Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 103 of 125
Found at i:31114804 original size:29 final size:31
Alignment explanation
Indices: 31114731--31114804 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
31114721 AATCAAGATT
* *
31114731 AAAGTTTCATGTATACATTTGAACCACAATT
1 AAAGTTTCATGTATACAATTGAACCACAATC
* * *
31114762 AAAGTTTCACGTATATAATTGTACCA-AATC
1 AAAGTTTCATGTATACAATTGAACCACAATC
31114792 AAAG-TTCATGTAT
1 AAAGTTTCATGTAT
31114805 CAAATTACAC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 8 0.22
30 7 0.19
31 22 0.59
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (31 bp):
AAAGTTTCATGTATACAATTGAACCACAATC
Found at i:31118417 original size:20 final size:20
Alignment explanation
Indices: 31118373--31118417 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
31118363 TCCCCTTATT
* **
31118373 TTTTATTTATAATATTATTA
1 TTTTATTTATAAAATTAACA
*
31118393 ATTTATTTATAAAATTAACA
1 TTTTATTTATAAAATTAACA
31118413 TTTTA
1 TTTTA
31118418 ATAAATAAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTTATTTATAAAATTAACA
Found at i:31126575 original size:14 final size:14
Alignment explanation
Indices: 31126558--31126603 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
31126548 TAAAATTAAA
31126558 AAAATATAAAAATT
1 AAAATATAAAAATT
31126572 AAAAT-TAACTAAATT
1 AAAATATAA--AAATT
*
31126587 AATATATAAAAATT
1 AAAATATAAAAATT
31126601 AAA
1 AAA
31126604 TCTGCAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 12 0.44
15 9 0.33
16 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:31126585 original size:23 final size:22
Alignment explanation
Indices: 31126538--31126603 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
31126528 TTAAGTTGTG
31126538 ATTAAAAATTTAAAATTAAAAAA
1 ATTAAAAA-TTAAAATTAAAAAA
**
31126561 ATATAAAAATTAAAATTAACTAA
1 AT-TAAAAATTAAAATTAAAAAA
* *
31126584 ATTAATATATAAAAATTAAA
1 ATTAA-AAATTAAAATTAAA
31126604 TCTGCAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 3 0.08
23 27 0.75
24 6 0.17
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTAAAAATTAAAATTAAAAAA
Found at i:31141156 original size:19 final size:19
Alignment explanation
Indices: 31141132--31141174 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
31141122 AAACATAAAT
31141132 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
31141151 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
31141170 TAAAT
1 TAAAT
31141175 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:31142734 original size:27 final size:28
Alignment explanation
Indices: 31142704--31142758 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 28
31142694 GAACCCAAAT
* * *
31142704 AATATACTCATTATTACCCAAA-CTCAA
1 AATAAACTAATTATAACCCAAATCTCAA
*
31142731 AATAAACTAATTATAACCTAAATCTCAA
1 AATAAACTAATTATAACCCAAATCTCAA
31142759 GTCCAAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 18 0.78
28 5 0.22
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (28 bp):
AATAAACTAATTATAACCCAAATCTCAA
Found at i:31143247 original size:37 final size:38
Alignment explanation
Indices: 31143179--31143288 Score: 102
Period size: 37 Copynumber: 2.9 Consensus size: 38
31143169 ATATAATATA
* *
31143179 TAATATATTA-ATAGTTTTTATATATATTATAATATCAT-G
1 TAATACATTATATA-TTATTATAT-TA-TATAATATCATAG
* * *
31143218 TAATAC-TATATGTTTTATTATATTATATAATATAATAG
1 TAATACAT-TATATATTATTATATTATATAATATCATAG
*
31143256 TAATACATTATATATTAAT-TATTATATAATATC
1 TAATACATTATATATTATTATATTATATAATATC
31143289 CTTTATAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
37 23 0.40
38 18 0.31
39 16 0.28
40 1 0.02
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (38 bp):
TAATACATTATATATTATTATATTATATAATATCATAG
Found at i:31151646 original size:101 final size:101
Alignment explanation
