ATATTATAAAATATGAAAAT
1 ATTAAATATAATACTATAAAATATGAAAAT
* *
2880282 ATAAATATTATAATACTATAAAATATTAAATAT
1 ATTAA-A-TATAATACTATAAAATATGAAA-AT
2880315 ATTAAATATAAT
1 ATTAAATATAAT
2880327 TACAACACAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
28 4 0.11
29 1 0.03
31 8 0.22
32 17 0.47
33 6 0.17
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
ATTAAATATAATACTATAAAATATGAAAAT
Found at i:2880366 original size:19 final size:19
Alignment explanation
Indices: 2880342--2880379 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2880332 CACATAAAAA
* *
2880342 ATAATATATATATATATAT
1 ATAATATAAATATACATAT
2880361 ATAATATAAATATACATAT
1 ATAATATAAATATACATAT
2880380 TATTATATCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
ATAATATAAATATACATAT
Found at i:2881475 original size:29 final size:30
Alignment explanation
Indices: 2881412--2881480 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
2881402 TTCAATTTAG
* *
2881412 ATTACTATTTAATTAATAAAAAAATATATT
1 ATTAATATTTAATTAATAAAAAAATATAAT
* *
2881442 TTTAA-ATTTAATT-ATAAAAATATATTAAT
1 ATTAATATTTAATTAATAAAAAAATA-TAAT
2881471 ATTAATATTT
1 ATTAATATTT
2881481 TAGATAGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.31
29 15 0.47
30 7 0.22
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (30 bp):
ATTAATATTTAATTAATAAAAAAATATAAT
Found at i:2882474 original size:23 final size:25
Alignment explanation
Indices: 2882441--2882496 Score: 71
Period size: 23 Copynumber: 2.3 Consensus size: 25
2882431 TATAGTAATG
*
2882441 TATAAATATATTATTATT-TAT-TA
1 TATAAAAATATTATTATTATATCTA
*
2882464 TATAAAAATATTTTTATTATATCTA
1 TATAAAAATATTATTATTATATCTA
2882489 TCATAAAA
1 T-ATAAAA
2882497 TATAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 16 0.57
24 3 0.11
25 3 0.11
26 6 0.21
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (25 bp):
TATAAAAATATTATTATTATATCTA
Found at i:2885502 original size:25 final size:25
Alignment explanation
Indices: 2885441--2885516 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
2885431 TATAAATTAT
* *
2885441 AAAAATAAAATATATATTATGTTTAA
1 AAAAATAAAA-ATATAATATATTTAA
** * *
2885467 ATCAATTAAAATTTAATATATTTAA
1 AAAAATAAAAATATAATATATTTAA
2885492 AAAAATAAAAACTAT-ATAT-TTTAA
1 AAAAATAAAAA-TATAATATATTTAA
2885516 A
1 A
2885517 TTTATAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
24 6 0.15
25 24 0.62
26 9 0.23
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.38
Consensus pattern (25 bp):
AAAAATAAAAATATAATATATTTAA
Found at i:2885730 original size:21 final size:20
Alignment explanation
Indices: 2885698--2885749 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
2885688 TTAAAATTTT
2885698 AATTTAATTTAAATTAAAAATTA
1 AATTT-ATTTAAATT--AAATTA
2885721 AA-TTATTTAAATTAAATTA
1 AATTTATTTAAATTAAATTA
2885740 AATTTATTTA
1 AATTTATTTA
2885750 TTTATTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.29
20 7 0.25
21 9 0.32
22 2 0.07
23 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATTTATTTAAATTAAATTA
Found at i:2885770 original size:26 final size:26
Alignment explanation
Indices: 2885738--2885787 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
2885728 TAAATTAAAT
*
2885738 TAAATTTATTTATTTATT-TTTAAAAA
