Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 103066607
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: 103066607
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 238 characters in sequence are not A, C, G, or T
File 2 of 345
Found at i:467050 original size:14 final size:14
Alignment explanation
Indices: 467009--467042 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
466999 ATATTCTTTA
467009 TAAA-TTTAA-ATT
1 TAAATTTTAATATT
467021 TAAATTTTAATATT
1 TAAATTTTAATATT
467035 TAAATTTT
1 TAAATTTT
467043 TATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAAATTTTAATATT
Found at i:467448 original size:11 final size:11
Alignment explanation
Indices: 467434--467473 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
467424 GTTTTCTCCT
467434 TATTTTGCTAC
1 TATTTTGCTAC
* *
467445 TATTTTACTTC
1 TATTTTGCTAC
*
467456 TATGTTGCTAC
1 TATTTTGCTAC
467467 TATTTTG
1 TATTTTG
467474 TTGTTATTGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.57
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:467450 original size:22 final size:23
Alignment explanation
Indices: 467411--467472 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
467401 TTTTTAAATA
* * *
467411 TTATTTTGTTATTGTTTT-CTCC
1 TTATTTTGCTACTATTTTACTCC
*
467433 TTATTTTGCTACTATTTTACTTC
1 TTATTTTGCTACTATTTTACTCC
*
467456 -TATGTTGCTACTATTTT
1 TTATTTTGCTACTATTTT
467473 GTTGTTATTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 31 0.91
23 3 0.09
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.63
Consensus pattern (23 bp):
TTATTTTGCTACTATTTTACTCC
Found at i:467557 original size:30 final size:31
Alignment explanation
Indices: 467510--467573 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
467500 ACTTATTTTA
* *
467510 TTGTTAAATTTTTTTATTATTTTA-AAGACAT
1 TTGTTAAATTTTATTATTACTTTAGAA-ACAT
467541 TTGTT-AATTTTATTATTACTTTAGAAACAT
1 TTGTTAAATTTTATTATTACTTTAGAAACAT
467571 TTG
1 TTG
467574 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 23 0.77
31 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (31 bp):
TTGTTAAATTTTATTATTACTTTAGAAACAT
Found at i:467677 original size:18 final size:18
Alignment explanation
Indices: 467656--467694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
467646 GAAATATTTA
*
467656 TTTGA-TGTTTTTAATATT
1 TTTGATTGTTTAT-ATATT
467674 TTTGATTGTTTATATATT
1 TTTGATTGTTTATATATT
467692 TTT
1 TTT
467695 TAAAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (18 bp):
TTTGATTGTTTATATATT
Found at i:467694 original size:19 final size:18
Alignment explanation
Indices: 467649--467695 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
467639 TTGTTGAGAA
*
467649 ATATTTATTTGATGTTTTT
1 ATATTT-TTTGATGTTTAT
467668 A-ATATTTTTGATTGTTTAT
1 ATAT-TTTTTGA-TGTTTAT
467687 ATATTTTTT
1 ATATTTTTT
467696 AAAATTATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 7 0.29
19 15 0.62
20 2 0.08
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
ATATTTTTTGATGTTTAT
Found at i:467726 original size:12 final size:12
Alignment explanation
Indices: 467696--467728 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
467686 TATATTTTTT
467696 AAAATT-ATATA
1 AAAATTAATATA
467707 AAAA-TAATATA
1 AAAATTAATATA
467718 AAAATTAATAT
1 AAAATTAATAT
467729 GGGTGGGCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:470252 original size:22 final size:22
Alignment explanation
Indices: 470224--470267 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
470214 AACTAAATTA
470224 ATTTTTTTAAAGAGTGCCTGTG
1 ATTTTTTTAAAGAGTGCCTGTG
*
470246 ATTTTTTTAAAGAGTGCTTGTG
1 ATTTTTTTAAAGAGTGCCTGTG
470268 GCATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.48
Consensus pattern (22 bp):
ATTTTTTTAAAGAGTGCCTGTG
Found at i:471243 original size:123 final size:122
Alignment explanation
Indices: 470993--471259 Score: 320
Period size: 123 Copynumber: 2.2 Consensus size: 122
470983 CAAACTCGAA
* * **
470993 CGAAAGCTGGACCTAATCAACTCAAATCCAAAATAATATCTAACCCTATGTGACCATAAAAACAA
1 CGAAAACTAGACCTAATCAACTCAAATAAAAAATAATATCTAACCCTATGTGACCATAAAAACAA
* * * * * **
471058 TTCAACCCAAACATGAAATAATTGAAACTTGGAGTGATCGGAATTTGAATCTGAACC
66 CTCAACCCAAACATAAAATAATTGAAACTTGGAGCGATCAGAACTCAAATCTGAACC
* * * * *
471115 TGAAAACTAGACCTAATCAACTTAAATAAAAAAATCATATCTAACTCTATGTGACCATAAAAATA
1 CGAAAACTAGACCTAATCAACTCAAAT-AAAAAATAATATCTAACCCTATGTGACCATAAAAACA
* * *
471180 ACTCAACCCAGACATAAAATAATTGAAACTTGGAGCGATTAGAACTCAAAT-TTAGACC
65 ACTCAACCCAAACATAAAATAATTGAAACTTGGAGCGATCAGAACTCAAATCTGA-ACC
* *
471238 CGAAAATTAGACCTAATTAACT
1 CGAAAACTAGACCTAATCAACT
471260 AATATTCAAA
Statistics
Matches: 121, Mismatches: 22, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
122 25 0.21
123 96 0.79
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.24
Consensus pattern (122 bp):
CGAAAACTAGACCTAATCAACTCAAATAAAAAATAATATCTAACCCTATGTGACCATAAAAACAA
CTCAACCCAAACATAAAATAATTGAAACTTGGAGCGATCAGAACTCAAATCTGAACC
Found at i:473702 original size:2 final size:2
Alignment explanation
Indices: 473697--473723 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
473687 ATATACAGAC
473697 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
473724 CACACTATAA
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:479590 original size:6 final size:6
Alignment explanation
Indices: 479579--479604 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
479569 AATGACTTAA
479579 ATATAG ATATAG ATATAG ATATAG AT
1 ATATAG ATATAG ATATAG ATATAG AT
479605 GGTATTTTAA
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:0.50, C:0.00, G:0.15, T:0.35
Consensus pattern (6 bp):
ATATAG
Found at i:480855 original size:15 final size:15
Alignment explanation
Indices: 480835--480866 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
480825 GAAAATACAT
*
480835 AATTTTAAATTTTAA
1 AATTTTAAAATTTAA
480850 AATTTTAAAATTTAA
1 AATTTTAAAATTTAA
480865 AA
1 AA
480867 AATGTACGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTTAAAATTTAA
Found at i:480867 original size:8 final size:8
Alignment explanation
Indices: 480835--480866 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
480825 GAAAATACAT
480835 AATTTT-A
1 AATTTTAA
480842 AATTTTAA
1 AATTTTAA
480850 AATTTTAA
1 AATTTTAA
480858 AA-TTTAA
1 AATTTTAA
480865 AA
1 AA
480867 AATGTACGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 13 0.54
8 11 0.46
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AATTTTAA
Found at i:495768 original size:18 final size:18
Alignment explanation
Indices: 495732--495773 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
495722 AACAGATTGG
*
495732 AAATTTAATTACTATAAT
1 AAATTTAATTACTAAAAT
495750 AAATTTAATTTA-TAAAAT
1 AAATTTAA-TTACTAAAAT
*
495768 ATATTT
1 AAATTT
495774 TTTCTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 18 0.86
19 3 0.14
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
AAATTTAATTACTAAAAT
Found at i:505588 original size:2 final size:2
Alignment explanation
Indices: 505581--505613 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
505571 TTTGATTAAT
*
505581 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
505614 TATTTTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:506574 original size:19 final size:21
Alignment explanation
Indices: 506517--506575 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
506507 AGTAATTTAC
*
506517 TATATTTCATGCTATTTTATTG
1 TATATTT-ATGATATTTTATTG
*
506539 TATATTTATGATTTTTTATT-
1 TATATTTATGATATTTTATTG
506559 T-TA-TTATGAATATTTTA
1 TATATTTATG-ATATTTTA
506576 AAATTTTTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 5 0.15
19 9 0.27
20 1 0.03
21 11 0.33
22 7 0.21
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (21 bp):
TATATTTATGATATTTTATTG
Found at i:507490 original size:18 final size:18
Alignment explanation
Indices: 507467--507507 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
507457 TACTTTTCTC
507467 TTTCTA-TCACAATTCTAA
1 TTTCTATTCACAATTC-AA
*
507485 TTTCTATTCATAATTCAA
1 TTTCTATTCACAATTCAA
507503 TTTCT
1 TTTCT
507508 TTTTCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.29, C:0.20, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTCTATTCACAATTCAA
Found at i:508674 original size:12 final size:12
Alignment explanation
Indices: 508659--508689 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
508649 TTCTCTTTTA
508659 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
508671 TTTTTCTTTCTC
1 TTTTTCTTTCCC
508683 TTTTTCT
1 TTTTTCT
508690 CCCCTACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:523756 original size:16 final size:15
Alignment explanation
Indices: 523733--523767 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
523723 TTCCATGTTC
523733 TTTATTTTGATATTT
1 TTTATTTTGATATTT
*
523748 TTTAGTTTTTATATTT
1 TTTA-TTTTGATATTT
523764 TTTA
1 TTTA
523768 AATTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTATTTTGATATTT
Found at i:523773 original size:16 final size:17
Alignment explanation
Indices: 523736--523773 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
523726 CATGTTCTTT
523736 ATTTTGATATTTTTT-A
1 ATTTTGATATTTTTTAA
* *
523752 GTTTTTATATTTTTTAA
1 ATTTTGATATTTTTTAA
523769 ATTTT
1 ATTTT
523774 TAAAATTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (17 bp):
ATTTTGATATTTTTTAA
Found at i:524403 original size:20 final size:20
Alignment explanation
Indices: 524367--524405 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
524357 ATCTTTTTTT
524367 GGGTCTAACTAAAAATTTTAA
1 GGGTCTAAC-AAAAATTTTAA
524388 GGGTCTAA-AAAGAATTTT
1 GGGTCTAACAAA-AATTTT
524406 CGAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.18
20 6 0.35
21 8 0.47
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (20 bp):
GGGTCTAACAAAAATTTTAA
Found at i:530803 original size:2 final size:2
Alignment explanation
Indices: 530796--530828 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
530786 TGATAAAGTG
530796 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
530829 GTGAATGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:532625 original size:21 final size:21
Alignment explanation
Indices: 532564--532626 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
532554 GTGGGGCTAA
532564 ATTATAAAATTGGACCTAAAT
1 ATTATAAAATTGGACCTAAAT
* * * *
532585 ATTAT--TA-T--CCCCAAAA
1 ATTATAAAATTGGACCTAAAT
532601 ATTATAAAATTGGACCTAAAT
1 ATTATAAAATTGGACCTAAAT
532622 ATTAT
1 ATTAT
532627 TATCCCAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 10
0.62 0.17 0.21
Matches are distributed among these distances:
16 10 0.34
18 2 0.07
19 2 0.07
21 15 0.52
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (21 bp):
ATTATAAAATTGGACCTAAAT
Found at i:532664 original size:37 final size:37
Alignment explanation
Indices: 532562--532653 Score: 175
Period size: 37 Copynumber: 2.5 Consensus size: 37
532552 GTGTGGGGCT
*
532562 AAATTATAAAATTGGACCTAAATATTATTATCCCCAA
1 AAATTATAAAATTGGACCTAAATATTATTATCCCAAA
532599 AAATTATAAAATTGGACCTAAATATTATTATCCCAAA
1 AAATTATAAAATTGGACCTAAATATTATTATCCCAAA
532636 AAATTATAAAATTGGACC
1 AAATTATAAAATTGGACC
532654 AACCCATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.48, C:0.14, G:0.07, T:0.32
Consensus pattern (37 bp):
AAATTATAAAATTGGACCTAAATATTATTATCCCAAA
Found at i:533571 original size:2 final size:2
Alignment explanation
Indices: 533566--533592 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
533556 TTTTACACAC
533566 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
533593 GGGGTGAAGC
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:534932 original size:20 final size:22
Alignment explanation
Indices: 534906--534949 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
534896 TTTTGATCGC
*
534906 TTTTTTTTGGTGAAAAAA-ATA
1 TTTTTTTGGGTGAAAAAATATA
534927 TTTTTTTGGGTGAAAAAATATA
1 TTTTTTTGGGTGAAAAAATATA
534949 T
1 T
534950 ATAATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (22 bp):
TTTTTTTGGGTGAAAAAATATA
Found at i:535742 original size:31 final size:31
Alignment explanation
Indices: 535677--535742 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
535667 TCAGCATAAA
**
535677 AACTTAAATAAAAATTTTTAAATAGTTCGTT
1 AACTTAAATAAAAATTTTTAAATAGTTCAAT
* *
535708 AACTTAAATGAAAAA-TTTTGAATAGTTTAAT
1 AACTTAAAT-AAAAATTTTTAAATAGTTCAAT
535739 AACT
1 AACT
535743 ATGTTGTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (31 bp):
AACTTAAATAAAAATTTTTAAATAGTTCAAT
Found at i:540327 original size:21 final size:21
Alignment explanation
Indices: 540302--540343 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
540292 AATGAATCAT
*
540302 TATGAGTTTTTTGATAAATTA
1 TATGAGCTTTTTGATAAATTA
540323 TATGAGCTTTTTGATAAATTA
1 TATGAGCTTTTTGATAAATTA
540344 GGTAAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (21 bp):
TATGAGCTTTTTGATAAATTA
Found at i:541278 original size:22 final size:22
Alignment explanation
Indices: 541233--541278 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
541223 TTTAGCTCCA
* *
541233 TCTCTGTTTCTTCAAATCTCTG
1 TCTCTGTTTCTTCAAAACTATG
541255 TCTCTGTTTCTTCAAAACTATG
1 TCTCTGTTTCTTCAAAACTATG
541277 TC
1 TC
541279 GATGGTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.26, G:0.09, T:0.48
Consensus pattern (22 bp):
TCTCTGTTTCTTCAAAACTATG
Found at i:542664 original size:29 final size:27
Alignment explanation
Indices: 542632--542692 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 27
542622 CAATGGAAAT
*
542632 AAATATATAAAAAT-TCATAAATTTATATA
1 AAATATAGAAAAATAT-ATAAA-TTATA-A
*
542661 AAATCTAGAAAAATATATAAATTATAA
1 AAATATAGAAAAATATATAAATTATAA
542688 AAATA
1 AAATA
542693 AAATTTACAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.18
28 5 0.18
29 17 0.61
30 1 0.04
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (27 bp):
AAATATAGAAAAATATATAAATTATAA
Found at i:542796 original size:10 final size:10
Alignment explanation
Indices: 542754--542799 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
542744 TATTATTACA
542754 AAAAAATTGT
1 AAAAAATTGT
542764 AAAAAGATTGT
1 AAAAA-ATTGT
* *
542775 -AGAAATTAT
1 AAAAAATTGT
542784 AAAAAATTGT
1 AAAAAATTGT
542794 AAAAAA
1 AAAAAA
542800 ATATTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
9 4 0.13
10 21 0.70
11 5 0.17
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (10 bp):
AAAAAATTGT
Found at i:542800 original size:11 final size:11
Alignment explanation
Indices: 542753--542801 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
542743 ATATTATTAC
542753 AAAAAAATTGT
1 AAAAAAATTGT
*
542764 AAAAAGATTGT
1 AAAAAAATTGT
* *
542775 --AGAAATTAT
1 AAAAAAATTGT
542784 -AAAAAATTGT
1 AAAAAAATTGT
542794 AAAAAAAT
1 AAAAAAAT
542802 ATTTTTAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
9 6 0.20
10 7 0.23
11 17 0.57
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (11 bp):
AAAAAAATTGT
Found at i:548215 original size:7 final size:7
Alignment explanation
Indices: 548203--548236 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
548193 AGGTAAGGAT
548203 GAAATTA
1 GAAATTA
548210 GAAATTA
1 GAAATTA
548217 GAAATTA
1 GAAATTA
548224 GAAATTA
1 GAAATTA
*
548231 AAAATT
1 GAAATT
548237 TAAGGGATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (7 bp):
GAAATTA
Found at i:548250 original size:29 final size:29
Alignment explanation
Indices: 548217--548284 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
548207 TTAGAAATTA
548217 GAAATTAGAAAT-TAAAAATTTAAGGGATT
1 GAAATTA-AAATATAAAAATTTAAGGGATT
* *
548246 GAAA-TAAAATAATAAAATTTTGAGGGATT
1 GAAATTAAAAT-ATAAAAATTTAAGGGATT
548275 -AAATTTAAAA
1 GAAA-TTAAAA
548285 AGAATGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 4 0.12
28 5 0.15
29 19 0.58
30 5 0.15
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (29 bp):
GAAATTAAAATATAAAAATTTAAGGGATT
Found at i:551118 original size:19 final size:17
Alignment explanation
Indices: 551086--551122 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
551076 AAAATATTTA
551086 ATATTATATTTTTAATT
1 ATATTATATTTTTAATT
551103 ATATTATATATATTTAATT
1 ATATTATAT-T-TTTAATT
551122 A
1 A
551123 AATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 1 0.06
19 8 0.44
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATTATATTTTTAATT
Found at i:556013 original size:19 final size:20
Alignment explanation