Indices: 31151468--31151666 Score: 389
Period size: 101 Copynumber: 2.0 Consensus size: 101
31151458 TCTGTTTTAC
31151468 TACAGTTTTATCGGGTGATATTCAATCTAATTAAAATGGAAAACTTGAAATTAATTGGAAATGGA
1 TACAGTTTTATCGGGTGATATTCAATCTAATTAAAATGGAAAACTTGAAATTAATTGGAAATGGA
*
31151533 TTGGTATCCTTCTAACTTGATATGTGTTATGTGATT
66 TTGGTATACTTCTAACTTGATATGTGTTATGTGATT
31151569 TACAGTTTTATCGGGTGATATTCAATCTAATTAAAATGGAAAACTTGAAATTAATTGGAAATGGA
1 TACAGTTTTATCGGGTGATATTCAATCTAATTAAAATGGAAAACTTGAAATTAATTGGAAATGGA
31151634 TTGGTATACTTCTAACTTGATATGTGTTATGTG
66 TTGGTATACTTCTAACTTGATATGTGTTATGTG
31151667 TATTGTTCAT
Statistics
Matches: 97, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (101 bp):
TACAGTTTTATCGGGTGATATTCAATCTAATTAAAATGGAAAACTTGAAATTAATTGGAAATGGA
TTGGTATACTTCTAACTTGATATGTGTTATGTGATT
Found at i:31169435 original size:9 final size:9
Alignment explanation
Indices: 31169421--31169445 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
31169411 AACTCTGATC
31169421 CAAGAAAAT
1 CAAGAAAAT
31169430 CAAGAAAAT
1 CAAGAAAAT
31169439 CAAGAAA
1 CAAGAAA
31169446 CCTTGCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.08
Consensus pattern (9 bp):
CAAGAAAAT
Found at i:31170238 original size:25 final size:25
Alignment explanation
Indices: 31170204--31170253 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
31170194 TGCTTGCTGG
31170204 TTCAGTGCAACAACAGCCACAACAA
1 TTCAGTGCAACAACAGCCACAACAA
*
31170229 TTCAGTGCAAGAACAGCCACAACAA
1 TTCAGTGCAACAACAGCCACAACAA
31170254 AGAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.30, G:0.14, T:0.12
Consensus pattern (25 bp):
TTCAGTGCAACAACAGCCACAACAA
Found at i:31170496 original size:58 final size:58
Alignment explanation
Indices: 31170432--31170550 Score: 166
Period size: 58 Copynumber: 2.1 Consensus size: 58
31170422 AAAAGAGCTA
* **
31170432 TTTATGAGTGTTATTTAGGAATAAAATTATATTTAGATTTAAAAATATTTGGGTTTAG
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTGAATTTAG
* * * * *
31170490 TTTATGAGTGTTTTTTAATAATGAAATTATATTTGGGTTTAAAAATATTTGAATTTAG
1 TTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTGAATTTAG
31170548 TTT
1 TTT
31170551 GTTGATGGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (58 bp):
TTTATGAGTGTTATTTAAGAATAAAATTATATTTAGATTTAAAAATATTTGAATTTAG
Found at i:31170564 original size:58 final size:58
Alignment explanation
Indices: 31170455--31170565 Score: 143
Period size: 58 Copynumber: 1.9 Consensus size: 58
31170445 TTTAGGAATA
** **
31170455 AAATTATATTTAGATTTAAAAATATTTGGGTTTAGTTTATGAGTGTTTTTTAATAATG
1 AAATTATATTTAGATTTAAAAATATTTGAATTTAGTTTATGAGTGGGTTTTAATAATG
* * *
31170513 AAATTATATTTGGGTTTAAAAATATTTGAATTTAGTTTGTTGA-TGGGTTTTAA
1 AAATTATATTTAGATTTAAAAATATTTGAATTTAGTTT-ATGAGTGGGTTTTAA
31170566 ATATTAGGGG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 42 0.93
59 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (58 bp):
AAATTATATTTAGATTTAAAAATATTTGAATTTAGTTTATGAGTGGGTTTTAATAATG
Found at i:31173672 original size:41 final size:41
Alignment explanation
Indices: 31173612--31173694 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
31173602 TGAAAGTTTA
* *
31173612 AAACTTATGAAGACGCTGACGAGGGACTCTTGCATCAACCT
1 AAACTTATGAAAACACTGACGAGGGACTCTTGCATCAACCT
31173653 AAACTTATGAAAACACTGACGAGGGACTCTTGCATCAACCT
1 AAACTTATGAAAACACTGACGAGGGACTCTTGCATCAACCT
31173694 A
1 A
31173695 TATAAATAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (41 bp):
AAACTTATGAAAACACTGACGAGGGACTCTTGCATCAACCT
Found at i:31181594 original size:21 final size:20
Alignment explanation
Indices: 31181560--31181601 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
31181550 TAAATGAATT
31181560 ATAAAATTAAAATATATTAA
1 ATAAAATTAAAATATATTAA
*
31181580 ATAATAATTACAATATATTAA
1 ATAA-AATTAAAATATATTAA
31181601 A
1 A
