Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 95 of 318
Found at i:31564311 original size:24 final size:24
Alignment explanation
Indices: 31564284--31564333 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
31564274 ACCACCAACT
* *
31564284 CCACTTCCGTATCCGGATCCAGAC
1 CCACTTCCATATCCAGATCCAGAC
*
31564308 CCACTTTCATATCCAGATCCAGAC
1 CCACTTCCATATCCAGATCCAGAC
31564332 CC
1 CC
31564334 TTCTCCACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.24, C:0.42, G:0.12, T:0.22
Consensus pattern (24 bp):
CCACTTCCATATCCAGATCCAGAC
Found at i:31564465 original size:12 final size:12
Alignment explanation
Indices: 31564448--31564501 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
31564438 ACCTATACCT
31564448 ATACCCAGACCC
1 ATACCCAGACCC
* * *
31564460 ATACCCTGATCT
1 ATACCCAGACCC
* * *
31564472 AGATCCTGACCC
1 ATACCCAGACCC
31564484 ATACCCAGACCC
1 ATACCCAGACCC
31564496 ATACCC
1 ATACCC
31564502 CGATCCGGAT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.30, C:0.44, G:0.09, T:0.17
Consensus pattern (12 bp):
ATACCCAGACCC
Found at i:31564488 original size:36 final size:36
Alignment explanation
Indices: 31564448--31564525 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
31564438 ACCTATACCT
* *
31564448 ATACCCAGACCCATACCCTGATCTAGATCCTGACCC
1 ATACCCAGACCCATACCCCGATCCAGATCCTGACCC
*
31564484 ATACCCAGACCCATACCCCGATCCGGATCCTGACCC
1 ATACCCAGACCCATACCCCGATCCAGATCCTGACCC
31564520 ATACCC
1 ATACCC
31564526 TGATCCTTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.27, C:0.45, G:0.12, T:0.17
Consensus pattern (36 bp):
ATACCCAGACCCATACCCCGATCCAGATCCTGACCC
Found at i:31564698 original size:15 final size:15
Alignment explanation
Indices: 31564680--31564720 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
31564670 GGCACCACCC
*
31564680 CCTCCGCCACCTCCA
1 CCTCCACCACCTCCA
* *
31564695 CCTCCACCACTTCCT
1 CCTCCACCACCTCCA
31564710 CCTCCACCACC
1 CCTCCACCACC
31564721 ACTAAGTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.66, G:0.02, T:0.17
Consensus pattern (15 bp):
CCTCCACCACCTCCA
Found at i:31564710 original size:18 final size:18
Alignment explanation
Indices: 31564689--31564723 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31564679 CCCTCCGCCA
*
31564689 CCTCCACCTCCACCACTT
1 CCTCCACCACCACCACTT
*
31564707 CCTCCTCCACCACCACT
1 CCTCCACCACCACCACT
31564724 AAGTGACCTA
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:0.17, C:0.63, G:0.00, T:0.20
Consensus pattern (18 bp):
CCTCCACCACCACCACTT
Found at i:31569475 original size:18 final size:18
Alignment explanation
Indices: 31569452--31569544 Score: 105
Period size: 18 Copynumber: 5.2 Consensus size: 18
31569442 CCCAACTACT
*
31569452 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
**
31569470 GTATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
* * *
31569488 GTATATGTAAATAGTACT
1 GTATACGTGAATAGTACC
* **
31569506 ATATACGTGAATAGTGTC
1 GTATACGTGAATAGTACC
31569524 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
31569542 GTA
1 GTA
31569545 AACGGTCGTA
Statistics
Matches: 58, Mismatches: 17, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 58 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:31569504 original size:36 final size:36
Alignment explanation
Indices: 31569452--31569544 Score: 132
Period size: 36 Copynumber: 2.6 Consensus size: 36
31569442 CCCAACTACT
* *
31569452 GTATACGTGAACAGTACCGTATACGTGAATAGTGTC
1 GTATACGTAAATAGTACCGTATACGTGAATAGTGTC
* **
31569488 GTATATGTAAATAGTACTATATACGTGAATAGTGTC
1 GTATACGTAAATAGTACCGTATACGTGAATAGTGTC
*
31569524 GTATACGTGAATAGTACCGTA
1 GTATACGTAAATAGTACCGTA
31569545 AACGGTCGTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.31
Consensus pattern (36 bp):
GTATACGTAAATAGTACCGTATACGTGAATAGTGTC
Found at i:31574191 original size:29 final size:27
Alignment explanation
Indices: 31574135--31574192 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
31574125 TATTTTGATA
*
31574135 TTTTAATTCAATATTTTAGTAATTTAT
1 TTTTAATTCAATATTTTAATAATTTAT
31574162 TTTTAAATGTCAAGTATTTTAATAA-TTAT
1 TTTT-AAT-TCAA-TATTTTAATAATTTAT
31574191 TT
1 TT
31574193 AATTACATAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 3 0.11
29 10 0.37
30 10 0.37
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (27 bp):
TTTTAATTCAATATTTTAATAATTTAT
Found at i:31574193 original size:27 final size:26
Alignment explanation
Indices: 31574133--31574194 Score: 63
Period size: 30 Copynumber: 2.3 Consensus size: 26
31574123 AATATTTTGA
* *
31574133 TATTTTAATTCAATATTTTAGTAATT
1 TATTTAAATTCAATATTTTAATAATT
31574159 TATTTTTAAATGTCAAGTATTTTAATAA-T
1 TA--TTTAAAT-TCAA-TATTTTAATAATT
31574188 TATTTAA
1 TATTTAA
31574195 TTACATACAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
26 2 0.07
27 5 0.17
28 6 0.20
29 7 0.23
30 10 0.33
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (26 bp):
TATTTAAATTCAATATTTTAATAATT
Found at i:31577641 original size:5 final size:5
Alignment explanation
Indices: 31577631--31577702 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
31577621 GTTAAAAAAA
* *
31577631 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
31577677 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
31577703 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:31577684 original size:19 final size:19
Alignment explanation
Indices: 31577660--31577702 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
31577650 ATTATGTTTT
31577660 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
31577679 TATATTATATTATATTATA
1 TATATTATATTATATTATA
31577698 TATAT
1 TATAT
31577703 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:31577735 original size:18 final size:19
Alignment explanation
Indices: 31577707--31577746 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
31577697 ATATATACAT
*
31577707 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
31577726 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
31577744 AAA
1 AAA
31577747 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:31577813 original size:4 final size:4
Alignment explanation
Indices: 31577806--31577833 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
31577796 GAGAAGGAAG
31577806 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA
31577834 AAGAAAAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:31578678 original size:46 final size:44
Alignment explanation
Indices: 31578626--31578739 Score: 138
Period size: 44 Copynumber: 2.5 Consensus size: 44
31578616 AGAACAGAAA
*
31578626 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAGGAT
* * *
31578672 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACATGAA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
* ** *
31578716 TAATTCATGTAAGTCCATGTTAAA
1 TGAGCCATGTAAGTCCATATTAAA
31578740 GACATGGCAT
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 38 0.64
46 21 0.36
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAGGAT
Found at i:31578725 original size:44 final size:45
Alignment explanation
Indices: 31578619--31578752 Score: 144
Period size: 46 Copynumber: 3.0 Consensus size: 45
31578609 ACAGGACAGA
* * *
31578619 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * *
31578665 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
31578709 ACATGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
31578753 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:31586376 original size:21 final size:22
Alignment explanation
Indices: 31586350--31586402 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
31586340 AAAATGGATT
31586350 AATAAAATAAA-TATAATGAA-A-
1 AATAAAATAAAGTA-AAT-AATAG
*
31586371 AATAAAAAAAAGTAAATAATAG
1 AATAAAATAAAGTAAATAATAG
31586393 AATAAAATAA
1 AATAAAATAA
31586403 TATGCTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 11 0.41
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (22 bp):
AATAAAATAAAGTAAATAATAG
Found at i:31589004 original size:53 final size:53
Alignment explanation
Indices: 31588940--31589047 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
31588930 AAGGGTTTTA
31588940 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
1 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
31588993 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
1 TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
31589046 TG
1 TG
31589048 AACTTTATAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.22, C:0.09, G:0.21, T:0.47
Consensus pattern (53 bp):
TGTAGCAAAATTACCCTTTTATTTGATAGTGGTCGGTTGTTATATGTTTTAGT
Found at i:31590243 original size:14 final size:14
Alignment explanation
Indices: 31590224--31590254 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31590214 GAGTTTTTTT
*
31590224 TAATCTAAATTTAC
1 TAATCTAAATTGAC
31590238 TAATCTAAATTGAC
1 TAATCTAAATTGAC
31590252 TAA
1 TAA
31590255 GAACGCAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.03, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTGAC
Found at i:31600360 original size:6 final size:7
Alignment explanation
Indices: 31600312--31600343 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31600302 TAAACACAAG
*
31600312 AAAACGT
1 AAAAAGT
31600319 AAAAAGT
1 AAAAAGT
31600326 AAAAAGT
1 AAAAAGT
31600333 AAAAAGT
1 AAAAAGT