Indices: 555976--556012 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
555966 TGCTTGTTTA
*
555976 TTTTTATCTGTAGAATTTTC
1 TTTTTATCTGTACAATTTTC
555996 TTTTTAT-TGTAC-ATTTT
1 TTTTTATCTGTACAATTTT
556013 TTTCTAATGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 5 0.31
19 4 0.25
20 7 0.44
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (20 bp):
TTTTTATCTGTACAATTTTC
Found at i:563940 original size:26 final size:25
Alignment explanation
Indices: 563915--563962 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
563905 TATATTAATA
563915 ATACTATTAAATATAAAAT-TTAAAT
1 ATACTATTAAA-ATAAAATCTTAAAT
**
563940 ATTTTATTAAAATAAAATCTTAA
1 ATACTATTAAAATAAAATCTTAA
563963 CTAAAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (25 bp):
ATACTATTAAAATAAAATCTTAAAT
Found at i:564697 original size:12 final size:12
Alignment explanation
Indices: 564680--564722 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
564670 AAAAATAATG
564680 TTATATTAATAA
1 TTATATTAATAA
564692 TTATATTAATAA
1 TTATATTAATAA
*
564704 TT-TA-TAAAAA
1 TTATATTAATAA
*
564714 TTAAATTAA
1 TTATATTAA
564723 ATTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 17 0.63
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:564727 original size:39 final size:38
Alignment explanation
Indices: 564666--564740 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 38
564656 AATACATAAA
* *
564666 TATAAAAAATAATGTTATATTAATAATTATATTAATAATT
1 TATAAAAAATAATATTAAATTAA-AATT-TATTAATAATT
* *
564706 TATAAAAATTAA-ATTAAATTAAAATTTATTTATAA
1 TATAAAAAATAATATTAAATTAAAATTTATTAATAA
564741 AATTACATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 8 0.26
38 4 0.13
39 8 0.26
40 11 0.35
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
TATAAAAAATAATATTAAATTAAAATTTATTAATAATT
Found at i:564797 original size:6 final size:6
Alignment explanation
Indices: 564768--564796 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
564758 GTTAATGTAC
564768 AATTTT AATTTT AATTTT AATTTT -ATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
564797 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
AATTTT
Found at i:568410 original size:24 final size:24
Alignment explanation
Indices: 568383--568431 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
568373 ACATAGCTTC
568383 TTACACCAGGAGTTGT-AGCCGGTG
1 TTACACCAGGAGTTGTCA-CCGGTG
568407 TTACACCAGGAGTTGTCACCGGTG
1 TTACACCAGGAGTTGTCACCGGTG
568431 T
1 T
568432 CCACGACGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (24 bp):
TTACACCAGGAGTTGTCACCGGTG
Found at i:571671 original size:91 final size:91
Alignment explanation
Indices: 571496--571673 Score: 252
Period size: 91 Copynumber: 2.0 Consensus size: 91
571486 ATTTCGTACA
* * ** * * *
571496 GGTGCCGGTCATTAGAAGGCTAGCACCAGAATTTTTTTTAAATACTGGTATCTGGTGCCGGCCAT
1 GGTGCCGGCCATTAGAAGGCCAAAACCAGAATTTTTTTTAAATACTCGTATCTAGTGCCGGCAAT
571561 TAGAAGGCCAACACCAAAAAATTACT
66 TAGAAGGCCAACACCAAAAAATTACT
*
571587 GGTGCCGGCCATTAGAAGGCCAAAACCA-ATTTTTTTTTTAAATACTCGTA-CTAGTGCCGGCAA
1 GGTGCCGGCCATTAGAAGGCCAAAACCAGA-ATTTTTTTTAAATACTCGTATCTAGTGCCGGCAA
*
571650 TTAGAAGGCCAGCACCAAAAAATT
65 TTAGAAGGCCAACACCAAAAAATT
571674 TTGAATTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
90 35 0.45
91 42 0.55
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (91 bp):
GGTGCCGGCCATTAGAAGGCCAAAACCAGAATTTTTTTTAAATACTCGTATCTAGTGCCGGCAAT
TAGAAGGCCAACACCAAAAAATTACT
Found at i:571823 original size:51 final size:50
Alignment explanation
Indices: 571729--571835 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 50
571719 AAAAAAAAAA
* * *
571729 TTAAATATTCGTACTGGTACCGGCCATTAGAAGGCTAAAACCAATTTTTTT
1 TTAAATACTCGTACTGGTACCGGCCATTACAAGGCTAAAACCAA-TTTTAT
* * * * **
571780 TTAAATACTCGTACTGGTGCTGGCCGTTACAAGTCTAGCACCAATTTTAT
1 TTAAATACTCGTACTGGTACCGGCCATTACAAGGCTAAAACCAATTTTAT
571830 TTAAAT
1 TTAAAT
571836 TTTTTAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
50 11 0.23
51 36 0.77
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.36
Consensus pattern (50 bp):
TTAAATACTCGTACTGGTACCGGCCATTACAAGGCTAAAACCAATTTTAT
Found at i:571884 original size:59 final size:60
Alignment explanation
Indices: 571776--571895 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
571766 AAACCAATTT
* * * * * * * *
571776 TTTTTTAAATACTCGTACTGGTGCTGGCCGTTACAAGTCTAGCACCAA-TTTTATTTAAA
1 TTTTTTAAATACTCGTAATAGTACCGGCCATTACAAGGCAAACACCAATTTTTATTTAAA
* * *
571835 TTTTTTAAATACTCGTAATAGTACCGGTCATTACAAGGCAAACATCAATTTTTTTTTAAA
1 TTTTTTAAATACTCGTAATAGTACCGGCCATTACAAGGCAAACACCAATTTTTATTTAAA
571895 T
1 T
571896 ACTCATACTG
Statistics
Matches: 49, Mismatches: 11, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
59 38 0.78
60 11 0.22
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (60 bp):
TTTTTTAAATACTCGTAATAGTACCGGCCATTACAAGGCAAACACCAATTTTTATTTAAA
Found at i:573230 original size:3 final size:3
Alignment explanation
Indices: 573224--573254 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
573214 CTACTACTTT
573224 TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
573255 TATTTTCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:580929 original size:23 final size:22
Alignment explanation
Indices: 580857--580944 Score: 92
Period size: 21 Copynumber: 4.1 Consensus size: 22
580847 TACCTGATCA
*
580857 GAATACGACACATAA-GTGCCT
1 GAATACGACACACAAGGTGCCT
*
580878 GAA-ACGACACACGAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
580899 G-CTGCGACACACAAGGTGCCT
1 GAATACGACACACAAGGTGCCT
* *
580920 GAAATACGACACATAAAGTGCCT
1 G-AATACGACACACAAGGTGCCT
580943 GA
1 GA
580945 TCAGTAAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
20 9 0.17
21 27 0.50
22 1 0.02
23 17 0.31
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (22 bp):
GAATACGACACACAAGGTGCCT
Found at i:580941 original size:44 final size:41
Alignment explanation
Indices: 580862--580943 Score: 101
Period size: 44 Copynumber: 1.9 Consensus size: 41
580852 GATCAGAATA
* * *
580862 CGACACATAAGTGCCTGAAACGACACACGAGGTGCCTGCTG
1 CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
*
580903 CGACACACAAGGTGCCTGAAATACGACACATAAAGTGCCTG
1 CGACACACAA-GTGCCTG-AA-ACGACACACAAAGTGCCTG
580944 ATCAGTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 7 0.21
43 2 0.06
44 16 0.47
ACGTcount: A:0.33, C:0.28, G:0.24, T:0.15
Consensus pattern (41 bp):
CGACACACAAGTGCCTGAAACGACACACAAAGTGCCTGCTG
Found at i:581134 original size:14 final size:13
Alignment explanation
Indices: 581115--581150 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
581105 GATTCCATCC
581115 AAACACACCACCA
1 AAACACACCACCA
581128 AAA-ACACCAACCA
1 AAACACACC-ACCA
581141 AAACACACCA
1 AAACACACCA
581151 GTATAATCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 5 0.24
13 11 0.52
14 5 0.24
ACGTcount: A:0.58, C:0.42, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACACACCACCA
Found at i:581204 original size:37 final size:38
Alignment explanation
Indices: 581125--581209 Score: 133
Period size: 36 Copynumber: 2.3 Consensus size: 38
581115 AAACACACCA
*
581125 CCAAAA-ACACC-AACCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAAAACAAAACACACCAGTATAATCCT
581161 CC-AAACACACCAAAACAAAACACA-CAGTATAATCCT
1 CCAAAACACACCAAAACAAAACACACCAGTATAATCCT
581197 CCAAAACACACCA
1 CCAAAACACACCA
581210 GTATCATATA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
35 3 0.07
36 21 0.47
37 21 0.47
ACGTcount: A:0.52, C:0.36, G:0.02, T:0.09
Consensus pattern (38 bp):
CCAAAACACACCAAAACAAAACACACCAGTATAATCCT
Found at i:581223 original size:28 final size:27
Alignment explanation
Indices: 581188--581270 Score: 130
Period size: 28 Copynumber: 3.0 Consensus size: 27
581178 AAACACACAG
*
581188 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAAT-A
*
581216 TATAATCCTCCCAAACACACCAGAATA
1 TATAATCCTCCAAAACACACCAGAATA
581243 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
581271 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
27 9 0.18
28 42 0.82
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (27 bp):
TATAATCCTCCAAAACACACCAGAATA
Found at i:584260 original size:29 final size:27
Alignment explanation
Indices: 584209--584303 Score: 127