31181602 ATTACATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAAAATTAAAATATATTAA
Found at i:31181631 original size:29 final size:27
Alignment explanation
Indices: 31181591--31181655 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
31181581 TAATAATTAC
* * *
31181591 AATATATTAAAATTACATTTATGTTAAA
1 AATAT-TTAAAATAAAATTTATATTAAA
31181619 TAATATTTCAAAATAAAATTTATATTAAA
1 -AATATTT-AAAATAAAATTTATATTAAA
31181648 ACATATTT
1 A-ATATTT
31181656 TTGTTGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 3 0.10
29 28 0.90
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (27 bp):
AATATTTAAAATAAAATTTATATTAAA
Found at i:31182684 original size:22 final size:22
Alignment explanation
Indices: 31182640--31182684 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
31182630 TATATTTTAA
*
31182640 TTTTTTTTTTATAATTTGATATT
1 TTTTTTTTTTATAATAT-ATATT
31182663 TTTTATTTTTTATAATAT-TATT
1 TTTT-TTTTTTATAATATATATT
31182685 ACTCAAGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 4 0.20
24 12 0.60
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (22 bp):
TTTTTTTTTTATAATATATATT
Found at i:31191051 original size:19 final size:18
Alignment explanation
Indices: 31191027--31191080 Score: 60
Period size: 17 Copynumber: 3.0 Consensus size: 18
31191017 GTTTGATCAA
31191027 ATAAAATATTAAAAAAATT
1 ATAAAATA-TAAAAAAATT
31191046 ATAAAATA-AAAAAATATT
1 ATAAAATATAAAAAA-ATT
31191064 -TAAAA-ATAGAAAAAATT
1 ATAAAATATA-AAAAAATT
31191081 GATTCAATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 1 0.03
17 15 0.47
18 8 0.25
19 8 0.25
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (18 bp):
ATAAAATATAAAAAAATT
Found at i:31191069 original size:18 final size:16
Alignment explanation
Indices: 31191036--31191080 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
31191026 AATAAAATAT
31191036 TAAAAAAATTATAAAA
1 TAAAAAAATTATAAAA
*
31191052 TAAAAAAATATTTAAAAA
1 TAAAAAAAT-TAT-AAAA
31191070 TAGAAAAAATT
1 TA-AAAAAATT
31191081 GATTCAATCG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 9 0.36
17 2 0.08
18 7 0.28
19 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
TAAAAAAATTATAAAA
Found at i:31205514 original size:2 final size:2
Alignment explanation
Indices: 31205507--31205541 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
31205497 TTCTTCTTTA
31205507 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31205542 GCCCAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:31205685 original size:5 final size:5
Alignment explanation
Indices: 31205675--31205702 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
31205665 ATTCCATGCT
31205675 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTT
31205703 CAACTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:31206957 original size:30 final size:30
Alignment explanation
Indices: 31206921--31206994 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 30
31206911 AATAGCTTAT
*
31206921 ATTTTTATAATTTTTA-AATGATTAAATTAA
1 ATTTTTATAATTTTTATAA-AATTAAATTAA
* **
31206951 ATTTTTATTATTTTTATAAAATTAAATTTT
1 ATTTTTATAATTTTTATAAAATTAAATTAA
31206981 ATTTTTATCAATTT
1 ATTTTTAT-AATTT
31206995 AAAATTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 31 0.84
31 6 0.16
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
ATTTTTATAATTTTTATAAAATTAAATTAA
Found at i:31206984 original size:21 final size:22
Alignment explanation
Indices: 31206958--31207002 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
31206948 TAAATTTTTA
31206958 TTATTTTTATAAAATT-AAATT
1 TTATTTTTATAAAATTAAAATT
* *
31206979 TTATTTTTATCAATTTAAAATT
1 TTATTTTTATAAAATTAAAATT
31207001 TT
1 TT
31207003 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATTTTTATAAAATTAAAATT
Found at i:31207356 original size:20 final size:20