31600340 AAAA
1 AAAA
31600344 GATGAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.72, C:0.03, G:0.12, T:0.12
Consensus pattern (7 bp):
AAAAAGT
Found at i:31602471 original size:21 final size:22
Alignment explanation
Indices: 31602445--31602488 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
31602435 TTCTCAAGGG
*
31602445 TTGGATCGA-AGGCTTGGATCT
1 TTGGATCGACAGACTTGGATCT
31602466 TTGGATCGATCAGACTTGGATCT
1 TTGGATCGA-CAGACTTGGATCT
31602489 AGCCATCGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
23 11 0.55
ACGTcount: A:0.20, C:0.16, G:0.30, T:0.34
Consensus pattern (22 bp):
TTGGATCGACAGACTTGGATCT
Found at i:31603005 original size:28 final size:28
Alignment explanation
Indices: 31602973--31603037 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
31602963 ATTTACTAGA
* * *
31602973 ATACCCCTATGTATGTAATATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
*
31603001 ATACCCCTATGTATGCAAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
31603029 ATACCCCTA
1 ATACCCCTA
31603038 GGGTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:31603184 original size:28 final size:27
Alignment explanation
Indices: 31603143--31603232 Score: 101
Period size: 27 Copynumber: 3.2 Consensus size: 27
31603133 AGGAAGCGTC
31603143 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* ** *
31603171 CTGGTGGCCCTGCCACGTATATCTTTT
1 CTGGTGGCACTGCCACAAATATCTGTT
31603198 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
31603227 CTGGTG
1 CTGGTG
31603233 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.33
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:31603243 original size:29 final size:28
Alignment explanation
Indices: 31603153--31603243 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 28
31603143 CTGGTGGCTA
* * *
31603153 TGCCACAAATTATCTGT-TCTGGTGGCCC
1 TGCCACAAAATATCT-TATCTGGTGACAC
** * *
31603181 TGCCAC-GTATATCTTTTCTGGTGGCAC
1 TGCCACAAAATATCTTATCTGGTGACAC
*
31603208 TGCCACAAAATATCTGTATCTGGTGACTC
1 TGCCACAAAATATCT-TATCTGGTGACAC
*
31603237 TGTCACA
1 TGCCACA
31603244 TTTTCTGTAT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
26 1 0.02
27 21 0.42
28 12 0.24
29 16 0.32
ACGTcount: A:0.21, C:0.26, G:0.20, T:0.33
Consensus pattern (28 bp):
TGCCACAAAATATCTTATCTGGTGACAC
Found at i:31607109 original size:15 final size:16
Alignment explanation
Indices: 31607084--31607113 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31607074 CTAATATACT
31607084 TAAACTAAAAATAAAA
1 TAAACTAAAAATAAAA
31607100 TAAA-TAAAAATAAA
1 TAAACTAAAAATAAA
31607114 TTTGGGTTGC
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:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
TAAACTAAAAATAAAA
Found at i:31612806 original size:18 final size:19
Alignment explanation
Indices: 31612775--31612817 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
31612765 AAAACGTAAA
31612775 AAATAAAAAGTAAAAAATG
1 AAATAAAAAGTAAAAAATG
*
31612794 AAATAAAAA-TAAATAATG
1 AAATAAAAAGTAAAAAATG
31612812 AAATAA
1 AAATAA
31612818 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (19 bp):
AAATAAAAAGTAAAAAATG
Found at i:31613731 original size:16 final size:16
Alignment explanation
Indices: 31613701--31613748 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
31613691 GAAAATTAAT
31613701 ATAAAATCT-AAAAT-A
1 ATAAAAT-TAAAAATAA
31613716 ATAATAATTAAAAATAA
1 ATAA-AATTAAAAATAA
31613733 ATAAAATT-AAAATAA
1 ATAAAATTAAAAATAA
31613748 A
1 A
31613749 CTTAAAATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.43
16 12 0.40
17 5 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAAATAA
Found at i:31613747 original size:11 final size:11
Alignment explanation
Indices: 31613692--31613762 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
31613682 ATAGCTTAAG
*
31613692 AAAATTAATAT
1 AAAATTAAAAT
31613703 AAAATCTAAAAT
1 AAAAT-TAAAAT
*
31613715 AATAA-T-AATT
1 AA-AATTAAAAT
*
31613725 AAAAAT-AAAT
1 AAAATTAAAAT
31613735 AAAATTAAAAT
1 AAAATTAAAAT
*
31613746 AAACTTAAAAT
1 AAAATTAAAAT
*
31613757 AGAATT
1 AAAATT
31613763 TCCTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 2 0.04
10 14 0.29
11 24 0.49
12 7 0.14
13 2 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (11 bp):
AAAATTAAAAT
Found at i:31614764 original size:28 final size:27
Alignment explanation
Indices: 31614733--31614787 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
31614723 TTTATTATTT
* *
31614733 TTCAATAGCAATTAATCAATCAGTAATA
1 TTCAATAACAATCAATCAATCAG-AATA
* *
31614761 TTCATTAACAATCAGTCAATCAGAATA
1 TTCAATAACAATCAATCAATCAGAATA
31614788 ATTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.45, C:0.16, G:0.07, T:0.31
Consensus pattern (27 bp):
TTCAATAACAATCAATCAATCAGAATA
Found at i:31614844 original size:18 final size:18
Alignment explanation
Indices: 31614822--31614866 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
31614812 TATTTGGTAA
31614822 CAATCAATTATTCAATAAT
1 CAATCAATTATTCAAT-AT
* *
31614841 -AATCAGTTATTCAGTAT
1 CAATCAATTATTCAATAT
31614858 CAATCAATT
1 CAATCAATT
31614867 GATCGGCAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.42, C:0.16, G:0.04, T:0.38
Consensus pattern (18 bp):
CAATCAATTATTCAATAT
Found at i:31614847 original size:36 final size:36
Alignment explanation
Indices: 31614759--31614866 Score: 101
Period size: 36 Copynumber: 3.0 Consensus size: 36
31614749 CAATCAGTAA
* * * * * *
31614759 TATTCATTAACAATCAGTCAATCAG-AATAATTATT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* * **
31614794 TATTCAGTAACAGTCAGTTATTTGGTAACAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
* *
31614830 TATTCAATAATAATCAGTTATTCAGTATCAATCAAT
1 TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
31614866 T
1 T
31614867 GATCGGCAGG
Statistics
Matches: 57, Mismatches: 15, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
35 19 0.33
36 38 0.67
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (36 bp):
TATTCAATAACAATCAGTTATTCAGTAACAATCAAT
Found at i:31614962 original size:18 final size:19
Alignment explanation
Indices: 31614916--31614962 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
31614906 TCGAGATAAT
*
31614916 GAAAAATAATTACTTTAAA
1 GAAAAATAATTACATTAAA
31614935 -AATAAA-AATTA-ATTAAA
1 GAA-AAATAATTACATTAAA
31614952 GAAAAATAATT
1 GAAAAATAATT
31614963 TAATAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.33
18 13 0.54
19 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (19 bp):
GAAAAATAATTACATTAAA
Found at i:31617536 original size:56 final size:56
Alignment explanation
Indices: 31617461--31617581 Score: 201
Period size: 56 Copynumber: 2.2 Consensus size: 56
31617451 ATCTTAAAAG
* *
31617461 ATAAAAA-AAAATTAATAACTATAAAATAAAATTA-AACTTTAAACTTTAAAACACA
1 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAA-TCTAAACTTTAAAACACA
31617516 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
1 ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
31617572 ATAAAAACAA
1 ATAAAAACAA
31617582 TTGTAAAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
55 7 0.11
56 53 0.85
57 2 0.03
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (56 bp):
ATAAAAACAAAATTAATAACTACAAAATAAAATTACAATCTAAACTTTAAAACACA
Found at i:31618091 original size:18 final size:19
Alignment explanation
Indices: 31618070--31618123 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
31618060 CCAATAACAG
31618070 TCAATTATTCAGTAA-AAA
1 TCAATTATTCAGTAACAAA
* * *
31618088 TCAAATATACAGTAACAAT
1 TCAATTATTCAGTAACAAA
*
31618107 TAAATTATTCAGTAACA
1 TCAATTATTCAGTAACA
31618124 GTCGATCTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
18 13 0.45
19 16 0.55
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (19 bp):
TCAATTATTCAGTAACAAA
Found at i:31618121 original size:19 final size:19
Alignment explanation
Indices: 31618072--31618123 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
31618062 AATAACAGTC
*
31618072 AATTATTCAGTAAAAATCA
1 AATTATTCAGTAACAATCA
* *
31618091 AA-TATACAGTAACAATTA
1 AATTATTCAGTAACAATCA
31618109 AATTATTCAGTAACA
1 AATTATTCAGTAACA
31618124 GTCGATCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTATTCAGTAACAATCA
Found at i:31618315 original size:6 final size:6
Alignment explanation
Indices: 31618304--31618334 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
31618294 ACAAACCCGA
*
31618304 AACAGT AACAGT AACGGT AACAGT AACAGT A
1 AACAGT AACAGT AACAGT AACAGT AACAGT A
31618335 GTCGGCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (6 bp):
AACAGT
Found at i:31627771 original size:3 final size:3
Alignment explanation
Indices: 31627763--31627787 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31627753 TTCTCGCCCA
31627763 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
31627788 TACTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31633251 original size:3 final size:3
Alignment explanation
Indices: 31633236--31633267 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
31633226 CCACAACTCG
*
31633236 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31633268 TACTTTGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31633572 original size:10 final size:9
Alignment explanation
Indices: 31633552--31633583 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