Period size: 27 Copynumber: 3.4 Consensus size: 27
584199 TAGTTGAACT
*
584209 ATGGCAAAGTGATAAAGTATGCCAAAC
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
584236 ATGGCAAAGTGTAATAAAGTGTGCCAAAC
1 ATGGCAAAGTG--ATAAAGTGTGCCAAAC
** * *
584265 ATGAAAAAGTGATAAAATGTGCCAAAT
1 ATGGCAAAGTGATAAAGTGTGCCAAAC
584292 ATGGCAAAGTGA
1 ATGGCAAAGTGA
584304 AATGTGACAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 35 0.59
29 24 0.41
ACGTcount: A:0.45, C:0.12, G:0.23, T:0.20
Consensus pattern (27 bp):
ATGGCAAAGTGATAAAGTGTGCCAAAC
Found at i:585087 original size:12 final size:11
Alignment explanation
Indices: 585049--585091 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
585039 GTATATTTAC
585049 TTATTATATAAG
1 TTATTAT-TAAG
585061 TATATTATTAAG
1 T-TATTATTAAG
*
585073 TTATTATTATTG
1 TTATTATTA-AG
585085 TTATTAT
1 TTATTAT
585092 ATATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 8 0.29
12 14 0.50
13 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (11 bp):
TTATTATTAAG
Found at i:585096 original size:2 final size:2
Alignment explanation
Indices: 585089--585116 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
585079 TTATTGTTAT
585089 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
585117 AAACAAAACA
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:585702 original size:57 final size:59
Alignment explanation
Indices: 585612--585737 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 59
585602 ATGTGTCAAC
* *
585612 TACTGTGACTGTTCCGGATTCGTTCCGAAGAGGTAC-TCCGTACTTC-ACTGTTACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTCCGTACTGCTACTGTTACTGT
* * * **
585669 TACTGTTACTGTTTCGGATTTGTTCCGATGAGGTACTTTGTGTACTGCTACTGTTACTGT
1 TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTAC-TTCCGTACTGCTACTGTTACTGT
585729 TACTGTTAC
1 TACTGTTAC
585738 CGTTACGGTG
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
57 32 0.54
59 7 0.12
60 20 0.34
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (59 bp):
TACTGTTACTGTTCCGGATTCGTTCCGAAGAGGTACTTCCGTACTGCTACTGTTACTGT
Found at i:585914 original size:18 final size:19
Alignment explanation
Indices: 585873--585908 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
585863 GACTGCTACG
*
585873 GAATAATTGACTGTT-CTT
1 GAATAAATGACTGTTACTT
585891 GAATAAATGACTGTTACT
1 GAATAAATGACTGTTACT
585909 GCATAACTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (19 bp):
GAATAAATGACTGTTACTT
Found at i:588127 original size:53 final size:54
Alignment explanation
Indices: 587988--588138 Score: 193
Period size: 53 Copynumber: 2.8 Consensus size: 54
587978 ATAAGTGCGC
* * *
587988 CCGTTTAAGACCATAGCTGGGCTATGGCATC-AT-TGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATG-AATGTGATAATGTGACT
* *
588041 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTAT-AATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGATATGGCATCGGTATGAATGTGATAATGTGACT
*
588094 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGATATGGCATCGGTATGA-ATGTGA
588139 ATCGTGTAAG
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
52 1 0.01
53 78 0.89
54 2 0.02
55 7 0.08
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (54 bp):
CCGTATAAGACCATAGCTGGGATATGGCATCGGTATGAATGTGATAATGTGACT
Found at i:588150 original size:46 final size:48
Alignment explanation
Indices: 588028--588173 Score: 125
Period size: 53 Copynumber: 3.0 Consensus size: 48
588018 CATTGCAATG
* * ** * *
588028 TGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAA
1 TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGG--T-A
* * **
588079 TGTGATAATGTGATTCCGTATAAGACCATGTCTGGGATATGGCTTCGGTA
1 --TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGTA
* *
588129 TGAT-ATGTGAAT-CGTGTAAGACCATGGCAAGGCTATGGCTTCGGT
1 TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGT
588174 GTGTGATGCG
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
46 28 0.34
47 7 0.09
48 4 0.05
50 1 0.01
51 1 0.01
53 41 0.50
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (48 bp):
TGATAATGTGAATCCGTATAAGACCATGGCAAGGATATGGCTTCGGTA
Found at i:590875 original size:17 final size:17
Alignment explanation
Indices: 590853--590906 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
590843 ATTTTTGTGA
590853 TTATTTTTGAACTTGGG
1 TTATTTTTGAACTTGGG
*
590870 TTATTTTTGTA-TT--G
1 TTATTTTTGAACTTGGG
590884 -T-TTTTT-AACTTGGG
1 TTATTTTTGAACTTGGG
590898 TTATTTTTG
1 TTATTTTTG
590907 TAAATATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
11 1 0.03
12 7 0.24
13 1 0.03
14 2 0.07
15 1 0.03
16 7 0.24
17 10 0.34
ACGTcount: A:0.15, C:0.04, G:0.19, T:0.63
Consensus pattern (17 bp):
TTATTTTTGAACTTGGG
Found at i:590887 original size:28 final size:28
Alignment explanation
Indices: 590843--590908 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
590833 ATTTCAGGTC
590843 ATTTTTGTGATTATTTTTGAACTTGGGTT
1 ATTTTTGT-ATTATTTTTGAACTTGGGTT
* *
590872 ATTTTTGTATTGTTTTTTAACTTGGGTT
1 ATTTTTGTATTATTTTTGAACTTGGGTT
590900 ATTTTTGTA
1 ATTTTTGTA
590909 AATATTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 27 0.77
29 8 0.23
ACGTcount: A:0.17, C:0.03, G:0.18, T:0.62
Consensus pattern (28 bp):
ATTTTTGTATTATTTTTGAACTTGGGTT
Found at i:591187 original size:54 final size:54
Alignment explanation
Indices: 591110--591312 Score: 150
Period size: 54 Copynumber: 3.8 Consensus size: 54
591100 ATTGAATTTA
* * * *
591110 TTTTTT-GTAATGATGCCGTCCATTAGAAGGCCAGCACCAAAAAATTTTGACTT
1 TTTTTTCGTACTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAATTTTGACTT
** * * *
591163 TTTTTTCGTACTGGTGTTGGCCATTAGAAGTCCA--A--AATTAAATTTT--CTTT
1 TTTTTTCGTACTGGTGCCGGCCATTACAAGGCCAGCACCAA-AAAATTTTGAC-TT
* * * *
591213 TTTTAAATACTCGTATTGGTGCCGGCCATTACAATGTCAGCACCAAAAAATTTTGAATT
1 TTTT---T--TCGTACTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAATTTTGACTT
* * *
591272 TTTTTTCGTACTAGTGCCGGCTATTACAAGGCCTGCACCAA
1 TTTTTTCGTACTGGTGCCGGCCATTACAAGGCCAGCACCAA
591313 TTTTTTTTTT
Statistics
Matches: 114, Mismatches: 22, Indels: 27
0.70 0.13 0.17
Matches are distributed among these distances:
49 1 0.01
50 8 0.07
51 7 0.06
52 1 0.01
53 7 0.06
54 51 0.45
55 22 0.19
56 1 0.01
57 1 0.01
58 7 0.06
59 8 0.07
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (54 bp):
TTTTTTCGTACTGGTGCCGGCCATTACAAGGCCAGCACCAAAAAATTTTGACTT
Found at i:591242 original size:109 final size:107
Alignment explanation
Indices: 591123--591358 Score: 274
Period size: 109 Copynumber: 2.2 Consensus size: 107
591113 TTTGTAATGA
* * * **
591123 TGCCGTCCATTAGAAGGCCAGCACCAAAAAATTTTGACTTTTTTTTCGTACTGGTGTTGGCCATT
1 TGCCGGCCATTAGAAGGCCAGCACCAAAAAATTTTGAATTTTTTTTCGTACTAGTGCCGGCCATT
* * * * * *
591188 AGAAGTCCAAAATTAAATTTTCTTTTTTTAAATACTCGTATTGG
66 ACAAGGCCAAAA-CAAATTTT-TTTTTTAAAATACTCGTACTAG
* * * *
591232 TGCCGGCCATTACAATGTCAGCACCAAAAAATTTTGAATTTTTTTTCGTACTAGTGCCGGCTATT
1 TGCCGGCCATTAGAAGGCCAGCACCAAAAAATTTTGAATTTTTTTTCGTACTAGTGCCGGCCATT
*** * *
591297 ACAAGGCCTGCACCAATTTTTTTTTTAAAATACTCGTCCTAG
66 ACAAGGCCAAAACAAATTTTTTTTTTAAAATACTCGTACTAG
591339 TGCCGGCCATTAGAAGGCCA
1 TGCCGGCCATTAGAAGGCCA
591359 AAAAAAAATA
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
107 35 0.34
108 6 0.06
109 63 0.61
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (107 bp):
TGCCGGCCATTAGAAGGCCAGCACCAAAAAATTTTGAATTTTTTTTCGTACTAGTGCCGGCCATT
ACAAGGCCAAAACAAATTTTTTTTTTAAAATACTCGTACTAG
Found at i:591475 original size:52 final size:49
Alignment explanation
Indices: 591414--591553 Score: 154
Period size: 52 Copynumber: 2.7 Consensus size: 49
591404 AATTTTTTTT
* **
591414 TAAATACTCGTACTGGTGCCGGTCATTAGAAGGTTAAAACCAAAAAAAAAAA
1 TAAATACTCGTACTGGTGCCGGACATTA-AAGGCCAAAA-C-AAAAAAAAAA
* ** *
591466 TAAATACTCGTACTGGTGCCGGCCATTACAAGGCCAGCACAAAAAAAAAT
1 TAAATACTCGTACTGGTGCCGGACATTA-AAGGCCAAAACAAAAAAAAAA
*
591516 TAAAATATTCGTACTGGTGCCGGACATTAAAGGGCCAA
1 T-AAATACTCGTACTGGTGCCGGACATTAAA-GGCCAA
591554 CTCCAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
50 12 0.16
51 31 0.41
52 33 0.43
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.21
Consensus pattern (49 bp):
TAAATACTCGTACTGGTGCCGGACATTAAAGGCCAAAACAAAAAAAAAA