1 TAAATTTAATTATTT-TTATTTAAAAA
2885764 TAAATTTAATTATTTTTATTTAAA
1 TAAATTTAATTATTTTTATTTAAA
2885788 TTTTGGCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (26 bp):
TAAATTTAATTATTTTTATTTAAAAA
Found at i:2885835 original size:20 final size:20
Alignment explanation
Indices: 2885798--2885836 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2885788 TTTTGGCTTG
*
2885798 AATTAAAAAAATTTAATATT
1 AATTAAAAAAATTAAATATT
2885818 AATTAAAATAAA-TAAATAT
1 AATTAAAA-AAATTAAATAT
2885837 AAAAAAATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTAAAAAAATTAAATATT
Found at i:2885939 original size:16 final size:18
Alignment explanation
Indices: 2885901--2885941 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
2885891 TTTGATTCAT
*
2885901 TTAATAAATAAAATTTAAC
1 TTAAT-AATAAAATTTAAA
2885920 TTAATAAT-AAA-TTAAA
1 TTAATAATAAAATTTAAA
2885936 TTAATA
1 TTAATA
2885942 TATATTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 10 0.48
17 3 0.14
18 3 0.14
19 5 0.24
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAATAATAAAATTTAAA
Found at i:2889227 original size:96 final size:96
Alignment explanation
Indices: 2889059--2889252 Score: 361
Period size: 96 Copynumber: 2.0 Consensus size: 96
2889049 GATTTGCGAA
2889059 TCAAAACTTCTGTCACAATTGTGCTTCGAACCGGACATCTGCTGGTTCCCTCTTAGATTTCTTGG
1 TCAAAACTTCTGTCACAATTGTGCTTCGAACCGGACATCTGCTGGTTCCCTCTTAGATTTCTTGG
*
2889124 CACATAATGCAAGTGTTAAAGACTCGCAACT
66 CAAATAATGCAAGTGTTAAAGACTCGCAACT
*
2889155 TCAAAACTTCTGTCACCATTGTGCTTCGAACCGGACATCTGCTGGTTCCCTCTTAGATTTCTTGG
1 TCAAAACTTCTGTCACAATTGTGCTTCGAACCGGACATCTGCTGGTTCCCTCTTAGATTTCTTGG
*
2889220 CAAATAATGCAGGTGTTAAAGACTCGCAACT
66 CAAATAATGCAAGTGTTAAAGACTCGCAACT
2889251 TC
1 TC
2889253 TTCAGTGTTG
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (96 bp):
TCAAAACTTCTGTCACAATTGTGCTTCGAACCGGACATCTGCTGGTTCCCTCTTAGATTTCTTGG
CAAATAATGCAAGTGTTAAAGACTCGCAACT
Found at i:2891291 original size:46 final size:44
Alignment explanation
Indices: 2891232--2891332 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 44
2891222 ATTTAAAATG
* * *
2891232 TATATTATTATTTAAATATTATTAAAAATTA-TTTTATATTAATATT
1 TATATTA-AATTTAAATATAAATAAAAATTATTTTTA-ATT-ATATT
* *
2891278 TATAATTAAATTTAAATATAAATAATAATTATTTTTAATTTTATT
1 TAT-ATTAAATTTAAATATAAATAAAAATTATTTTTAATTATATT
2891323 TATATTAAAT
1 TATATTAAAT
2891333 ATAATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
44 7 0.15
45 7 0.15
46 25 0.52
47 9 0.19
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (44 bp):
TATATTAAATTTAAATATAAATAAAAATTATTTTTAATTATATT
Found at i:2891314 original size:23 final size:23
Alignment explanation
Indices: 2891235--2891315 Score: 58
Period size: 23 Copynumber: 3.5 Consensus size: 23
2891225 TAAAATGTAT
* * *
2891235 ATTATTATTTAAATATTATTAAAA
1 ATTATT-TTTAAATATAAATAATA
* *
2891259 ATTA-TTTTATAT-TAATATTTATA
1 ATTATTTTTAAATATAA-A-TAATA
**
2891282 ATTAAATTTAAATATAAATAATA
1 ATTATTTTTAAATATAAATAATA
2891305 ATTATTTTTAA
1 ATTATTTTTAA
2891316 TTTTATTTAT
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
21 2 0.05
22 6 0.14
23 21 0.49
24 11 0.26
25 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTATTTTTAAATATAAATAATA
Found at i:2891317 original size:33 final size:31
Alignment explanation
Indices: 2891274--2891344 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
2891264 TTTATATTAA
*
2891274 TATTTATAATTAAATTTAAATATAAATAATAAT
1 TATTTTTAATTAAATTTAAAT-TAAAT-ATAAT
** *
2891307 TATTTTTAATTTTATTTATATTAAATATAAT
1 TATTTTTAATTAAATTTAAATTAAATATAAT
*
2891338 TTTTTTT
1 TATTTTT
2891345 TAATAATGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 11 0.33
32 5 0.15
33 17 0.52
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (31 bp):
TATTTTTAATTAAATTTAAATTAAATATAAT
Found at i:2896087 original size:2 final size:2
Alignment explanation
Indices: 2896080--2896104 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2896070 GCTCCTAAAA
2896080 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
2896105 TCCAAAAAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2902129 original size:26 final size:27
Alignment explanation
Indices: 2902081--2902131 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
2902071 GACTTCGGTG
*
2902081 CTTTTCTAATTAAACGAACTGATTGGT
1 CTTTTCTAATTAAACAAACTGATTGGT
* *
2902108 CTTTT-TAATTAACCAAATTGATTG
1 CTTTTCTAATTAAACAAACTGATTG
2902132 AAATATGAGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTTTCTAATTAAACAAACTGATTGGT
Found at i:2903521 original size:15 final size:15
Alignment explanation
Indices: 2903479--2903521 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
2903469 TTATAAAATT
* *
2903479 ATTTATTCAAATTTA
1 ATTTATTAAAATTAA
*
2903494 ATTTAATATAAATTAA
1 ATTTATTA-AAATTAA
2903510 ATTTATTAAAAT
1 ATTTATTAAAAT
2903522 ACAAAGATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTAAAATTAA
Found at i:2903672 original size:2 final size:2
Alignment explanation
Indices: 2903665--2903696 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2903655 GATTAATGTA
2903665 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
2903697 TTTAATGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2904158 original size:19 final size:19
Alignment explanation
Indices: 2904134--2904176 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2904124 TAAATGATTG
2904134 ATTTAA-ATAAGAGATAAAT
1 ATTTAATATAA-AGATAAAT
* *
2904153 ATTTAATTTAATGATAAAT
1 ATTTAATATAAAGATAAAT
2904172 ATTTA
1 ATTTA
2904177 TATTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTTAATATAAAGATAAAT
Found at i:2904348 original size:4 final size:4
Alignment explanation
Indices: 2904339--2904367 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2904329 GAGCTTAAAC
2904339 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
2904368 CTTCTAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:2909760 original size:156 final size:156
Alignment explanation
Indices: 2909476--2909789 Score: 592
Period size: 156 Copynumber: 2.0 Consensus size: 156
2909466 GTTGGTGCAG
* *
2909476 GATCAGATTAAGGCAGCTTTGGAGGAGCTTCGATCGATGGGTGGGTGATTTCAGACTATGGGTGC
1 GATCAGATTAAGGCAGCGTTGGAGGAGCTTCGATCGATGGGTGGGTGATTTCAGACTATGGATGC
*
2909541 TTATTTCCATGAAATATTTCTTGGTTATTGACGGATAGAGCTGATAATGTAGGGAAGTAACTGGA
66 TTATTTCCATGAAATATTTCTTGGTAATTGACGGATAGAGCTGATAATGTAGGGAAGTAACTGGA
2909606 GTTTGAGTTTCTTTTTGGGTTTATTT
131 GTTTGAGTTTCTTTTTGGGTTTATTT