31633542 ATTAGTATGA
*
31633552 TTTTTTATT
1 TTTTTTCTT
31633561 TTTTTTCTT
1 TTTTTTCTT
31633570 TTTTTTCTT
1 TTTTTTCTT
31633579 TTTTT
1 TTTTT
31633584 GTATATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.06, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:31637040 original size:19 final size:19
Alignment explanation
Indices: 31637018--31637069 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
31637008 TTTAGAAAAT
31637018 TTTTAAATATTTTCATTAA
1 TTTTAAATATTTTCATTAA
* *
31637037 TTTTAAAT-TTATTTA-TAT
1 TTTTAAATATT-TTCATTAA
31637055 TTTTAAA-ATTTTCAT
1 TTTTAAATATTTTCAT
31637070 AATAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTAAATATTTTCATTAA
Found at i:31637663 original size:5 final size:5
Alignment explanation
Indices: 31637653--31637677 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
31637643 GCCCCATCTG
31637653 CCTCT CCTCT CCTCT CCTCT CCTCT
1 CCTCT CCTCT CCTCT CCTCT CCTCT
31637678 ATCCTACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CCTCT
Found at i:31646083 original size:28 final size:30
Alignment explanation
Indices: 31646044--31646101 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
31646034 GTGGAATAAA
31646044 AAAATATATTATAAA-TATAT-TAAAAATT
1 AAAATATATTATAAATTATATATAAAAATT
*
31646072 AAAATGAT-TTATAAATTATATATAATAATT
1 AAAAT-ATATTATAAATTATATATAAAAATT
31646102 TATTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 12 0.46
29 7 0.27
30 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAATATATTATAAATTATATATAAAAATT
Found at i:31652467 original size:44 final size:44
Alignment explanation
Indices: 31652411--31652996 Score: 245
Period size: 51 Copynumber: 12.7 Consensus size: 44
31652401 CCACTTCAGT
*
31652411 CTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAAC
* * *
31652455 CTGCTCCACTGCAACTTCAGGGAGATAATGTCTGTAATTTCTAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAA-----G--ACTTGTAGCTTCAAC
* * * * * **
31652506 CTACTCCACTGTAACTCCAAGGAGATAAGA-TTCGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G-TAGCTTCAAC
* * *
31652551 CTGCTCCACTGCAACTTAAGGGAGATAAGACTTGTAACTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAAC
** *
31652595 CTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGT-GATTTCCAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAG-CTT-CAAC
* * **
31652640 TTAAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
1 ------CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAAC
* * * * * ** *
31652691 CTGCTCCACTGTAACTTTAGGAAGATAAAAC-T-TA-TTTTGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAAC
* * * ** *
31652732 CTGCTCTATTGCAACTTCAGAGAGATAAGA-TCTGTAATTTATATCCTTAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGT-A--GCT-T-C--AAC
* * * * * * * *
31652783 CTGTTCAATTGCAACTTCAGGAAGATAAGATTTGCTATCTTTAGC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAAC
* ** *
31652828 CTGCTCCATTGCAACTTCAGGGAGATAAGACTTGT---TTTGAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAAC
* * * * *
31652869 CTACTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGA-C------TTGTAGCTTCAAC
* * * * * * * *
31652920 CTGTTCTACTACAACTTTAGGGAAATAAGATTTGCTATCTTCAGC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-TAGCTTCAAC
*
31652965 CTGTTCCACTGCAACTTCAGGGAGATAAGACT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGACT
31652997 GTGAATTTAC
Statistics
Matches: 410, Mismatches: 88, Indels: 87
0.70 0.15 0.15
Matches are distributed among these distances:
41 55 0.13
42 4 0.01
43 3 0.01
44 73 0.18
45 128 0.31
46 3 0.01
47 1 0.00
48 5 0.01
49 3 0.01
51 130 0.32
52 5 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (44 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAAC
Found at i:31652567 original size:96 final size:95
Alignment explanation
Indices: 31652404--31652578 Score: 237
Period size: 96 Copynumber: 1.8 Consensus size: 95
31652394 ATATGCTCCA
* * *
31652404 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
1 CTTCAATCTACTCCACTGCAACTCCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
*
31652469 CTTCAGGGAGATAATGTCTGTAATTTCTAG
66 CTTAAGGGAGATAATGTCTGTAATTTCTAG
* * **
31652499 CTTCAATCTACTCCACTGTAACTCCAAGG-AGATAAGA-TTCGCTATCTTCAGTCTGCTCCACTG
1 CTTCAATCTACTCCACTGCAACTCC-AGGAAGATAAGACTT-G-TAGCTTCAACCTGCTCCACTG
31652562 CAACTTAAGGGAGATAA
63 CAACTTAAGGGAGATAA
31652579 GACTTGTAAC
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 2 0.03
95 30 0.43
96 37 0.54
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (95 bp):
CTTCAATCTACTCCACTGCAACTCCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
CTTAAGGGAGATAATGTCTGTAATTTCTAG
Found at i:31652809 original size:137 final size:139
Alignment explanation
Indices: 31652404--31652996 Score: 680
Period size: 137 Copynumber: 4.3 Consensus size: 139
31652394 ATATGCTCCA
* *
31652404 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTA-CTTTAACCTGCTCCACTGCAA
* * * * *
31652469 CTTCAGGGAGATAATG-TCTGTAATTTCTAGCTTCAATCTACTCCACTGTAACTCCAAGG-AGAT
65 CTTCAGAGAGATAA-GATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTC-AGGAAGAT
*
31652532 AAGATTCGCTAT
128 AAGATTTGCTAT
*
31652544 CTTCAGTCTGCTCCACTGCAACTTAAGGGAGATAAGACTTGTAACTTTAACCTGCTCCACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGT-ACTTTAACCTGCTCCACTGCAA
* * * * ** * * *
31652609 CTTCAGGGAGATAAGGTTTGTGATTTCCAACTTAAATCTGCTCCACTGCAACTTCAGGGAGATAA
65 CTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAA
31652674 GATTTGCTAT
130 GATTTGCTAT
* * * * * * * * *
31652684 CTTCAGTCTGCTCCACTGTAACTTTAGGAAGATAAAAC-T-TATTTTGATCTGCTCTATTGCAAC
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTGCTCCACTGCAAC
* * * *
31652747 TTCAGAGAGATAAGATCTGTAATTTATATCCTT-AATCTGTTCAATTGCAACTTCAGGAAGATAA
66 TTCAGAGAGATAAGATCTGTAATTTATA-GCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAA
31652811 GATTTGCTAT
130 GATTTGCTAT
* * * * * * *
31652821 CTTTAGCCTGCTCCATTGCAACTTCAGGGAGATAAGACTTGT--TTTGATCTACTCTACTGCAAC
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTGCTCCACTGCAAC
* * * *
31652884 TTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCTACTACAACTTTAGGGAA-ATAA
66 TTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCA-GGAAGATAA
31652948 GATTTGCTAT
130 GATTTGCTAT
* *
31652958 CTTCAGCCTGTTCCACTGCAACTTCAGGGAGATAAGACT
1 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
31652997 GTGAATTTAC
Statistics
Matches: 396, Mismatches: 49, Indels: 19
0.85 0.11 0.04
Matches are distributed among these distances:
136 3 0.01
137 223 0.56
138 9 0.02
139 6 0.02
140 154 0.39
141 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (139 bp):
CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTGCTCCACTGCAAC
TTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAG
ATTTGCTAT
Found at i:31660625 original size:19 final size:20
Alignment explanation
Indices: 31660603--31660646 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
31660593 GGGCATTTTC
* *
31660603 ATGAAATTTAGTGCATATG-
1 ATGAAATGTAGTGCAAATGA
31660622 ATGAAATGTAGTGCAAATGA
1 ATGAAATGTAGTGCAAATGA
31660642 ATGAA
1 ATGAA
31660647 TGCAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.30
Consensus pattern (20 bp):
ATGAAATGTAGTGCAAATGA
Found at i:31664779 original size:18 final size:18
Alignment explanation
Indices: 31664756--31664797 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
31664746 AAAAATAATG
31664756 ATAATAGTAATGATA-AT
1 ATAATAGTAATGATATAT
*
31664773 ATCAATAGTGATGATATAT
1 AT-AATAGTAATGATATAT
31664792 ATAATA
1 ATAATA
31664798 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (18 bp):
ATAATAGTAATGATATAT
Found at i:31664834 original size:21 final size:22
Alignment explanation
Indices: 31664804--31664844 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31664794 AATAATAAAA
* *
31664804 TAAAATAAAATAAATGTGTTTT
1 TAAAATAAAAGAAATATGTTTT
31664826 TAAAA-AAAAGAAATATGTT
1 TAAAATAAAAGAAATATGTT
31664845 AACTCGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (22 bp):
TAAAATAAAAGAAATATGTTTT
Found at i:31666163 original size:19 final size:20
Alignment explanation
Indices: 31666139--31666178 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31666129 TTGCTACTAT
31666139 TTTGC-TTCGTTTCTGCTTC
1 TTTGCTTTCGTTTCTGCTTC
* *
31666158 TTTGCTTTCTTTTCTGTTTC
1 TTTGCTTTCGTTTCTGCTTC
31666178 T
1 T
31666179 ATTTTGCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTGCTTTCGTTTCTGCTTC
Found at i:31670979 original size:20 final size:20
Alignment explanation
Indices: 31670956--31670994 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31670946 TTATATATAT
31670956 ATATTAT-ATTATATAATTGA
1 ATATTATAATTAT-TAATTGA
31670976 ATATTATAATTATTAATTG
1 ATATTATAATTATTAATTG
31670995 TTATGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATTATAATTATTAATTGA
Found at i:31672597 original size:45 final size:45
Alignment explanation
Indices: 31672547--31672657 Score: 172
Period size: 45 Copynumber: 2.5 Consensus size: 45
31672537 CGACTACTGT
31672547 TACTGTTATCGTTACTGTTATCA-ATTC-GACACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTA-CAGATTCAG-CACTTTGTGTGTTGAA
31672592 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
* *
31672637 TACTGCTACCGTTACTGTTAC
1 TACTGTTATCGTTACTGTTAC
31672658 TGTTACTGCT
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