Found at i:591530 original size:51 final size:51
Alignment explanation
Indices: 591414--591621 Score: 159
Period size: 54 Copynumber: 4.0 Consensus size: 51
591404 AATTTTTTTT
* **
591414 TAAATACTCGTACTGGTGCCGGTCATTAGAAGGTTAAAACCAAAAAAAAAAA
1 TAAATACTCGTACTGGTGCCGGACATTA-AAGGCCAAAACCAAAAAAAAAAA
* ** *
591466 TAAATACTCGTACTGGTGCCGGCCATTACAAGGCCAGCA-C-AAAAAAAAAT
1 TAAATACTCGTACTGGTGCCGGACATTA-AAGGCCAAAACCAAAAAAAAAAA
* ** *****
591516 TAAAATATTCGTACTGGTGCCGGACATTAAAGGGCCAACTCCAAAAATTATTTTT
1 T-AAATACTCGTACTGGTGCCGGACATTAAA-GGCCAAAACCAAAAA--AAAAAA
** * * *
591571 TAAATACTCGTACTGGTGTTGGCCATTAGAAGGCCAAAACTAAAAAGAAAA
1 TAAATACTCGTACTGGTGCCGGACATTA-AAGGCCAAAACCAAAAAAAAAA
591622 CTTTTTATTT
Statistics
Matches: 122, Mismatches: 27, Indels: 14
0.75 0.17 0.09
Matches are distributed among these distances:
50 12 0.10
51 32 0.26
52 34 0.28
53 4 0.03
54 35 0.29
55 5 0.04
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (51 bp):
TAAATACTCGTACTGGTGCCGGACATTAAAGGCCAAAACCAAAAAAAAAAA
Found at i:592319 original size:109 final size:105
Alignment explanation
Indices: 592197--592405 Score: 312
Period size: 109 Copynumber: 2.0 Consensus size: 105
592187 ACCAAGAAAA
*
592197 TTTGAATTTTTTTTTCGTACTGGTGTCGGCCATTAGAAGGCCAAAACCAATTTTTTTTTTAAAAA
1 TTTGAAATTTTTTTTCGTACTGGTGTCGGCCATTAGAAGGCCAAAA-CAA-TTTTTTTTT--AAA
*
592262 TACTCGTACT-AGTGCCAGCTATTATAAGACCAGCACCAAAAGAT
62 TACTCGTACTGA-TGCCAGCCATTATAAGACCAGCACCAAAAGAT
* *
592306 TTTGAAATTTTTTTTCGTACTGGTGTCGGCCATTAGAAGGCTAAAACTATTTTTTTTTAAATACT
1 TTTGAAATTTTTTTTCGTACTGGTGTCGGCCATTAGAAGGCCAAAACAATTTTTTTTTAAATACT
* *
592371 CGTACTGATGCCGGCCATTATAAGGCCAGCACCAA
66 CGTACTGATGCCAGCCATTATAAGACCAGCACCAA
592406 TTTTTTTTTA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
105 37 0.40
106 1 0.01
107 9 0.10
108 2 0.02
109 44 0.47
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (105 bp):
TTTGAAATTTTTTTTCGTACTGGTGTCGGCCATTAGAAGGCCAAAACAATTTTTTTTTAAATACT
CGTACTGATGCCAGCCATTATAAGACCAGCACCAAAAGAT
Found at i:592480 original size:47 final size:48
Alignment explanation
Indices: 592320--592581 Score: 193
Period size: 51 Copynumber: 5.0 Consensus size: 48
592310 AAATTTTTTT
* * * *
592320 TCGTACTGGTGTCGGCCATTAGAAGGCTAAAACTATTTTTTTTTAAATAC
1 TCGTACTGGTGCCGGCCATTACAAGGC--CAACAATTTTTTTTTAAATAC
* *
592370 TCGTACTGATGCCGGCCATTATAAGGCCAGCACCAATTTTTTTTTAAATAC
1 TCGTACTGGTGCCGGCCATTACAAGGCCA--A-CAATTTTTTTTTAAATAC
* * * * **
592421 TCGTACTAGTGCCGACCATTAGAAAGCCAA-TTTTTTTTTTTAAATAC
1 TCGTACTGGTGCCGGCCATTACAAGGCCAACAATTTTTTTTTAAATAC
*
592468 TTGTACTGGTGCCGGCCATTACAAGGCCAACACCAAAAATATATATTTTTTAAAATAC
1 TCGTACTGGTGCCGGCCATTACAAGGCC-A-A-C---AAT-T-T-TTTTTT-AAATAC
* *
592526 TCGTATTGGTACCGGCCATTACAAGGCCAGCACCAAATTTTTTCTTTTAAATAC
1 TCGTACTGGTGCCGGCCATTACAAGGCCA--A-C-AA-TTTTT-TTTTAAATAC
592580 TC
1 TC
592582 TTATTTTTGT
Statistics
Matches: 173, Mismatches: 22, Indels: 30
0.77 0.10 0.13
Matches are distributed among these distances:
47 38 0.22
48 2 0.01
49 2 0.01
50 25 0.14
51 41 0.24
54 11 0.06
55 6 0.03
56 5 0.03
57 8 0.05
58 35 0.20
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (48 bp):
TCGTACTGGTGCCGGCCATTACAAGGCCAACAATTTTTTTTTAAATAC
Found at i:595451 original size:51 final size:51
Alignment explanation
Indices: 595380--595480 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
595370 CTGATCACAT
595380 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
*
595431 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCA
595481 ATTGTCGCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.32
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
Found at i:595492 original size:51 final size:51
Alignment explanation
Indices: 595380--595493 Score: 192
Period size: 51 Copynumber: 2.2 Consensus size: 51
595370 CTGATCACAT
*
595380 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAA
*
595431 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAA
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAA
* *
595482 TTGTCGCTTGTC
1 TTATCACTTGTC
595494 GCTTGTCACT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 59 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAA
Found at i:597213 original size:21 final size:22
Alignment explanation
Indices: 597189--597238 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 22
597179 CTTTTTATTC
*
597189 AATTAACTATCGAAACTTTAA-
1 AATTAACTAACGAAACTTTAAT
*
597210 AATT-TCTTAACGAAACTTTAAT
1 AATTAAC-TAACGAAACTTTAAT
597232 AA-TAACT
1 AATTAACT
597239 TATTAACACT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
20 1 0.04
21 19 0.83
22 3 0.13
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (22 bp):
AATTAACTAACGAAACTTTAAT
Found at i:598147 original size:33 final size:33
Alignment explanation
Indices: 598110--598197 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
598100 TACCTAAAAG
*
598110 GTACAACTGGAAAAGGAAATGTACACTATGTGT
1 GTACAACTTGAAAAGGAAATGTACACTATGTGT
* * * *
598143 GTACAACTTAAAAATGAAACGTACACTTTGTGT
1 GTACAACTTGAAAAGGAAATGTACACTATGTGT
598176 GTAC-ACTTGAAAAGGAAATGTA
1 GTACAACTTGAAAAGGAAATGTA
598198 TGCCTTATGT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 15 0.32
33 32 0.68
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.26
Consensus pattern (33 bp):
GTACAACTTGAAAAGGAAATGTACACTATGTGT
Found at i:598254 original size:31 final size:31
Alignment explanation
Indices: 598215--598361 Score: 213
Period size: 31 Copynumber: 4.7 Consensus size: 31
598205 TGTGTACAAT
598215 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
598246 GCGAAAAGTGGTAGCTTCGGCTACCTGATTA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* * **
598277 GTGAAAAGTAGTAGCTTCGACTACCTGATTG
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
* *
598308 GTGAAAAGTGGTAGCTCCAGCTACCTGATCA
1 GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
*
598339 GTGAATAGTGGTAGCTTCGGCTA
1 GTGAAAAGTGGTAGCTTCGGCTA
598362 AAAGTGACAA
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 101 1.00
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.27
Consensus pattern (31 bp):
GTGAAAAGTGGTAGCTTCGGCTACCTGATCA
Found at i:598487 original size:27 final size:27
Alignment explanation
Indices: 598456--598543 Score: 131
Period size: 27 Copynumber: 3.3 Consensus size: 27
598446 TGAACAATGG
*
598456 CAAAGTGATAAAGTGAGCCAATCATGA
1 CAAAGTGATAAAGTGTGCCAATCATGA
598483 CAAAGTGATAAAGTGTGCCAATCATGA
1 CAAAGTGATAAAGTGTGCCAATCATGA
* * * *
598510 CAAAGTGATATAGTCTGCCAAACATAA
1 CAAAGTGATAAAGTGTGCCAATCATGA
598537 CAAAGTG
1 CAAAGTG
598544 TTCAGTGATC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.20
Consensus pattern (27 bp):
CAAAGTGATAAAGTGTGCCAATCATGA
Found at i:598670 original size:34 final size:34
Alignment explanation
Indices: 598598--598671 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
598588 CATGGCAATG
598598 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
1 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
* * *
598632 TGTGAAACGTAGGTATGGTGTTTCCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
598666 TGTGAA
1 TGTGAA
598672 TCGTGGCACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.32
Consensus pattern (34 bp):
TGTGAAACGTAGGTATGGTATTTCCATACCGAGC
Found at i:600033 original size:104 final size:104
Alignment explanation
Indices: 599841--600069 Score: 282
Period size: 105 Copynumber: 2.2 Consensus size: 104
599831 ATATAAGTTT
* *
599841 TGGTGTCGGCCATTAGAAGGCCAGCACAAAAAAAATGAATTTTTTTTCGTACTGGTGTCGGCCAT
1 TGGTGCCGGCCATTAGAAGGCCAGCACAAAAAAAATGAATTTTTTTTCGTACTGGTGCCGGCCAT
* * *
599906 TAGAAGGCCAAAACCATTTTTTTTTAAAAATATTTGTAC
66 TAGAAGGCCAAAACCATATTTTTTTAAAAATACTCGTAC
* *
599945 TGGTGCCGGCCATTACAAGGCCAGCACAAAAAAATTTTG-ATTTTTTATTCGTACTGGTGCCGGC
1 TGGTGCCGGCCATTAGAAGGCCAGCACAAAAAAA--ATGAATTTTTT-TTCGTACTGGTGCCGGC
** * ** **
600009 GGTTATAAGGCCAGCACCA-ATTTTTTTTTAAATACTCGTAC
63 CATTAGAAGGCCAAAACCATATTTTTTTAAAAATACTCGTAC
*
600050 TGGTGCCGACCATTAGAAGG
1 TGGTGCCGGCCATTAGAAGG
600070 TGTGAAAATA
Statistics
Matches: 106, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
104 32 0.30
105 42 0.40
106 32 0.30
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (104 bp):