2909632 GATCAGATTAAGGCAGCGTTGGAGGAGCTTCGATCGATGGGTGGGTGATTTCAGACTATGGATGC
1 GATCAGATTAAGGCAGCGTTGGAGGAGCTTCGATCGATGGGTGGGTGATTTCAGACTATGGATGC
*
2909697 TTATTTCCATGAAATATTTCTTGGTAATTGACGGATAGAGCTGATAGTGTAGGGAAGTAACTGGA
66 TTATTTCCATGAAATATTTCTTGGTAATTGACGGATAGAGCTGATAATGTAGGGAAGTAACTGGA
2909762 GTTTGAGTTTCTTTTTGGGTTTATTT
131 GTTTGAGTTTCTTTTTGGGTTTATTT
2909788 GA
1 GA
2909790 GTGAAATGAA
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 154 1.00
ACGTcount: A:0.24, C:0.10, G:0.30, T:0.36
Consensus pattern (156 bp):
GATCAGATTAAGGCAGCGTTGGAGGAGCTTCGATCGATGGGTGGGTGATTTCAGACTATGGATGC
TTATTTCCATGAAATATTTCTTGGTAATTGACGGATAGAGCTGATAATGTAGGGAAGTAACTGGA
GTTTGAGTTTCTTTTTGGGTTTATTT
Found at i:2915061 original size:2 final size:2
Alignment explanation
Indices: 2915054--2915081 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2915044 CTTAAAAGGC
2915054 TA 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 TA
2915082 CACCTGGCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2923016 original size:32 final size:32
Alignment explanation
Indices: 2922947--2923031 Score: 88
Period size: 31 Copynumber: 2.7 Consensus size: 32
2922937 AAAAAATATA
*
2922947 TAAATATAAAT-AAATTTATT-TAAATGTAAAT
1 TAAATTTAAATAAAATTT-TTATAAATGTAAAT
2922978 TAAATTTTAAATAAAATTTTTATAAAT-TAATAT
1 TAAA-TTTAAATAAAATTTTTATAAATGTAA-AT
* *
2923011 T-AATTTAATTAAAATTATTAT
1 TAAATTTAAATAAAATTTTTAT
2923032 TTAATAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 20 0.43
32 13 0.28
33 14 0.30
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
TAAATTTAAATAAAATTTTTATAAATGTAAAT
Found at i:2930239 original size:17 final size:16
Alignment explanation
Indices: 2930188--2930254 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 16
2930178 AATATTTTAA
2930188 AAAATT-TATATAATAT
1 AAAATTATATA-AATAT
2930204 -AAATTATTAATAAAT-T
1 AAAATTA-T-ATAAATAT
2930220 AAAATGTATATAAATAT
1 AAAAT-TATATAAATAT
* *
2930237 -AAATCAAATAAATAT
1 AAAATTATATAAATAT
2930252 AAA
1 AAA
2930255 CTTGCCAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
15 14 0.33
16 13 0.31
17 10 0.24
18 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (16 bp):
AAAATTATATAAATAT
Found at i:2943948 original size:2 final size:2
Alignment explanation
Indices: 2943937--2943979 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
2943927 TTGAGAGATG
*
2943937 TA TA TC TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
2943979 T
1 T
2943980 TCATTCATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2958607 original size:46 final size:46
Alignment explanation
Indices: 2958540--2958638 Score: 191
Period size: 46 Copynumber: 2.2 Consensus size: 46
2958530 CATCTTCATC
2958540 GCTTTCCAAATTGTTTTGTTTACATTAACAGATTCTGCAACGACTT
1 GCTTTCCAAATTGTTTTGTTTACATTAACAGATTCTGCAACGACTT
2958586 GCTTTCCAAATTGTTTTGTTTACATTAACAGATTCTGCAACGACTT
1 GCTTTCCAAATTGTTTTGTTTACATTAACAGATTCTGCAACGACTT
2958632 G-TTTCCA
1 GCTTTCCA
2958639 CCTTGGATCG
Statistics
Matches: 53, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
45 6 0.11
46 47 0.89
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (46 bp):
GCTTTCCAAATTGTTTTGTTTACATTAACAGATTCTGCAACGACTT
Done.