44 2 0.03
45 59 0.95
46 1 0.02
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (45 bp):
TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
Found at i:31672662 original size:12 final size:12
Alignment explanation
Indices: 31672637--31672673 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
31672627 GTGTGTTGAA
31672637 TACTGCTACCGT
1 TACTGCTACCGT
* *
31672649 TACTGTTACTGT
1 TACTGCTACCGT
31672661 TACTGCTACCGT
1 TACTGCTACCGT
31672673 T
1 T
31672674 TCTGATTCTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.16, T:0.41
Consensus pattern (12 bp):
TACTGCTACCGT
Found at i:31680097 original size:9 final size:9
Alignment explanation
Indices: 31680083--31680123 Score: 55
Period size: 9 Copynumber: 4.3 Consensus size: 9
31680073 TTAAATTTTT
31680083 AAAAATTAAA
1 AAAAATT-AA
31680093 AAAATATTAA
1 AAAA-ATTAA
31680103 AAAAATTAA
1 AAAAATTAA
*
31680112 AAACATTAA
1 AAAAATTAA
31680121 AAA
1 AAA
31680124 TATTTTTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 16 0.55
10 10 0.34
11 3 0.10
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAAATTAA
Found at i:31680725 original size:22 final size:20
Alignment explanation
Indices: 31680688--31680727 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31680678 TTAAAATATT
*
31680688 TTTTTATTCATTAAACTTAA
1 TTTTTATTCATAAAACTTAA
31680708 TTTTTATTCTATCAAAACTT
1 TTTTTATTC-AT-AAAACTT
31680728 GTAAGAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTATTCATAAAACTTAA
Found at i:31698942 original size:20 final size:20
Alignment explanation
Indices: 31698917--31698954 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31698907 AATTTAGGAT
*
31698917 TTATTTTTATTTATCTTTAA
1 TTATTTGTATTTATCTTTAA
31698937 TTATTTGTATTTATCTTT
1 TTATTTGTATTTATCTTT
31698955 TGAAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTATTTGTATTTATCTTTAA
Found at i:31700334 original size:15 final size:16
Alignment explanation
Indices: 31700316--31700346 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31700306 TTAGTGCTCC
31700316 CTCCAAAGTTT-AAAA
1 CTCCAAAGTTTGAAAA
31700331 CTCCAAAGTTTGAAAA
1 CTCCAAAGTTTGAAAA
31700347 GTATAATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (16 bp):
CTCCAAAGTTTGAAAA
Found at i:31705663 original size:24 final size:24
Alignment explanation
Indices: 31705614--31705663 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
31705604 AAGTCTGTCT
*
31705614 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTAATAAG
* *
31705638 GGAGAGGATTTAGGAGCTAATTAG
1 GGAGAAGATTTAGGAGCTAATAAG
31705662 GG
1 GG
31705664 TGAACTGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTAATAAG
Found at i:31707135 original size:27 final size:26
Alignment explanation
Indices: 31707096--31707206 Score: 105
Period size: 27 Copynumber: 4.1 Consensus size: 26
31707086 GGAAGCGTCT
*
31707096 TGGTGGCTATGCCACAATTATCTGATC
1 TGGTGGCTCTGCCAC-ATTATCTGATC
*
31707123 TGGTGGCTCTGCCACATATATCTGTTC
1 TGGTGGCTCTGCCACAT-TATCTGATC
* * *
31707150 TAGTGGTTCTGACACGATTATCTGTATC
1 TGGTGGCTCTGCCAC-ATTATCTG-ATC
** * *
31707178 TGGTAACTCTGTCACATTATCTGTTC
1 TGGTGGCTCTGCCACATTATCTGATC
31707204 TGG
1 TGG
31707207 CAGCCATGCT
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.10
27 48 0.70
28 14 0.20
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
TGGTGGCTCTGCCACATTATCTGATC
Found at i:31709603 original size:44 final size:44
Alignment explanation
Indices: 31709498--31710052 Score: 306
Period size: 44 Copynumber: 12.5 Consensus size: 44
31709488 GATAATGGCG
* * * * * *
31709498 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAAATTGAAGATAGCA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTA-CA
* * *
31709543 AATCTTATCTCTCTGAAATTGCAGTAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
31709587 AATCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
31709631 AGTCTTATCTCCCT-AAAGTTGAAGTGGAGCAGACTAAAGATAGCG
1 AATCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGCTA-CA
* * *
31709676 AGTTTTATTTCCCTGAAATTGCAGTGGA--ATGATTAAAGCTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCA-GATTAAAGCTACA
*** ** * * * *
31709719 AATGACAAAT--CT--AATTGCAGTCGAGTAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTA-CA
* * * * * *
31709760 AATCTTATCTCTCT-AAAGTTGCAATAGAGTAGATTAAAGTTATA
1 AATCTTATCTCCCTGAAA-TTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * *
31709804 AACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAAAGTTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTACA
* * * * *
31709848 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAA-ATAACG
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGA-TTAAAGCT-ACA
* * *
31709893 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGC-------TACA
* * * *
31709944 AATCTTATCTCTCTGAAATTGCAGTAGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTACA
* * * * * **
31709988 AATCTTATCTCCATGAAGTCGCAAGTGGAGCAGATTGAAGTTATT
1 AATCTTATCTCCCTGAAATTGC-AGTGGAGCAGATTAAAGCTACA
31710033 AA---TATCTCCCTGAAATTGCA
1 AATCTTATCTCCCTGAAATTGCA
31710053 ATAGAGTAGA
Statistics
Matches: 392, Mismatches: 95, Indels: 50
0.73 0.18 0.09
Matches are distributed among these distances:
39 11 0.03
40 9 0.02
41 11 0.03
42 14 0.04
43 10 0.03
44 164 0.42
45 133 0.34
46 3 0.01
51 36 0.09
52 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAATTGCAGTGGAGCAGATTAAAGCTACA
Found at i:31709801 original size:173 final size:171
Alignment explanation
Indices: 31709559--31709875 Score: 391
Period size: 173 Copynumber: 1.8 Consensus size: 171
31709549 ATCTCTCTGA
* * * * * *
31709559 AATTGCAGTAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAA
1 AATTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTAAAGTTGCAATAGAGCAGATTAA
** * * *
31709624 AGTTACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGATAGCGAGTTTTATTTCCC
66 AGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGATA-CAAGTCTTATCTCCC
31709689 TGAAATTGCAGTGGAATGATTAAAGCTACAAATGACAAATCT
130 TGAAATTGCAGTGGAATGATTAAAGCTACAAATGACAAATCT
* * * * *
31709731 AATTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCTAAAGTTGCAATAGAGTAGATTA
1 AATTGCAGTAGAGCAGATTAAAGATA-CAAATCTTATCTCCCTAAAGTTGCAATAGAGCAGATTA
* * * * * ** *
31709796 AAGTTATAAACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAAAGTTACAAGTCTTATCTCCC
65 AAGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGATACAAGTCTTATCTCCC
*
31709861 TGAAGTTGCAGTGGA
130 TGAAATTGCAGTGGA
31709876 GCAGACTGAA
Statistics
Matches: 119, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
172 48 0.40
173 71 0.60
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (171 bp):
AATTGCAGTAGAGCAGATTAAAGATACAAATCTTATCTCCCTAAAGTTGCAATAGAGCAGATTAA
AGTTACAAACCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGATACAAGTCTTATCTCCCT
GAAATTGCAGTGGAATGATTAAAGCTACAAATGACAAATCT
Found at i:31709903 original size:217 final size:218
Alignment explanation
Indices: 31709516--31709948 Score: 656
Period size: 217 Copynumber: 2.0 Consensus size: 218
31709506 CTCCCTGAAG
* *
31709516 TTGCAGTGGAGTAAATTGAAGATAGCAAATCTTATCTCTCTGAAATTGCAGTAGAGCAGATTAAA
1 TTGCAGTCGAGTAAATTGAAGATAGCAAATCTTATCTCTCTGAAATTGCAATAGAGCAGATTAAA
*
31709581 GCTATAAATCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTACAAGTCTTATCTCCCTA
66 GCTATAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTACAAGTCTTATCTCCCTA
* * * *
31709646 AAGTTGAAGTGGAGCAGACTAAAGATAGCGAGTTTTATTTCCCTGAAATTGCAGTGGAA-TGATT
131 AAGTTGAAGTGGAGCAGACTAAAGATAACGAATCTTATTTCCCTGAAATTGCAGTGGAACAGATT
31709710 AAAGCTACAAATGACAAATCTAA
196 AAAGCTACAAATGACAAATCTAA
* *
31709733 TTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCT-AAAGTTGCAATAGAGTAGATTAA
1 TTGCAGTCGAGTAAATTGAAGATAGCAAATCTTATCTCTCTGAAA-TTGCAATAGAGCAGATTAA
* * * * *
31709797 AGTTATAAACCTTATCTCTCTTAAGTTGTAGTGGGGCAGGTTAAAGTTACAAGTCTTATCTCCCT
65 AGCTATAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTACAAGTCTTATCTCCCT
* * *
31709862 GAAGTTGCAGTGGAGCAGACTGAAA-ATAACGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGA
130 AAAGTTGAAGTGGAGCAGACT-AAAGATAACGAATCTTATTTCCCTGAAATTGCAGTGGAACAGA
* *
31709926 TTAAAGCTATAAATTACAAATCT
194 TTAAAGCTACAAATGACAAATCT
31709949 TATCTCTCTG
Statistics
Matches: 194, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
216 3 0.02
217 165 0.85
218 26 0.13
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (218 bp):
TTGCAGTCGAGTAAATTGAAGATAGCAAATCTTATCTCTCTGAAATTGCAATAGAGCAGATTAAA
GCTATAAACCTTATCTCCCTGAAGTTGCAATGGGGCAGGTTAAAGTTACAAGTCTTATCTCCCTA
AAGTTGAAGTGGAGCAGACTAAAGATAACGAATCTTATTTCCCTGAAATTGCAGTGGAACAGATT
AAAGCTACAAATGACAAATCTAA
Found at i:31709978 original size:51 final size:51
Alignment explanation
Indices: 31709893--31709990 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
31709883 GAAAATAACG
* * *
31709893 AATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTACA
1 AATCTTATCTCCCTGAAATTGCAGTAGAACAGATTAAAGCTATAAATTACA
* **
31709944 AATCTTATCTCTCTGAAATTGCAGTAGAGTAGATTAAAGCTATAAAT
1 AATCTTATCTCCCTGAAATTGCAGTAGAACAGATTAAAGCTATAAAT
31709991 CTTATCTCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAATTGCAGTAGAACAGATTAAAGCTATAAATTACA
Found at i:31710954 original size:20 final size:20
Alignment explanation