TGGTGCCGGCCATTAGAAGGCCAGCACAAAAAAAATGAATTTTTTTTCGTACTGGTGCCGGCCAT
TAGAAGGCCAAAACCATATTTTTTTAAAAATACTCGTAC
Found at i:600505 original size:238 final size:238
Alignment explanation
Indices: 600085--600558 Score: 912
Period size: 238 Copynumber: 2.0 Consensus size: 238
600075 AAATAAAACA
600085 AAATAAAGAACACACAGATTTTACATGGAAACTCTTTCAGGAAAAAACCACGGACAGAGAAGAAG
1 AAATAAAGAACACACAGATTTTACATGGAAACTCTTTCAGGAAAAAACCACGGACAGAGAAGAAG
*
600150 AAAATTTGCTATGTCGAATTCGAATTAATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTG
66 AAAATTCGCTATGTCGAATTCGAATTAATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTG
600215 TAAAGCTATATTCTAGTAAGACTGAAATACGTTATTCTAATCAATATCAAATAGATAGAATTTAA
131 TAAAGCTATATTCTAGTAAGACTGAAATACGTTATTCTAATCAATATCAAATAGATAGAATTTAA
600280 TAATAAGGTTTAAAAAACCTTATTCTAAATAAAATAAAAGACG
196 TAATAAGGTTTAAAAAACCTTATTCTAAATAAAATAAAAGACG
600323 AAATAAAGAACACACAGATTTTACATGGAAACTCTTTCAGGAAAAAACCACGGACAGAGAAGAAG
1 AAATAAAGAACACACAGATTTTACATGGAAACTCTTTCAGGAAAAAACCACGGACAGAGAAGAAG
*
600388 AAAATTCGCTATGTCGAATTTGAATTAATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTG
66 AAAATTCGCTATGTCGAATTCGAATTAATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTG
* *
600453 TAAAGCTATATTCTAGTAAGACTGAAATATGTTATTCTAATCAATGTCAAATAGATAGAATTTAA
131 TAAAGCTATATTCTAGTAAGACTGAAATACGTTATTCTAATCAATATCAAATAGATAGAATTTAA
600518 TAATAAGGTTTAAAAAACCTTATTCTAAATAAAATAAAAGA
196 TAATAAGGTTTAAAAAACCTTATTCTAAATAAAATAAAAGA
600559 AGTTTAATTC
Statistics
Matches: 232, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
238 232 1.00
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.28
Consensus pattern (238 bp):
AAATAAAGAACACACAGATTTTACATGGAAACTCTTTCAGGAAAAAACCACGGACAGAGAAGAAG
AAAATTCGCTATGTCGAATTCGAATTAATTACAAGAGAAATAGACTATGTCTATTTATAGGCTTG
TAAAGCTATATTCTAGTAAGACTGAAATACGTTATTCTAATCAATATCAAATAGATAGAATTTAA
TAATAAGGTTTAAAAAACCTTATTCTAAATAAAATAAAAGACG
Found at i:600729 original size:52 final size:53
Alignment explanation
Indices: 600651--600778 Score: 197
Period size: 52 Copynumber: 2.5 Consensus size: 53
600641 AACAGAAGGT
*
600651 AAAA-TTTTTTTTAAATACTCGTACTGGTGTTGGCCATTACAAGGCCAGCACC
1 AAAATTTTTTTTTAAATACTCGTACTGGTGTCGGCCATTACAAGGCCAGCACC
* *
600703 -AATTTTTTTTTTAAATACTCGTACTGGTGTCGGCCATTATAAGGCCAGCACC
1 AAAATTTTTTTTTAAATACTCGTACTGGTGTCGGCCATTACAAGGCCAGCACC
* *
600755 AAAATTTTTTTTTAAGTTCTCGTA
1 AAAATTTTTTTTTAAATACTCGTA
600779 TTTTTGTATA
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
51 2 0.03
52 46 0.68
53 20 0.29
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (53 bp):
AAAATTTTTTTTTAAATACTCGTACTGGTGTCGGCCATTACAAGGCCAGCACC
Found at i:602297 original size:33 final size:34
Alignment explanation
Indices: 602247--602312 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
602237 CACCAAAAGT
*
602247 TTTGTTCTTTTAAAAAAACCCTCCTCTTTGAAGA
1 TTTGTTCTTTTAAAAAAAACCTCCTCTTTGAAGA
602281 TTTGTTC-TTTAAAAAAAACCTCCTCTTTGAAG
1 TTTGTTCTTTTAAAAAAAACCTCCTCTTTGAAG
602313 GAAGGTGAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (34 bp):
TTTGTTCTTTTAAAAAAAACCTCCTCTTTGAAGA
Found at i:603266 original size:19 final size:20
Alignment explanation
Indices: 603234--603295 Score: 74
Period size: 19 Copynumber: 3.1 Consensus size: 20
603224 TTGAAAGACT
**
603234 AAAATAAATTTAAAAAAT-A
1 AAAATAAAAATAAAAAATCA
603253 AAAATAAAAATAAAAAGATCA
1 AAAATAAAAATAAAAA-ATCA
*
603274 AAATTAAAAA-AAAAAATCA
1 AAAATAAAAATAAAAAATCA
603293 AAA
1 AAA
603296 CTTTTAGGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 21 0.55
20 7 0.18
21 10 0.26
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.18
Consensus pattern (20 bp):
AAAATAAAAATAAAAAATCA
Found at i:616379 original size:31 final size:31
Alignment explanation
Indices: 616324--616424 Score: 94
Period size: 31 Copynumber: 3.3 Consensus size: 31
616314 CTTAACAGTC
* * *
616324 CAGTGACTTAAACAAAAATATTCAATTAGTT
1 CAGTGACTTAAATAAAAACATTCAAATAGTT
*
616355 CAGTGACTTAAATAAAAACGTTCAAATAGTT
1 CAGTGACTTAAATAAAAACATTCAAATAGTT
* * * * * **
616386 TAGTAATTTAAATGAAAACTTTTGAATAGTT
1 CAGTGACTTAAATAAAAACATTCAAATAGTT
*
616417 CAATGACT
1 CAGTGACT
616425 ATTTTGTAAC
Statistics
Matches: 55, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.44, C:0.11, G:0.12, T:0.34
Consensus pattern (31 bp):
CAGTGACTTAAATAAAAACATTCAAATAGTT
Found at i:619804 original size:30 final size:30
Alignment explanation
Indices: 619770--619896 Score: 106
Period size: 30 Copynumber: 4.4 Consensus size: 30
619760 GCGATTATTA
619770 AATTTTA-TATTTTTATAAGAGTTAAAATTT
1 AATTTTATTATTTTTA-AAGAGTTAAAATTT
*
619800 AATTTTATTA-TTTTAATA-ACG-TATAATTT
1 AATTTTATTATTTTTAA-AGA-GTTAAAATTT
* **
619829 --TTTTACTATTTTTAAAGA-TTAAAATAA
1 AATTTTATTATTTTTAAAGAGTTAAAATTT
* ** *
619856 AATTTTATTATTTTTAAAAAGTTAACGTAT
1 AATTTTATTATTTTTAAAGAGTTAAAATTT
619886 AATTTTATTAT
1 AATTTTATTAT
619897 ATACTAATTT
Statistics
Matches: 78, Mismatches: 10, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
27 13 0.17
28 7 0.09
29 25 0.32
30 31 0.40
31 2 0.03
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
AATTTTATTATTTTTAAAGAGTTAAAATTT
Found at i:620389 original size:16 final size:16
Alignment explanation
Indices: 620343--620389 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
620333 TAAAAATATT
620343 TATATTATTTTATTTTA
1 TATATT-TTTTATTTTA
* *
620360 -ATATTTAATAATTTTA
1 TATATTT-TTTATTTTA
620376 TATATTTTTTATTT
1 TATATTTTTTATTT
620390 ATTGAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 1 0.04
16 17 0.71
17 6 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TATATTTTTTATTTTA
Found at i:621408 original size:54 final size:53
Alignment explanation
Indices: 621343--621444 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
621333 ATTTATTTGA
* * *
621343 ATTTAATTTTAAT-GTTAAATTTAGTTTTTTAATTTTTTTTAATTTGATACCTGC
1 ATTTAATTTTAATAGTTAAA-TTAG-TGTCTAAGTTTTTTTAATTTGATACCTGC
* *
621397 ATTTGATTTTAATATTTAAATTAGTGTCTAAGTTTTTTTAATTTGATA
1 ATTTAATTTTAATAGTTAAATTAGTGTCTAAGTTTTTTTAATTTGATA
621445 TTTGAGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 21 0.50
54 16 0.38
55 5 0.12
ACGTcount: A:0.29, C:0.04, G:0.09, T:0.58
Consensus pattern (53 bp):
ATTTAATTTTAATAGTTAAATTAGTGTCTAAGTTTTTTTAATTTGATACCTGC
Found at i:627963 original size:23 final size:23
Alignment explanation
Indices: 627919--627964 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
627909 ATTTTATTTT
*
627919 TATTTATATATTACATACATAAA
1 TATTTATATATTACAAACATAAA
*
627942 TATTTATAT-TTATCAAATATAAA
1 TATTTATATATTA-CAAACATAAA
627965 AATAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTTATATATTACAAACATAAA
Found at i:648634 original size:22 final size:21
Alignment explanation
Indices: 648603--648645 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
648593 CCCTAAATTT
*
648603 TAAAAAATTATAAAATAATTAA
1 TAAAAAATTAAAAAAT-ATTAA
*
648625 TAAAATATTAAAAAATATTAA
1 TAAAAAATTAAAAAATATTAA
648646 AGTCATTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAAAAAATTAAAAAATATTAA
Found at i:655621 original size:25 final size:26
Alignment explanation
Indices: 655556--655622 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
655546 GCCTTTTATC
* * *
655556 TATT-TTATTCTTTTTAAAATTATTT
1 TATTATTATACTTTTTAAAATTAATA
*
655581 TATTATTATA-TATTTAAAATTAATA
1 TATTATTATACTTTTTAAAATTAATA
655606 TATTATT-TACTTTTTAA
1 TATTATTATACTTTTTAA
655623 TTGCAGTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 2 0.06
25 29 0.83
26 4 0.11
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTATTATACTTTTTAAAATTAATA
Found at i:660735 original size:2 final size:2
Alignment explanation
Indices: 660728--660755 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
660718 TCTCAACACA
660728 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
660756 TGCATTTAGA
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):
AT
Found at i:660802 original size:2 final size:2
Alignment explanation
Indices: 660795--660824 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
660785 AGAGTTGAAA
660795 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
660825 GAATAAGCTC
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:664322 original size:17 final size:16