Alignment explanation
Indices: 31207333--31207372 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31207323 AAACAATTAT
*
31207333 TATAAATTGTAATTTAAATA
1 TATAAATTATAATTTAAATA
*
31207353 TATAAATTATATTTTAAATA
1 TATAAATTATAATTTAAATA
31207373 AGGGTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (20 bp):
TATAAATTATAATTTAAATA
Found at i:31212106 original size:23 final size:21
Alignment explanation
Indices: 31212083--31212121 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
31212073 AGATTATTAT
31212083 TATTATT-TTAAATATAATAA
1 TATTATTATTAAATATAATAA
31212103 TATTATTATTAAATATAAT
1 TATTATTATTAAATATAAT
31212122 TTAATAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTATTATTAAATATAATAA
Found at i:31212189 original size:24 final size:23
Alignment explanation
Indices: 31212168--31212229 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 23
31212158 TAATATAATT
31212168 ATTATTAAATATAATTTAATAAA
1 ATTATTAAATATAATTTAATAAA
* *
31212191 AATA-TAAATATAAAATTTAATAAC
1 ATTATTAAATAT--AATTTAATAAA
31212215 ATTATT-AATATAATT
1 ATTATTAAATATAATT
31212230 ATTTTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 11 0.33
23 3 0.09
24 18 0.55
25 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTATTAAATATAATTTAATAAA
Found at i:31212192 original size:61 final size:62
Alignment explanation
Indices: 31212104--31212232 Score: 183
Period size: 61 Copynumber: 2.1 Consensus size: 62
31212094 ATATAATAAT
* *
31212104 ATTATTATTAAATATAATTTAATAAAAAAGAT-AATA-AATAACTTAATTATATT-TTAATATA
1 ATTATTATTAAATATAATTTAAT-AAAAAGATAAATATAA-AACTTAATAACATTATTAATATA
* *
31212165 ATTATTATTAAATATAATTTAATAAAAATATAAATATAAAATTTAATAACATTATTAATATA
1 ATTATTATTAAATATAATTTAATAAAAAGATAAATATAAAACTTAATAACATTATTAATATA
31212227 ATTATT
1 ATTATT
31212233 TTTATATTAA
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
60 7 0.11
61 38 0.62
62 16 0.26
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (62 bp):
ATTATTATTAAATATAATTTAATAAAAAGATAAATATAAAACTTAATAACATTATTAATATA
Found at i:31212775 original size:19 final size:20
Alignment explanation
Indices: 31212739--31212778 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
31212729 ATCATATTTC
*
31212739 AAAATTTTATAATACCACTA
1 AAAATATTATAATACCACTA
*
31212759 AAAATATTA-AATTCCACTA
1 AAAATATTATAATACCACTA
31212778 A
1 A
31212779 TCAAATAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATATTATAATACCACTA
Found at i:31213677 original size:58 final size:59
Alignment explanation
Indices: 31213573--31213688 Score: 157
Period size: 57 Copynumber: 2.0 Consensus size: 59
31213563 CTCATTTTGA
* *
31213573 TACCTGAACTAGATTTCAAGGTTCAAATTGATACTTAAGA-TTTTTTTGCCCAATTAGG
1 TACCTAAAATAGATTTCAAGGTTCAAATTGATACTTAAGATTTTTTTTGCCCAATTAGG
* *
31213631 TACCTAAAATAGA-TTCAAGGTTCAAATTGGTACTTAA-ACCTTTTTTTTGTCCAATTAG
1 TACCTAAAATAGATTTCAAGGTTCAAATTGATACTTAAGA--TTTTTTTTGCCCAATTAG
31213689 ATACTTGAAC
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
56 1 0.02
57 23 0.45
58 11 0.22
59 16 0.31
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (59 bp):
TACCTAAAATAGATTTCAAGGTTCAAATTGATACTTAAGATTTTTTTTGCCCAATTAGG
Found at i:31219824 original size:23 final size:23
Alignment explanation
Indices: 31219789--31219840 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
31219779 ATCATTACTT
31219789 ATTAAATTATTGATAATTAAAAA
1 ATTAAATTATTGATAATTAAAAA
* *
31219812 ATTATAATT-TTGATCATTAAAAT
1 ATTA-AATTATTGATAATTAAAAA
31219835 ATTAAA
1 ATTAAA
31219841 AAAATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 2 0.08
23 20 0.77
24 4 0.15
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (23 bp):
ATTAAATTATTGATAATTAAAAA
Found at i:31221833 original size:13 final size:14
Alignment explanation
Indices: 31221815--31221867 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