Indices: 31710929--31710970 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
31710919 GGACGGTGGC
*
31710929 GCCGTCATCGGCGACCGACG
1 GCCGTCATAGGCGACCGACG
*
31710949 GCCGTCATAGGCGATCGACG
1 GCCGTCATAGGCGACCGACG
31710969 GC
1 GC
31710971 AGCCACAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.36, G:0.36, T:0.12
Consensus pattern (20 bp):
GCCGTCATAGGCGACCGACG
Found at i:31711609 original size:14 final size:14
Alignment explanation
Indices: 31711592--31711623 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31711582 CTACTGCGCA
31711592 TTTTATTCTTATTT
1 TTTTATTCTTATTT
*
31711606 TTTTATTTTTATTT
1 TTTTATTCTTATTT
31711620 TTTT
1 TTTT
31711624 CTATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTATTCTTATTT
Found at i:31711757 original size:14 final size:15
Alignment explanation
Indices: 31711731--31711770 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
31711721 CTTGCACATT
*
31711731 TTATTAGTATTACCA
1 TTATTATTATTACCA
31711746 TT-TTATTATTACCA
1 TTATTATTATTACCA
31711760 TTATTATTATT
1 TTATTATTATT
31711771 GTTTAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (15 bp):
TTATTATTATTACCA
Found at i:31717277 original size:20 final size:20
Alignment explanation
Indices: 31717235--31717281 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31717225 AAAATTACAA
* *
31717235 AAAAAATTCAATATAATTTT
1 AAAAAATTCAAAATAATTAT
31717255 AAAAAATTCAAAAT-ATTCAT
1 AAAAAATTCAAAATAATT-AT
31717275 AAAAAAT
1 AAAAAAT
31717282 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTAT
Found at i:31718366 original size:13 final size:13
Alignment explanation
Indices: 31718348--31718400 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
31718338 AGTTTGGTAA
31718348 TACTTTTGAAAAG
1 TACTTTTGAAAAG
*
31718361 TACTTTTCAAAAG
1 TACTTTTGAAAAG
* *
31718374 TGCTTTTGATAAG
1 TACTTTTGAAAAG
31718387 TACTTTTGAAAAG
1 TACTTTTGAAAAG
31718400 T
1 T
31718401 TTGGTTTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.42
Consensus pattern (13 bp):
TACTTTTGAAAAG
Found at i:31726893 original size:18 final size:18
Alignment explanation
Indices: 31726850--31726893 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
31726840 TTGTGGAGTT
*
31726850 TATTT-ATGAGTATTTTA
1 TATTTGATGAATATTTTA
31726867 TATAATTGATGAATATTTTA
1 TAT--TTGATGAATATTTTA
31726887 TATTTGA
1 TATTTGA
31726894 AATTTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 4 0.17
19 2 0.09
20 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TATTTGATGAATATTTTA
Found at i:31738250 original size:11 final size:10
Alignment explanation
Indices: 31738236--31738286 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
31738226 AAAGAAAAAC
31738236 AAAAAGGAGAG
1 AAAAAGGA-AG
31738247 AAAAAGGAAG
1 AAAAAGGAAG
* *
31738257 GAAAATGAA-
1 AAAAAGGAAG
*
31738266 AAAAAGAGAGG
1 AAAAAG-GAAG
31738277 AAAAAGGAAG
1 AAAAAGGAAG
31738287 CATGGTGTGA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
9 4 0.12
10 14 0.44
11 14 0.44
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (10 bp):
AAAAAGGAAG
Found at i:31740298 original size:29 final size:31
Alignment explanation
Indices: 31740231--31740302 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 31
31740221 TTACATTTAA
*
31740231 ATATTTAAAATAAATCTTTAACTTTTAATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
* * *
31740262 ATA-GTAAAAT-AAGC-TTCACTTTTTATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
31740290 ATATTT-AAATAAA
1 ATATTTAAAATAAA
31740303 TTATTAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 19 0.56
29 6 0.18
30 6 0.18
31 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTAAAATAAAGCTTTAACTTTTAATTT
Found at i:31741010 original size:3 final size:3
Alignment explanation
Indices: 31741002--31741031 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31740992 GAGCCAATGG
31741002 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31741032 AGCAGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31742581 original size:17 final size:17
Alignment explanation
Indices: 31742559--31742604 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
31742549 AGAACAAGGA
31742559 AAGAAAAGAA-AGGAAG
1 AAGAAAAGAAGAGGAAG
31742575 AAGGAAAAGAAAAGAGGAAG
1 AA-GAAAAG--AAGAGGAAG
31742595 AAGAAAAGAA
1 AAGAAAAGAA
31742605 CTAACGTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 2 0.08
17 8 0.31
19 8 0.31
20 8 0.31
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
AAGAAAAGAAGAGGAAG
Found at i:31742589 original size:14 final size:15
Alignment explanation
Indices: 31742572--31742604 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31742562 AAAAGAAAGG
31742572 AAGAAGGAA-AAGAA
1 AAGAAGGAAGAAGAA
31742586 AAG-AGGAAGAAGAA
1 AAGAAGGAAGAAGAA
31742600 AAGAA
1 AAGAA
31742605 CTAACGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 11 0.65
15 1 0.06
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AAGAAGGAAGAAGAA
Found at i:31743400 original size:16 final size:18
Alignment explanation
Indices: 31743368--31743400 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31743358 ATTAAGAGAA
31743368 TGAATTTAGTGTTAATTG
1 TGAATTTAGTGTTAATTG
31743386 TGAATTT-GT-TTAATT
1 TGAATTTAGTGTTAATT
31743401 TTATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (18 bp):
TGAATTTAGTGTTAATTG
Found at i:31744456 original size:18 final size:18
Alignment explanation
Indices: 31744383--31744475 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
31744373 TATTTAAAAT
*
31744383 ATTATAAAAACA-TATTAA
1 ATTATAAAAA-ATTATAAA
* *
31744401 ATTCTATAAAAATCATAAA
1 ATTATA-AAAAATTATAAA
* *
31744420 A-AATAAAAAAAGTATTAAA
1 ATTAT-AAAAAATTA-TAAA
*
31744439 ATTGAT-ATAAATTATAAA
1 ATT-ATAAAAAATTATAAA
31744457 ATTATAAAAAATTATAAA
1 ATTATAAAAAATTATAAA
31744475 A
1 A
31744476 ACTTAAATTA
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
17 2 0.04
18 32 0.56
19 21 0.37
21 2 0.04
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTATAAAAAATTATAAA
Found at i:31744475 original size:9 final size:9
Alignment explanation
Indices: 31744281--31744476 Score: 90
Period size: 10 Copynumber: 20.4 Consensus size: 9
31744271 ATTAAATATT
31744281 AAAATATATA
1 AAAAT-TATA
31744291 AAAATTGATA
1 AAAATT-ATA
*
31744301 TAAACTTATA
1 -AAAATTATA
31744311 AAAATTTATA
1 AAAA-TTATA
* *
31744321 AGAATTGTA
1 AAAATTATA
*
31744330 AAAGATGTAAA
1 AAA-AT-TATA
* *
31744341 AAAAATCTA
1 AAAATTATA
31744350 ACAAATTATA
1 A-AAATTATA
* * *
31744360 AAAGTAACCA
1 AAAATTA-TA
31744370 AAATATT-TA
1 AAA-ATTATA
31744379 AAATATTATA
1 AAA-ATTATA
* *
31744389 AAAACATATT
1 AAAA-TTATA
*
31744399 AAATTCTATA
1 AAAAT-TATA
*
31744409 AAAATCATA
1 AAAATTATA
* *
31744418 AAAAATAAA
1 AAAATTATA
* *
31744427 AAAAGTATT
1 AAAATTATA
31744436 AAAATTGATA
1 AAAATT-ATA
*
31744446 TAAATTAT-
1 AAAATTATA
31744454 AAAATTATAA
1 AAAATTAT-A
31744464 AAAATTATA
1 AAAATTATA
31744473 AAAA
1 AAAA
31744477 CTTAAATTAG
Statistics
Matches: 137, Mismatches: 35, Indels: 29
0.68 0.17 0.14
Matches are distributed among these distances:
8 7 0.05
9 53 0.39
10 66 0.48
11 11 0.08
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:31745848 original size:9 final size:9
Alignment explanation
Indices: 31745829--31745865 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
31745819 GGATTCTTTA
31745829 TTTTC-GGG
1 TTTTCGGGG
31745837 TTTTCGGGG
1 TTTTCGGGG
*
31745846 TTTT-TGGG
1 TTTTCGGGG
31745854 TTTTCGGGG
1 TTTTCGGGG
31745863 TTT
1 TTT
31745866 AGTCTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 12 0.48
9 13 0.52
ACGTcount: A:0.00, C:0.08, G:0.38, T:0.54
Consensus pattern (9 bp):
TTTTCGGGG
Found at i:31745854 original size:17 final size:17
Alignment explanation
Indices: 31745829--31745865 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
31745819 GGATTCTTTA
31745829 TTTTCGGGTTTTCGGGG
1 TTTTCGGGTTTTCGGGG
*
31745846 TTTTTGGGTTTTCGGGG
1 TTTTCGGGTTTTCGGGG
31745863 TTT
1 TTT
31745866 AGTCTTTATC
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:0.00, C:0.08, G:0.38, T:0.54
Consensus pattern (17 bp):
TTTTCGGGTTTTCGGGG
Found at i:31748086 original size:36 final size:36
Alignment explanation
Indices: 31748045--31748121 Score: 154
Period size: 36 Copynumber: 2.1 Consensus size: 36
31748035 TTTTATGATT
31748045 AATTTAAGAGAGAAAATTTACAAATCAAATCATTTA
1 AATTTAAGAGAGAAAATTTACAAATCAAATCATTTA
31748081 AATTTAAGAGAGAAAATTTACAAATCAAATCATTTA
1 AATTTAAGAGAGAAAATTTACAAATCAAATCATTTA
31748117 AATTT
1 AATTT
31748122 TTTATTTTCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (36 bp):
AATTTAAGAGAGAAAATTTACAAATCAAATCATTTA
Found at i:31749226 original size:15 final size:15
Alignment explanation
Indices: 31749203--31749241 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
31749193 GTTTAGTCCC
* * *
31749203 TAGGATTTTTTGGTT
1 TAGGGTTTTTAGGGT
31749218 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
31749233 TAGGGTTTT
1 TAGGGTTTT
31749242 GCTAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:31749402 original size:34 final size:34
Alignment explanation
Indices: 31749319--31749443 Score: 128
Period size: 34 Copynumber: 3.6 Consensus size: 34
31749309 TCTTTTTTAA
* * **
31749319 AAATTAATTAAATTAAGGTTTATGATTTTTAAAT
1 AAATTAATTAAATTAGGGTTTAAGGGTTTTAAAT
*
31749353 AAATTAAGTAAATTAGGGTTTAAGGGTTTTAAAT
1 AAATTAATTAAATTAGGGTTTAAGGGTTTTAAAT