Alignment explanation
Indices: 664302--664357 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
664292 TTATAAATTC
664302 TAAAAACATCTAAAAAA
1 TAAAAACAT-TAAAAAA
* *
664319 TAAATA-GTATAAAAAA
1 TAAAAACAT-TAAAAAA
*
664335 TAAAAACAATTAATAAA
1 TAAAAAC-ATTAAAAAA
664352 TAAAAA
1 TAAAAA
664358 TATGATTACG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 13 0.42
17 17 0.55
18 1 0.03
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.21
Consensus pattern (16 bp):
TAAAAACATTAAAAAA
Found at i:666653 original size:11 final size:11
Alignment explanation
Indices: 666637--666665 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
666627 TTTGAGCATT
666637 TAATTATAAAA
1 TAATTATAAAA
666648 TAATTATAAAA
1 TAATTATAAAA
666659 TAATTAT
1 TAATTAT
666666 TTAACTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TAATTATAAAA
Found at i:668496 original size:18 final size:16
Alignment explanation
Indices: 668475--668509 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
668465 TAATATTATG
668475 TTAATAAATAAGATTAAA
1 TTAAT-AATAA-ATTAAA
668493 TTAATAATAAATTAAA
1 TTAATAATAAATTAAA
668509 T
1 T
668510 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 5 0.29
18 5 0.29
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
TTAATAATAAATTAAA
Found at i:668502 original size:21 final size:21
Alignment explanation
Indices: 668476--668517 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
668466 AATATTATGT
*
668476 TAATAAA-TAAGATTAAATTAA
1 TAATAAATTAA-ATAAAATTAA
668497 TAATAAATTAAATAAAATTAA
1 TAATAAATTAAATAAAATTAA
668518 AAGAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATAAATTAAATAAAATTAA
Found at i:668534 original size:23 final size:24
Alignment explanation
Indices: 668498--668542 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
668488 TTAAATTAAT
*
668498 AATAAATTAAATAAA-ATTAAAAG
1 AATAAAATAAATAAATATTAAAAG
*
668521 AATAAAATATATAAATATTAAA
1 AATAAAATAAATAAATATTAAA
668543 TTTGCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (24 bp):
AATAAAATAAATAAATATTAAAAG
Found at i:673483 original size:22 final size:21
Alignment explanation
Indices: 673454--673496 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
673444 ACATGCAGGG
*
673454 GCAGCAAAAGCAATGGCAGCA
1 GCAGCAAAAGCAACGGCAGCA
*
673475 GCAGCCAAAAGCAGCGGCAGCA
1 GCAG-CAAAAGCAACGGCAGCA
673497 ACAGGAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.28, G:0.30, T:0.02
Consensus pattern (21 bp):
GCAGCAAAAGCAACGGCAGCA
Found at i:677422 original size:24 final size:25
Alignment explanation
Indices: 677395--677448 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
677385 ATATATCTCA
* * *
677395 TAATAATATATATAAATCAAATT-T
1 TAATAATAAAAATAAATAAAATTAT
677419 TAATAATAAAAATAAATAAAATTAT
1 TAATAATAAAAATAAATAAAATTAT
677444 TAATA
1 TAATA
677449 GAAGAATCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (25 bp):
TAATAATAAAAATAAATAAAATTAT
Found at i:684379 original size:7 final size:7
Alignment explanation
Indices: 684367--684392 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
684357 CTAAAGATAC
684367 CACTTAT
1 CACTTAT
684374 CACTTAT
1 CACTTAT
684381 CACTTAT
1 CACTTAT
684388 CACTT
1 CACTT
684393 GTCATTGATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.42
Consensus pattern (7 bp):
CACTTAT
Found at i:684416 original size:58 final size:58
Alignment explanation
Indices: 684326--684449 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 58
684316 CTGATCACAT
*
684326 TTATCAATTGTCACTGATCAGATAAGTGTAGCTAAAGATACCACTTATCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGATACCACTTATCACTTATCAC
* * *
684384 TTATCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGATACCACTTATCACTTATCAC
*
684442 TTGTCACT
1 TTATCACT
684450 GATCAGAAGT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (58 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGATACCACTTATCACTTATCAC
Found at i:690056 original size:4 final size:4
Alignment explanation
Indices: 690049--690077 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
690039 AGACGCATGC
690049 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
690078 GGGTGTACTC
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:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:691308 original size:13 final size:13
Alignment explanation
Indices: 691290--691314 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
691280 AGGTACATGA
691290 ACAAAAAAAAAAG
1 ACAAAAAAAAAAG
691303 ACAAAAAAAAAA
1 ACAAAAAAAAAA
691315 CATAAAATAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (13 bp):
ACAAAAAAAAAAG
Found at i:696670 original size:58 final size:57
Alignment explanation
Indices: 696570--696689 Score: 143
Period size: 58 Copynumber: 2.1 Consensus size: 57
696560 AACCCTAAAG
* * * *
696570 TTCAAGTCCCAACGTGGGAATAATTGCCAAATTCAAAGCTTAATTTGGATAAAAAAAA
1 TTCAAGTCCCAACGTAGGAATAATTACCAAATTCAAAGCTTAACTTGAAT-AAAAAAA
* * * *
696628 TTCAAGTCCCAATGTAGGAATAATTACCAAGTTC-AGGACTTAACTTGAATTAAAAAA
1 TTCAAGTCCCAACGTAGGAATAATTACCAAATTCAAAG-CTTAACTTGAATAAAAAAA
696685 TTCAA
1 TTCAA
696690 ACCTTAATAT
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
57 13 0.25
58 40 0.75
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (57 bp):
TTCAAGTCCCAACGTAGGAATAATTACCAAATTCAAAGCTTAACTTGAATAAAAAAA
Found at i:706093 original size:13 final size:14
Alignment explanation
Indices: 706068--706109 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
706058 GTCACCAATT
706068 ATTATATTAAATAA
1 ATTATATTAAATAA
706082 ATTATA-TAAATAA
1 ATTATATTAAATAA
*
706095 ACTTAAAATTAAATA
1 A-TT-ATATTAAATA
706110 CTCTCTTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 2 0.08
16 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATTATATTAAATAA
Found at i:711234 original size:44 final size:45
Alignment explanation
Indices: 711144--711272 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
711134 GACAGAACGA
*
711144 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
711190 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
711234 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
711273 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:713200 original size:35 final size:35
Alignment explanation
Indices: 713037--713197 Score: 225
Period size: 35 Copynumber: 4.6 Consensus size: 35
713027 CATGGCAAAG
*
713037 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGATATGTAGGTATGGTATCATCCATACTGAGT
*
713072 TGTGATATATAGGTATGGTATCATCCATACTGAGT
1 TGTGATATGTAGGTATGGTATCATCCATACTGAGT
*
713107 TGTGATATGTAGGTATGGTATCATCCATACTAAGT
1 TGTGATATGTAGGTATGGTATCATCCATACTGAGT
* * *
713142 TGTGATATGTAGGTATGGCAT-TTCCCATACCGAGT
1 TGTGATATGTAGGTATGGTATCAT-CCATACTGAGT
** *
713177 TGAAAAATGTAGGTATGGTAT
1 TGTGATATGTAGGTATGGTAT
713198 TTCAATGAGA
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 1 0.01
35 112 0.99
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.35
Consensus pattern (35 bp):
TGTGATATGTAGGTATGGTATCATCCATACTGAGT
Found at i:719992 original size:35 final size:35
Alignment explanation
Indices: 719934--720094 Score: 216
Period size: 35 Copynumber: 4.6 Consensus size: 35
719924 CCTCATTGAA
* ** * *
719934 ATACCATACCTACATTTTTCAACTCGGTATGGGA-A
1 ATACCATACCTACATATCACAACTCAGTAT-GGATG
* *
719969 ATGCCATACCTACATATCACAACTTAGTATGGATG
1 ATACCATACCTACATATCACAACTCAGTATGGATG
*
720004 ATACCATACCTACATATCACAACTTAGTATGGATG
1 ATACCATACCTACATATCACAACTCAGTATGGATG
*
720039 ATACCATACCTATATATCACAACTCAGTATGGATG
1 ATACCATACCTACATATCACAACTCAGTATGGATG
*
720074 ATACCATACCTACATTTCACA
1 ATACCATACCTACATATCACA
720095 CTTTGCCATG
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
34 3 0.03
35 110 0.97
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.29
Consensus pattern (35 bp):
ATACCATACCTACATATCACAACTCAGTATGGATG
Found at i:720106 original size:35 final size:35
Alignment explanation
Indices: 719972--720094 Score: 219
Period size: 35 Copynumber: 3.5 Consensus size: 35
719962 ATGGGAAATG
719972 CCATACCTACATATCACAACTTAGTATGGATGATA
1 CCATACCTACATATCACAACTTAGTATGGATGATA
720007 CCATACCTACATATCACAACTTAGTATGGATGATA
1 CCATACCTACATATCACAACTTAGTATGGATGATA