31221805 TTTCACGAGT
31221815 TAAAAAATAAT-TA
1 TAAAAAATAATATA
*
31221828 TAAAAAGTAATGATA
1 TAAAAAATAAT-ATA
*
31221843 TTAAAAATAAGTAATA
1 TAAAAAATAA-T-ATA
31221859 TAAAAAATA
1 TAAAAAATA
31221868 TGCAATATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 10 0.31
15 10 0.31
16 12 0.38
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (14 bp):
TAAAAAATAATATA
Found at i:31228970 original size:6 final size:6
Alignment explanation
Indices: 31228959--31228987 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
31228949 ACGAAAGCAA
31228959 AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
1 AGGCAG AGGCAG AGGCAG AGGCAG AGGCA
31228988 AAGCATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.17, G:0.48, T:0.00
Consensus pattern (6 bp):
AGGCAG
Found at i:31231989 original size:32 final size:32
Alignment explanation
Indices: 31231929--31231990 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
31231919 ATAAAAAATC
*
31231929 AATCTAGACAAATGATTGTTCGGGTTCATTTG
1 AATCTAGACAAATGATTGTTCGGATTCATTTG
* *
31231961 AATCTAGACAATTGTTTGTCTC-GATTCATT
1 AATCTAGACAAATGATTGT-TCGGATTCATT
31231991 CAAGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (32 bp):
AATCTAGACAAATGATTGTTCGGATTCATTTG
Found at i:31233135 original size:22 final size:22
Alignment explanation
Indices: 31233104--31233148 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31233094 TGTGCAAATG
*
31233104 TAAATTCAAAATTAAGATATAA
1 TAAATCCAAAATTAAGATATAA
* *
31233126 TAAATCCAAAATTAGGATTTAA
1 TAAATCCAAAATTAAGATATAA
31233148 T
1 T
31233149 CTTTTTAGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
TAAATCCAAAATTAAGATATAA
Found at i:31233750 original size:12 final size:12
Alignment explanation
Indices: 31233715--31233804 Score: 92
Period size: 12 Copynumber: 7.6 Consensus size: 12
31233705 ATAACATCCA
*
31233715 AACAACCAAAAT
1 AACAACAAAAAT
* *
31233727 AGCAGC-AAAAT
1 AACAACAAAAAT
*
31233738 AATAACAAAAAT
1 AACAACAAAAAT
* * *
31233750 AGCAATAAAAAC
1 AACAACAAAAAT
31233762 AACAACAAAAAT
1 AACAACAAAAAT
* *
31233774 AACAGCAAAAAC
1 AACAACAAAAAT
31233786 AACAACAAAAAT
1 AACAACAAAAAT
31233798 AACAACA
1 AACAACA
31233805 TCAAAACAGT
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
11 8 0.13
12 53 0.87
ACGTcount: A:0.69, C:0.19, G:0.04, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:31233768 original size:24 final size:24
Alignment explanation
Indices: 31233715--31233826 Score: 102
Period size: 24 Copynumber: 4.7 Consensus size: 24
31233705 ATAACATCCA
* * *
31233715 AACAACCAAAATAGCAGC-AAAAT
1 AACAACAAAAATAGCAACAAAAAC
* *
31233738 AATAACAAAAATAGCAATAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
* *
31233762 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
*
31233786 AACAACAAAAATAACAACATCAAAAC
1 AACAACAAAAATAGCAACA--AAAAC
**
31233812 AGTAA-AAAAATAGCA
1 AACAACAAAAATAGCA
31233827 CCGAAACAAC
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
23 14 0.19
24 42 0.58
25 9 0.12
26 8 0.11
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:31233775 original size:36 final size:37
Alignment explanation
Indices: 31233732--31233826 Score: 95
Period size: 36 Copynumber: 2.6 Consensus size: 37
31233722 AAAATAGCAG
*
31233732 CAAAATAATAACAAAAATAGCAATAAAAACAACAACA
1 CAAAATAATAACAAAAATAGCAACAAAAACAACAACA
* * * * *
31233769 -AAAATAACAGCAAAAACAACAACAAAAATAACAACA
1 CAAAATAATAACAAAAATAGCAACAAAAACAACAACA
* *
31233805 TCAAAACAGTAA-AAAAATAGCA
1 -CAAAATAATAACAAAAATAGCA
31233827 CCGAAACAAC
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
36 30 0.68
37 8 0.18
38 6 0.14
ACGTcount: A:0.69, C:0.17, G:0.04, T:0.09
Consensus pattern (37 bp):
CAAAATAATAACAAAAATAGCAACAAAAACAACAACA
Found at i:31233789 original size:27 final size:26