* * * *
31749387 AAATAAATTAAATTAGAGATT-AGGG-TTTAAGGTT
1 AAATTAATTAAATTAGGGTTTAAGGGTTTTAA--AT
31749421 AAAGTTAATTAAATTAGGGTTTA
1 AAA-TTAATTAAATTAGGGTTTA
31749444 GTTTTTTCAA
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
32 5 0.07
33 4 0.05
34 50 0.68
35 15 0.20
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (34 bp):
AAATTAATTAAATTAGGGTTTAAGGGTTTTAAAT
Found at i:31749732 original size:125 final size:126
Alignment explanation
Indices: 31749504--31749866 Score: 500
Period size: 125 Copynumber: 2.9 Consensus size: 126
31749494 TTTTTACCCC
**
31749504 AAAAAATAATTTTGAGAAGACCTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCAC
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCAC
* * *
31749569 TATCAGCAAAATTACTAAAAAAAGCTACCACATGGACGCTCTTTTTCTA-TAGTAGTTCCT-
66 TATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACT-GTAGTTCCTA
* *
31749629 GAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCAC
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCAC
* * * * *
31749694 TGTCAGCAAAAGTACTGAAAAATGCTCCCACGTAGACGCAAT-TTTTTTTACTGTAGTTCCTA
66 TATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC--TCTTTTTCTACTGTAGTTCCTA
* *
31749756 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGT-AAAAATCACTTCAAGCAGGATGCA
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAA-CGCTTTAAGCAGGATGCA
* * * *
31749820 CTATCAGTAAAATTACTGAAAAAAGCTCTCATGTGGACGGTCTTTTT
65 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
31749867 TTACAATAGT
Statistics
Matches: 208, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
125 94 0.45
126 26 0.12
127 88 0.42
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (126 bp):
AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCAC
TATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACTGTAGTTCCTA
Found at i:31751719 original size:18 final size:18
Alignment explanation
Indices: 31751693--31751735 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31751683 GACTGGGAAA
* * *
31751693 AGGAAACATATAAGGGTT
1 AGGATACATATAAAGGCT
31751711 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
31751729 AGGATAC
1 AGGATAC
31751736 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:31752328 original size:7 final size:7
Alignment explanation
Indices: 31752318--31752342 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31752308 TTATATACAT
31752318 AATACTA
1 AATACTA
31752325 AATACTA
1 AATACTA
31752332 AATACTA
1 AATACTA
31752339 AATA
1 AATA
31752343 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:31755964 original size:15 final size:15
Alignment explanation
Indices: 31755941--31755983 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
31755931 AATTTAACAA
*
31755941 TTAAATTTTTCATAT
1 TTAAATTTTTAATAT
*
31755956 TTAACTTTTTAATAT
1 TTAAATTTTTAATAT
31755971 TTAAATTTTTAAT
1 TTAAATTTTTAAT
31755984 TTACCAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (15 bp):
TTAAATTTTTAATAT
Found at i:31757159 original size:30 final size:30
Alignment explanation
Indices: 31757125--31757188 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
31757115 AAATATCGAA
31757125 TCTTCCCAAGCTCCTAAATGCA-ATATTAAG
1 TCTTCCCAAGCTCCTAAATG-AGATATTAAG
* * *
31757155 TCTTCCCAAGCTTCTGAATGAGATATTAGG
1 TCTTCCCAAGCTCCTAAATGAGATATTAAG
31757185 TCTT
1 TCTT
31757189 ATCAATCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (30 bp):
TCTTCCCAAGCTCCTAAATGAGATATTAAG
Found at i:31759901 original size:33 final size:34
Alignment explanation
Indices: 31759853--31759916 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
31759843 AATAGATGTA
31759853 TTAACTATAAAAAATAA-TTACAAATAATTATCAT
1 TTAACTATAAAAAATAATTTA-AAATAATTATCAT
*
31759887 TTAA-TATAATAAATAATTTAAAATAATTAT
1 TTAACTATAAAAAATAATTTAAAATAATTAT
31759917 ATAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAACTATAAAAAATAATTTAAAATAATTATCAT
Found at i:31759922 original size:18 final size:17
Alignment explanation
Indices: 31759859--31759913 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
31759849 TGTATTAACT
*
31759859 ATAAAAAATAA-TTACAA
1 ATAATAAATAATTTA-AA
* * *
31759876 ATAAT-TATCATTTAAT
1 ATAATAAATAATTTAAA
31759892 ATAATAAATAATTTAAA
1 ATAATAAATAATTTAAA
31759909 ATAAT
1 ATAAT
31759914 TATATAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATAAATAATTTAAA
Found at i:31759924 original size:17 final size:17
Alignment explanation
Indices: 31759866--31759924 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
31759856 ACTATAAAAA
31759866 ATAATTACAAATAATTAT
1 ATAATTA-AAATAATTAT
* *
31759884 CAT--TTAATATAA-TAA
1 -ATAATTAAAATAATTAT
31759899 ATAATTTAAAATAATTAT
1 ATAA-TTAAAATAATTAT
31759917 ATAATTAA
1 ATAATTAA
31759925 TTAGAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 5 0.16
17 15 0.47
18 6 0.19
19 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATAATTAT
Found at i:31760461 original size:22 final size:23
Alignment explanation
Indices: 31760421--31760463 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
31760411 TATAAATTTA
*
31760421 TTTTAAATACAAAATTTTAAAGG
1 TTTTAAATACAAAAATTTAAAGG
31760444 TTTTAAATA-AAAAATTTAAA
1 TTTTAAATACAAAAATTTAAA
31760464 ATAAATTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (23 bp):
TTTTAAATACAAAAATTTAAAGG
Found at i:31764736 original size:26 final size:26
Alignment explanation
Indices: 31764701--31764808 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
31764691 TGAAATTCCC
*
31764701 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
31764727 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
31764753 ATCATGAAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31764779 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
31764805 ATCA
1 ATCA
31764809 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:31765590 original size:23 final size:23
Alignment explanation
Indices: 31765559--31766203 Score: 571
Period size: 23 Copynumber: 28.1 Consensus size: 23
31765549 AAATAAGTAC
* *
31765559 TTAAACACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
31765582 TTAAGCACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
*
31765605 TTAAACACTTCAATTTGCAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
31765628 TCAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
*
31765652 TT-AACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* *
31765675 TT-AACA-TATCAATTAACAACAT
1 TTAAACACT-TCAATTTACAGCAT
* *
31765697 TTATACACCTCAA-TTACAGCGA-
1 TTAAACACTTCAATTTACAGC-AT
* * * *
31765719 TAAAACA-TCTCAATGTCCAGCAA
1 TTAAACACT-TCAATTTACAGCAT
* * * *
31765742 CTAAACACTTCAATTTGCAGTAC
1 TTAAACACTTCAATTTACAGCAT
* *
31765765 TTAAACACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
*
31765788 TTAAGCACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
31765811 TTAAATACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
* **
31765834 TCAAACACTTCAATTTGTAGCACT
1 TTAAACACTTCAATTTACAGCA-T
31765858 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
*
31765880 TTAAACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
31765903 TCAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
*
31765927 TT-AACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
31765949 TAAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* * *
31765973 TT-AACATTTCAATTAACAACAT
1 TTAAACACTTCAATTTACAGCAT
31765995 TTAAACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
31766018 TCAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
31766042 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
31766064 TAAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* * *
31766088 TT-AACATTTCAATTAACAACAT
1 TTAAACACTTCAATTTACAGCAT
* * *
31766110 TTATACACCTCAA-TTACAACGA-
1 TTAAACACTTCAATTTACAGC-AT
* * *
31766132 TAAAACA-TCTCAATTTCCAGCAA
1 TTAAACACT-TCAATTTACAGCAT
* * * * *
31766155 CTAAACACTTCAAATTGCAGTAC
1 TTAAACACTTCAATTTACAGCAT
* *
31766178 TTAAACACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
31766201 TTA
1 TTA
31766204 CTACTAAATA
Statistics
Matches: 506, Mismatches: 92, Indels: 48
0.78 0.14 0.07
Matches are distributed among these distances:
22 48 0.09
23 444 0.88
24 14 0.03
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAAACACTTCAATTTACAGCAT
Found at i:31770813 original size:41 final size:41
Alignment explanation
Indices: 31770647--31770802 Score: 285
Period size: 41 Copynumber: 3.8 Consensus size: 41
31770637 TTTATCGTTA
* *
31770647 GTGACATAATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
31770688 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
31770729 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
*
31770770 GTGACACATTTCGGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
31770803 AAGAGCCGGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 112 1.00
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:31771073 original size:33 final size:32
Alignment explanation
Indices: 31771017--31771080 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
31771007 ATAGATATGT
31771017 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
31771049 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
31771081 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:31771097 original size:33 final size:33