* *
720042 CCATACCTATATATCACAACTCAGTATGGATGATA
1 CCATACCTACATATCACAACTTAGTATGGATGATA
*
720077 CCATACCTACATTTCACA
1 CCATACCTACATATCACA
720095 CTTTGCCATG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 84 1.00
ACGTcount: A:0.37, C:0.25, G:0.10, T:0.28
Consensus pattern (35 bp):
CCATACCTACATATCACAACTTAGTATGGATGATA
Found at i:747222 original size:47 final size:48
Alignment explanation
Indices: 747160--747259 Score: 175
Period size: 47 Copynumber: 2.1 Consensus size: 48
747150 AAGCTTCTAT
747160 GTTATTTAAAATTTTTATTTTAAATACTTATG-TTTTTTTAAATTAAA
1 GTTATTTAAAATTTTTATTTTAAATACTTATGTTTTTTTTAAATTAAA
747207 GTTATTTAAAATTTTTATTTTAAATACTTATGATTTTTTTTTAAATTAAA
1 GTTATTTAAAATTTTTATTTTAAATACTTATG--TTTTTTTTAAATTAAA
747257 GTT
1 GTT
747260 GGAGAGTAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
47 32 0.64
50 18 0.36
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (48 bp):
GTTATTTAAAATTTTTATTTTAAATACTTATGTTTTTTTTAAATTAAA
Found at i:747245 original size:24 final size:24
Alignment explanation
Indices: 747171--747246 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
747161 TTATTTAAAA
747171 TTTTTATTTTAAATACTTATG-TT
1 TTTTTATTTTAAATACTTATGATT
** * **
747194 TTTTTAAATTAAAGTTA-TT-TAAAA
1 TTTTTATTTTAAA--TACTTATGATT
747218 TTTTTATTTTAAATACTTATGATT
1 TTTTTATTTTAAATACTTATGATT
747242 TTTTT
1 TTTTT
747247 TTAAATTAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 9
0.67 0.18 0.16
Matches are distributed among these distances:
22 2 0.05
23 14 0.37
24 20 0.53
25 2 0.05
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTTTATTTTAAATACTTATGATT
Found at i:750561 original size:22 final size:23
Alignment explanation
Indices: 750515--750562 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
750505 AATTTAATTA
750515 TTTTAAAATTATAAAATATAAAT
1 TTTTAAAATTATAAAATATAAAT
* *
750538 TTTTAAAATTGTAAAAT-TACAT
1 TTTTAAAATTATAAAATATAAAT
750560 TTT
1 TTT
750563 ATACGATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTTTAAAATTATAAAATATAAAT
Found at i:751401 original size:29 final size:29
Alignment explanation
Indices: 751343--751404 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
751333 TATATTTATA
* * *
751343 ATTTTAAATAATTAAATTAAAATTTTATT
1 ATTTTAAAGAATTAAAGTAAAATTTAATT
* *
751372 ATTTTAGAGAATTAAAGTATAATTTAATT
1 ATTTTAAAGAATTAAAGTAAAATTTAATT
751401 ATTT
1 ATTT
751405 AATTATTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (29 bp):
ATTTTAAAGAATTAAAGTAAAATTTAATT
Found at i:752130 original size:14 final size:15
Alignment explanation
Indices: 752095--752128 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
752085 AAATTTTTTA
752095 AAAAATAAATAAATT
1 AAAAATAAATAAATT
*
752110 AAAAATAATTAAATT
1 AAAAATAAATAAATT
752125 AAAA
1 AAAA
752129 TACAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAAATAAATT
Found at i:764610 original size:23 final size:23
Alignment explanation
Indices: 764575--764619 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
764565 TTTTATCACT
764575 TAATTATAAAAAAAGTT-ATAAAA
1 TAATTATAAAAAAA-TTAATAAAA
**
764598 TAATTATTTAAAAATTAATAAA
1 TAATTATAAAAAAATTAATAAA
764620 TTTTTTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATTATAAAAAAATTAATAAAA
Found at i:799541 original size:14 final size:14
Alignment explanation
Indices: 799522--799549 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
799512 TACTTCGGGG
799522 ATTATTTGATGATT
1 ATTATTTGATGATT
799536 ATTATTTGATGATT
1 ATTATTTGATGATT
799550 TCATGTGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
ATTATTTGATGATT
Found at i:806538 original size:12 final size:11
Alignment explanation
Indices: 806508--806532 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
806498 TTCAACTAAT
806508 AAAGCAAACAA
1 AAAGCAAACAA
806519 AAAGCAAACAA
1 AAAGCAAACAA
806530 AAA
1 AAA
806533 CTCAAATAGA
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:0.76, C:0.16, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAGCAAACAA
Found at i:812390 original size:21 final size:21
Alignment explanation
Indices: 812366--812431 Score: 78
Period size: 25 Copynumber: 3.0 Consensus size: 21
812356 GTCTTGAATT
812366 TGTTAGATGTTGAATTTATTA
1 TGTTAGATGTTGAATTTATTA
*
812387 TGTTTTAAGCTTGTTGAATTTATTA
1 TG--TT-AG-ATGTTGAATTTATTA
*
812412 TGTTAGATATTGAATTTATT
1 TGTTAGATGTTGAATTTATT
812432 TAGTTGGATA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
21 14 0.37
22 2 0.05
23 4 0.11
24 2 0.05
25 16 0.42
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.55
Consensus pattern (21 bp):
TGTTAGATGTTGAATTTATTA
Found at i:813886 original size:22 final size:22
Alignment explanation
Indices: 813861--813902 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
813851 ACAATTTAAA
813861 ATATAAATTTATTAATATATAT
1 ATATAAATTTATTAATATATAT
813883 ATATAAATTTATTAATATAT
1 ATATAAATTTATTAATATAT
813903 GTAAAAACAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATAAATTTATTAATATATAT
Found at i:814012 original size:14 final size:15
Alignment explanation
Indices: 813993--814059 Score: 77
Period size: 14 Copynumber: 4.7 Consensus size: 15
813983 CCAGAAAAGT
*
813993 AAATCATTTTCTA-G
1 AAATCATTTTCCAGG
814007 AAATCATTTTCCAGG
1 AAATCATTTTCCAGG
*
814022 AAATCATTTTCCA-A
1 AAATCATTTTCCAGG
*
814036 AAATTATTTT-CAGG
1 AAATCATTTTCCAGG
*
814050 AAAACATTTT
1 AAATCATTTT
814060 ACCTGCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
13 2 0.04
14 29 0.64
15 14 0.31
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (15 bp):
AAATCATTTTCCAGG
Found at i:814039 original size:29 final size:28
Alignment explanation
Indices: 813993--814059 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 28
813983 CCAGAAAAGT
* *
813993 AAATCATTTTCTAGAAATCATTTTCCAGG
1 AAATCATTTTCCAAAAATCATTTT-CAGG
*
814022 AAATCATTTTCCAAAAATTATTTTCAGG
1 AAATCATTTTCCAAAAATCATTTTCAGG
*
814050 AAAACATTTT
1 AAATCATTTT
814060 ACCTGCAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (28 bp):
AAATCATTTTCCAAAAATCATTTTCAGG
Found at i:815318 original size:40 final size:40
Alignment explanation
Indices: 815274--815353 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
815264 ATTAAAAAAT
815274 GAGAATGATTTGTTTTTTTTATTCTTATATCTTTTAAGGA
1 GAGAATGATTTGTTTTTTTTATTCTTATATCTTTTAAGGA
815314 GAGAATGATTTGTTTTTTTTATTCTTATATCTTTTAAGGA
1 GAGAATGATTTGTTTTTTTTATTCTTATATCTTTTAAGGA
815354 CTATTTAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55
Consensus pattern (40 bp):
GAGAATGATTTGTTTTTTTTATTCTTATATCTTTTAAGGA
Found at i:816693 original size:20 final size:20
Alignment explanation
Indices: 816668--816709 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
816658 TAACTATATA
*
816668 ATAATATTATTTGAATAATT
1 ATAATATTAATTGAATAATT
816688 ATAATATTAATTGAATAATT
1 ATAATATTAATTGAATAATT
816708 AT
1 AT
816710 GTATTTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (20 bp):
ATAATATTAATTGAATAATT
Found at i:832126 original size:13 final size:13
Alignment explanation
Indices: 832108--832132 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
832098 ATTCTCTACA
832108 ATTTTTAATTTCT
1 ATTTTTAATTTCT
832121 ATTTTTAATTTC
1 ATTTTTAATTTC
832133 ATTAGTGATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTTAATTTCT
Found at i:835795 original size:58 final size:58
Alignment explanation
Indices: 835724--835837 Score: 192
Period size: 58 Copynumber: 2.0 Consensus size: 58
835714 AGAATTAAAT
*
835724 ATCAACTTAGATTTTGAAGTGATTATCTAAAACAAGTAACTTATAGTCATAAAAAAAA
1 ATCAACTCAGATTTTGAAGTGATTATCTAAAACAAGTAACTTATAGTCATAAAAAAAA
* * *
835782 ATCAACTCAGATTTTGAAGTGATTATCTAAAATATGTACCTTATAGTCATAAAAAA
1 ATCAACTCAGATTTTGAAGTGATTATCTAAAACAAGTAACTTATAGTCATAAAAAA
835838 TAGGCTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (58 bp):
ATCAACTCAGATTTTGAAGTGATTATCTAAAACAAGTAACTTATAGTCATAAAAAAAA
Found at i:840793 original size:13 final size:13
Alignment explanation
Indices: 840775--840800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
840765 CTCTATGCTT
840775 CTGTCATCATCAC
1 CTGTCATCATCAC
840788 CTGTCATCATCAC
1 CTGTCATCATCAC
840801 ATTTCTTCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (13 bp):
CTGTCATCATCAC
Done.