Alignment explanation
Indices: 31771024--31771097 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
31771014 TGTATATATA
* * **
31771024 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
31771056 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
31771089 TGTATGTAT
1 TATATGTAT
31771098 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:31774711 original size:41 final size:42
Alignment explanation
Indices: 31774666--31774796 Score: 106
Period size: 43 Copynumber: 3.1 Consensus size: 42
31774656 CGAGTGAAAG
*
31774666 TTTTTTGCGGCATTTTTA-CAAAAACACCACTATATCTCAAC
1 TTTTTTGCGGCATTTTTACCAAAAACGCCACTATATCTCAAC
** * * * * *
31774707 -TTTTTGCAACGTTTTCACCAAAATCGTCACTATAGCTCAAC
1 TTTTTTGCGGCATTTTTACCAAAAACGCCACTATATCTCAAC
* * ** *
31774748 TTTTTTACGGTATTTTTTAGAAAAAACGCCACTAT-TGCTCAAT
1 TTTTTTGCGGCA-TTTTTACCAAAAACGCCACTATAT-CTCAAC
31774791 TTTTTT
1 TTTTTT
31774797 TTCATTTTTA
Statistics
Matches: 66, Mismatches: 20, Indels: 6
0.72 0.22 0.07
Matches are distributed among these distances:
40 13 0.20
41 19 0.29
42 6 0.09
43 28 0.42
ACGTcount: A:0.29, C:0.21, G:0.09, T:0.40
Consensus pattern (42 bp):
TTTTTTGCGGCATTTTTACCAAAAACGCCACTATATCTCAAC
Found at i:31774949 original size:8 final size:8
Alignment explanation
Indices: 31774938--31774989 Score: 88
Period size: 8 Copynumber: 6.6 Consensus size: 8
31774928 AATATTAAAA
31774938 TTTTAAGT
1 TTTTAAGT
31774946 TTTTAAGT
1 TTTTAAGT
31774954 TTTTAAGT
1 TTTTAAGT
31774962 TTTTAAGT
1 TTTTAAGT
31774970 TTTTAA-T
1 TTTTAAGT
*
31774977 TTTTAATT
1 TTTTAAGT
31774985 TTTTA
1 TTTTA
31774990 TTTTAAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.16
8 36 0.84
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (8 bp):
TTTTAAGT
Found at i:31774959 original size:24 final size:23
Alignment explanation
Indices: 31774932--31774982 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
31774922 ATATTAAATA
31774932 TTAAAATTTTAAGTTTTTAAGTTT
1 TTAAAATTTTAAGTTTTTAA-TTT
**
31774956 TTAAGTTTTTAAGTTTTTAATTT
1 TTAAAATTTTAAGTTTTTAATTT
31774979 TTAA
1 TTAA
31774983 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (23 bp):
TTAAAATTTTAAGTTTTTAATTT
Found at i:31775007 original size:15 final size:15
Alignment explanation
Indices: 31774918--31775008 Score: 60
Period size: 15 Copynumber: 6.1 Consensus size: 15
31774908 AAATATGGAC
* * *
31774918 TAAAATATTAAATAT
1 TAAAATTTTTAATTT
31774933 TAAAA-TTTTAAGTTT
1 TAAAATTTTTAA-TTT
* *
31774948 TTAAGTTTTTAAGTTT
1 TAAAATTTTTAA-TTT
* *
31774964 TTAAGTTTTTAATTT
1 TAAAATTTTTAATTT
* *
31774979 T-TAATTTTTTATTT
1 TAAAATTTTTAATTT
*
31774993 TAAAATTTTCAATTT
1 TAAAATTTTTAATTT
31775008 T
1 T
31775009 TTTGAAGTTT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.24
15 25 0.40
16 22 0.35
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.59
Consensus pattern (15 bp):
TAAAATTTTTAATTT
Found at i:31775009 original size:8 final size:7
Alignment explanation
Indices: 31774938--31775009 Score: 72
Period size: 8 Copynumber: 9.6 Consensus size: 7
31774928 AATATTAAAA
31774938 TTTTAAGT
1 TTTTAA-T
31774946 TTTTAAGT
1 TTTTAA-T
31774954 TTTTAAGT
1 TTTTAA-T
31774962 TTTTAAGT
1 TTTTAA-T
31774970 TTTTAAT
1 TTTTAAT
31774977 TTTTAAT
1 TTTTAAT
*
31774984 TTTTTAT
1 TTTTAAT
*
31774991 TTTAAAAT
1 TTT-TAAT
*
31774999 TTTCAAT
1 TTTTAAT
31775006 TTTT
1 TTTT
31775010 TTGAAGTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
7 23 0.40
8 35 0.60
ACGTcount: A:0.26, C:0.01, G:0.06, T:0.67
Consensus pattern (7 bp):
TTTTAAT
Found at i:31776327 original size:13 final size:13
Alignment explanation
Indices: 31776309--31776333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31776299 ATAAGTCCAA
31776309 AAACAAAAATAAT
1 AAACAAAAATAAT
31776322 AAACAAAAATAA
1 AAACAAAAATAA
31776334 AATGAAATCC
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:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAACAAAAATAAT
Found at i:31776522 original size:18 final size:18
Alignment explanation
Indices: 31776455--31776585 Score: 187
Period size: 18 Copynumber: 7.3 Consensus size: 18
31776445 ATAATCTTCA
31776455 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
31776474 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
31776493 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31776510 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31776528 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31776546 ATGATAT--AATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
* *
31776563 ATGGTTGCAATCTTAAAT
1 ATGATTGCAATCTTAGAT
31776581 ATGAT
1 ATGAT
31776586 ATACTATCTT
Statistics
Matches: 103, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.01
17 30 0.29
18 48 0.47
19 24 0.23
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:31776526 original size:35 final size:36
Alignment explanation
Indices: 31776460--31776598 Score: 194
Period size: 35 Copynumber: 3.9 Consensus size: 36
31776450 CTTCAATGAT
31776460 ATGCAATCTTAGATATGATATGCAATCTTAGATATG
1 ATGCAATCTTAGATATGATATGCAATCTTAGATATG
*
31776496 ATACAATCTTAGATATGAT-TGCAATCTTAGATATG
1 ATGCAATCTTAGATATGATATGCAATCTTAGATATG
31776531 ATTGCAATCTTAGATATGATAT--AATCTTAGATATGG
1 A-TGCAATCTTAGATATGATATGCAATCTTAGATAT-G
* * * *
31776567 TTGCAATCTTAAATATGATATACTATCTTAGA
1 ATGCAATCTTAGATATGATATGCAATCTTAGA
31776599 AGATATGATT
Statistics
Matches: 93, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
35 48 0.52
36 36 0.39
37 9 0.10
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.38
Consensus pattern (36 bp):
ATGCAATCTTAGATATGATATGCAATCTTAGATATG
Found at i:31776542 original size:53 final size:54
Alignment explanation
Indices: 31776455--31776598 Score: 227
Period size: 53 Copynumber: 2.7 Consensus size: 54
31776445 ATAATCTTCA
31776455 ATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
*
31776510 ATGATTGCAATCTTAGATATGAT-TGCAATCTTAGATATGATATAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
* * * *
31776563 ATGGTTGCAATCTTAAATATGATATACTATCTTAGA
1 ATGATTGCAATCTTAGATATGATATGCAATCTTAGA
31776599 AGATATGATT
Statistics
Matches: 83, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
53 50 0.60
54 28 0.34
55 5 0.06
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (54 bp):
ATGATTGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
Found at i:31777117 original size:16 final size:15
Alignment explanation
Indices: 31777090--31777152 Score: 58
Period size: 16 Copynumber: 4.1 Consensus size: 15
31777080 TATTTTATAT
31777090 TTTTATATAATTATTA
1 TTTTATA-AATTATTA
*
31777106 TTCTTATAAATTATTT
1 TT-TTATAAATTATTA
*
31777122 TTATTATATATTA-TA
1 TT-TTATAAATTATTA
*
31777137 TTTTA-AATTTATTA
1 TTTTATAAATTATTA
31777151 TT
1 TT
31777153 AAATATCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.10
14 7 0.18
15 3 0.08
16 20 0.51
17 5 0.13
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATAAATTATTA
Found at i:31778436 original size:7 final size:7
Alignment explanation
Indices: 31778424--31778550 Score: 51
Period size: 7 Copynumber: 17.9 Consensus size: 7
31778414 CTAATTAATT
31778424 TAAACCC
1 TAAACCC
31778431 TAAACCTC
1 TAAACC-C
*
31778439 TTAACCC
1 TAAACCC
* *
31778446 TTATCCC
1 TAAACCC
*
31778453 ATAAACAC
1 -TAAACCC
**
31778461 TAAATAC
1 TAAACCC
*
31778468 TAAACCT
1 TAAACCC
*
31778475 TAAACTC
1 TAAACCC
* *
31778482 TTAACCT
1 TAAACCC
*
31778489 TTAACCC
1 TAAACCC
* *
31778496 TTAGCCC
1 TAAACCC
*
31778503 CAAACCC
1 TAAACCC
* *
31778510 TTACACCT
1 -TAAACCC
31778518 TAAACTCC
1 TAAAC-CC
*
31778526 --AACAC
1 TAAACCC
31778531 TAAACCC
1 TAAACCC
31778538 TAAACCC
1 TAAACCC
31778545 TAAACC
1 TAAACC
31778551 ATAATCCATA
Statistics
Matches: 88, Mismatches: 26, Indels: 12
0.70 0.21 0.10
Matches are distributed among these distances:
5 1 0.01
6 3 0.03
7 69 0.78
8 15 0.17
ACGTcount: A:0.39, C:0.37, G:0.01, T:0.24
Consensus pattern (7 bp):
TAAACCC
Found at i:31778634 original size:14 final size:14
Alignment explanation
Indices: 31778603--31778654 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
31778593 AATTAACTCC
* *
31778603 TAAACCTTAAACCC
1 TAAACCATAAACCT
* *
31778617 TAAACCATATATCT
1 TAAACCATAAACCT
31778631 TAAACCATAAACCT
1 TAAACCATAAACCT
*
31778645 TAAACTATAA
1 TAAACCATAA
31778655 TGATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:31778805 original size:15 final size:16
Alignment explanation
Indices: 31778754--31778823 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
31778744 AATAATTATT
*
31778754 GTTTTAGGGGTTAT-A
1 GTTTTAGGGTTTATGA
* *
31778769 G-ATTAGTGTTTATGA
1 GTTTTAGGGTTTATGA
*
31778784 TTTTTAGGGTTTA-GA
1 GTTTTAGGGTTTATGA
31778799 GTTTTAGGGGTTATATGA
1 GTTTTA-GGGTT-TATGA
*
31778817 CTTTTAG
1 GTTTTAG
31778824 CGGCGTTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
14 9 0.21
15 9 0.21
16 14 0.33
17 3 0.07
18 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.49
Consensus pattern (16 bp):
GTTTTAGGGTTTATGA
Found at i:31778863 original size:41 final size:41
Alignment explanation
Indices: 31778818--31779038 Score: 289
Period size: 41 Copynumber: 5.4 Consensus size: 41
31778808 GTTATATGAC
* * * *
31778818 TTTTAGCGGCGTTTTACCGAAAGTGCCGTTAATGTTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
31778859 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * * *
31778900 ATTAAGCGGCTTTTTATCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
** **
31778941 TTTTAATGGCATTTTATAGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * * *
31778982 TCTTAGCAGCATTTTACCAAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
31779023 TTTTAGCGGCGTTTTA
1 TTTTAGCGGCATTTTA
31779039 GCATAAAACA
Statistics
Matches: 155, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 155 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:31779067 original size:123 final size:123
Alignment explanation
Indices: 31778818--31779078 Score: 299
Period size: 123 Copynumber: 2.1 Consensus size: 123
31778808 GTTATATGAC
* * ** * * * * * *
31778818 TTTTAGCGGCGTTTTACCGAAAGTGCCGTTAATGTTCTGGTTTTTAGCGGCATTTTACCGAAAGC
1 TTTTAACGGCATTTTATAGAAAGCGCCGCTAATGCTCTGGTTCTTAGCAGCATTTTACCAAAAGC
* * * * * *
31778883 GCCGCTAATGCTCTGGTATTAAGCGGCTTTTTATCGAAAGCGCCGCTAATGCTCTGGT
66 GCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGCGAAAACACCGCTAATGCTCTGAT
*
31778941 TTTTAATGGCATTTTATAGAAAGCGCCGCTAATGCTCTGGTTCTTAGCAGCATTTTACCAAAAGC
1 TTTTAACGGCATTTTATAGAAAGCGCCGCTAATGCTCTGGTTCTTAGCAGCATTTTACCAAAAGC
* * * * *
31779006 GCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAGCATAAAACACCTCTATTGCTCT-AT
66 GCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGC-GAAAACACCGCTAATGCTCTGAT
*
31779064 TTTTAACGGCGTTTT
1 TTTTAACGGCATTTT
31779079 TGGTAAAACG
Statistics
Matches: 113, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
123 98 0.87
124 15 0.13
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.35
Consensus pattern (123 bp):
TTTTAACGGCATTTTATAGAAAGCGCCGCTAATGCTCTGGTTCTTAGCAGCATTTTACCAAAAGC
GCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGCGAAAACACCGCTAATGCTCTGAT
Found at i:31779109 original size:41 final size:41
Alignment explanation
Indices: 31779022--31779101 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
31779012 AATGCCCTGG
* *
31779022 TTTTTAGCGGCGTTTTAGCATAAAACACCTCTATTGCTCTA
1 TTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCTA
* * *
31779063 TTTTTAACGGCGTTTTTG-GTAAAACGCCACTATTGCTCT
1 TTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCT
31779102 GTGTTTTACA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 18 0.53
41 16 0.47
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (41 bp):
TTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCTA
Found at i:31780136 original size:21 final size:21
Alignment explanation
Indices: 31780110--31780153 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
31780100 GTCCAATCCA
*
31780110 AACAAACTCAAAACAAAACCC
1 AACAAACCCAAAACAAAACCC
31780131 AACAAACCCAAAACAAAACCC
1 AACAAACCCAAAACAAAACCC
31780152 AA
1 AA
31780154 ACACGAATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.34, G:0.00, T:0.02
Consensus pattern (21 bp):
AACAAACCCAAAACAAAACCC
Found at i:31780155 original size:11 final size:11
Alignment explanation
Indices: 31780107--31780156 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
31780097 ACAGTCCAAT
31780107 CCAAAC-AAAC
1 CCAAACAAAAC
*
31780117 TCAAAACAAAAC
1 -CCAAACAAAAC
31780129 CC-AAC-AAAC
1 CCAAACAAAAC
31780138 CCAAAACAAAAC
1 CC-AAACAAAAC
31780150 CCAAACA
1 CCAAACA
31780157 CGAATGGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 6 0.18
10 3 0.09
11 14 0.42
12 10 0.30
ACGTcount: A:0.62, C:0.36, G:0.00, T:0.02
Consensus pattern (11 bp):
CCAAACAAAAC
Found at i:31781226 original size:3 final size:3
Alignment explanation
Indices: 31781218--31781289 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
31781208 TTTAACATTG
* * * * *
31781218 TAT TAT TAT TAT TAT TAT CAT TAC TAT TAT CAT TAC TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
31781266 TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
31781290 ATTTCTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:31783100 original size:23 final size:23
Alignment explanation
Indices: 31783074--31783127 Score: 58
Period size: 26 Copynumber: 2.3 Consensus size: 23
31783064 GTTTACTTAT
*
31783074 ATTATAAGTA-AATAATAATATTA
1 ATTATAAATATAATAATAATA-TA
31783097 ATTACTAAAATATAATAATAATATA
1 ATTA-T-AAATATAATAATAATATA
31783122 A-TATAA
1 ATTATAA
31783128 TAATTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 2 0.07
23 5 0.19
24 3 0.11
25 7 0.26
26 10 0.37
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (23 bp):
ATTATAAATATAATAATAATATA
Found at i:31784176 original size:23 final size:24
Alignment explanation
Indices: 31784137--31784184 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
31784127 AGGTTAATCT
31784137 ATATAAGCAAAAATTATGTTTATA
1 ATATAAGCAAAAATTATGTTTATA
31784161 ATATAAGC-AAAATTATGTTTATA
1 ATATAAGCAAAAATTATGTTTATA
31784184 A
1 A
31784185 AATAGTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
ATATAAGCAAAAATTATGTTTATA
Found at i:31784483 original size:40 final size:42
Alignment explanation
Indices: 31784426--31784503 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
31784416 TTTTGAGTCT
*
31784426 ACACGGCATGTCACACGGGCGTG-TGATCAGA-CGTGTGAGAC
1 ACACGGCATGTCACACGGGCATGTTGAT-AGACCGTGTGAGAC
*
31784467 ACACGGCTTG-CACACGGGCATGTTGATAGACCGTGTG
1 ACACGGCATGTCACACGGGCATGTTGATAGACCGTGTG
31784504 TCCCTTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 14 0.42
41 19 0.58
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.19
Consensus pattern (42 bp):
ACACGGCATGTCACACGGGCATGTTGATAGACCGTGTGAGAC
Found at i:31784630 original size:17 final size:17
Alignment explanation
Indices: 31784588--31784630 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
31784578 CCACGGGCTG
*
31784588 GCCACACGACCATGGGA
1 GCCACACGGCCATGGGA
31784605 GCCACACGGCCATGGGA
1 GCCACACGGCCATGGGA
*
31784622 GCTACACGG
1 GCCACACGG
31784631 GTATGTGCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.35, G:0.33, T:0.07
Consensus pattern (17 bp):
GCCACACGGCCATGGGA
Found at i:31786218 original size:47 final size:44
Alignment explanation
Indices: 31786047--31786264 Score: 174
Period size: 47 Copynumber: 4.8 Consensus size: 44
31786037 GGTGATTCGT
* * * *
31786047 GTGCCAGTATAAGACCATGTCTGGGACATGGCATCGTCATTTAGA-TGA
1 GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC--TAAGAGT-A
* * * **
31786095 GGGCTAGTGTAAGACATGTCTGGGACATGCTTCAGCCATATTA-TGA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATC-GGC-TAAGAGT-A
* *
31786141 GTGCCAGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATA
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGG-CT--A-AGAG-TA
* *
31786190 GT-C-AGTGTAAGACATGTCTAGGACATGCATCGGCTAAGAGTT
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTA
31786232 GTGCTAGTGTAAGACATGTCTGGGACATGCATC
1 GTGCTAGTGTAAGACATGTCTGGGACATGCATC
31786265 ATCACGCATA
Statistics
Matches: 141, Mismatches: 20, Indels: 22
0.77 0.11 0.12
Matches are distributed among these distances:
42 3 0.02
43 5 0.04
44 28 0.20
45 2 0.01
46 41 0.29
47 45 0.32
48 13 0.09
49 3 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (44 bp):
GTGCTAGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTA
Found at i:31799710 original size:140 final size:139
Alignment explanation
Indices: 31799458--31799888 Score: 531
Period size: 140 Copynumber: 3.1 Consensus size: 139
31799448 ATGCTTACTA
** * * **
31799458 CGACACTTTTGAGG-CGACACTTTTTTAAATGTTGGGATAGACTTGTCGACATACGTTTTGGCCA
1 CGACACTTTTG-GGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCA
* * *
31799522 ACTATTTGTATAAGAGTTGGGATATACATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTC
65 AC-CTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC
*
31799587 CAACATTATGC
129 CAACACTATGC
*
31799598 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCAATATACACTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* * * * * *
31799663 TCCTTTATATAAGAGTTGGGATATGTATGCCTAAGGCAACGCTTAAATAGGAGCCGACTTTATCC
66 -CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC
31799728 AACACTATGC
130 AACACTATGC
* * * * * * *
31799738 CGAAACTTTTGGGCCAAAACTTTTCCTAAGTGTTGGGATAAACTTGTTGATGTACACTTTGTCCA
1 CGACACTTTTGGGCCGACAC-TTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCA
* * * * * *
31799803 ACCCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAATGCTTATATAAGATTAGGCTTTGTT
65 A-CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC
31799868 CAACACTATGC
129 CAACACTATGC
*
31799879 CGGCACTTTT
1 CGACACTTTT
31799889 CTAAGTGCTG
Statistics
Matches: 248, Mismatches: 40, Indels: 5
0.85 0.14 0.02
Matches are distributed among these distances:
139 2 0.01
140 135 0.54
141 111 0.45
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (139 bp):
CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
ACACTATGC
Found at i:31800462 original size:52 final size:52
Alignment explanation
Indices: 31800400--31800503 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
31800390 TTAATAATTT
31800400 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCATGAC
1 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCATGAC
31800452 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCATGAC
1 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCATGAC
31800504 AAGCATAGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (52 bp):
CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCATGAC
Done.