Alignment explanation
Indices: 31233750--31233810 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
31233740 TAACAAAAAT
*
31233750 AGCAATAAAAACAACAACAAA-AATAAC
1 AGCAA-AAAAACAACAA-AAATAACAAC
31233777 AGCAAAAACAACAACAAAAATAACAAC
1 AGCAAAAA-AACAACAAAAATAACAAC
*
31233804 ATCAAAA
1 AGCAAAA
31233811 CAGTAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.70, C:0.20, G:0.03, T:0.07
Consensus pattern (26 bp):
AGCAAAAAAACAACAAAAATAACAAC
Found at i:31237625 original size:16 final size:14
Alignment explanation
Indices: 31237598--31237641 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 14
31237588 TATTTCAACA
31237598 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
31237612 AAAAAATCTCAAAAAT
1 AAAAAAT-T-AAAAAT
*
31237628 AAATAATTATAAAA
1 AAAAAATTA-AAAA
31237642 AATTAAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.31
15 6 0.23
16 12 0.46
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Found at i:31238157 original size:7 final size:8
Alignment explanation
Indices: 31238139--31238185 Score: 51
Period size: 8 Copynumber: 5.6 Consensus size: 8
31238129 TAGATGTTGT
31238139 TTTTAATAA
1 TTTT-ATAA
31238148 TTTT-TAA
1 TTTTATAA
*
31238155 TTTTATTA
1 TTTTATAA
31238163 TTTTATAA
1 TTTTATAA
31238171 TTCTTAATAA
1 TT-TT-ATAA
31238181 TTTTA
1 TTTTA
31238186 AATAATTCTC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
7 7 0.21
8 12 0.36
9 8 0.24
10 6 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:31246439 original size:2 final size:2
Alignment explanation
Indices: 31246432--31246457 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31246422 TACTGGCATA
31246432 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
31246458 GAAAAAGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31251431 original size:22 final size:22
Alignment explanation
Indices: 31251379--31251459 Score: 117
Period size: 23 Copynumber: 3.6 Consensus size: 22
31251369 GCTGGGGAAA
*
31251379 CAGTAAGCACACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
31251401 CTAGTAGGCACACACAGTGCAAT
1 C-AGTAGGCACACACAGTGCAAT
* *
31251424 CAGTAGGCGCACATAGTGCAAAT
1 CAGTAGGCACACACAGTGC-AAT
31251447 CAGTAGGCACACA
1 CAGTAGGCACACA
31251460 AGGTACGAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 17 0.32
23 36 0.68
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:31251501 original size:23 final size:23
Alignment explanation
Indices: 31251475--31251551 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
31251465 CGAAACAGTA
31251475 AGCACATAAAGTGCTAATCAGAG
1 AGCACATAAAGTGCTAATCAGAG
*
31251498 AGCACATGAAGTGCTAATAACAGAG
1 AGCACATAAAGTGCTAAT--CAGAG
* *
31251523 AGCACGA-AACGTGCTAAACAGAG
1 AGCAC-ATAAAGTGCTAATCAGAG
31251546 AGCACA
1 AGCACA
31251552 CACAATGCTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
22 1 0.02
23 27 0.57
25 18 0.38
26 1 0.02
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (23 bp):
AGCACATAAAGTGCTAATCAGAG
Found at i:31254561 original size:18 final size:16
Alignment explanation
Indices: 31254529--31254564 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
31254519 ATGGAATGAG
31254529 AATAAATTTTTAATTA
1 AATAAATTTTTAATTA
31254545 AATAAATTTAATTAATTA
1 AATAAATTT--TTAATTA
31254563 AA
1 AA
31254565 AATTTTAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AATAAATTTTTAATTA
Found at i:31255793 original size:29 final size:29
Alignment explanation
Indices: 31255753--31255818 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
31255743 CAGTTATACT
*
31255753 TGGTGGAAACTTAATGTTGACTCTTGAGG
1 TGGTGGAAACTTAATGTTGACTCCTGAGG
31255782 TGGTGGAAACTTAATGTTGACTCCTGAGG
1 TGGTGGAAACTTAATGTTGACTCCTGAGG
*
31255811 TGGAGGAA
1 TGGTGGAA
31255819 TTTAATAAGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.26, C:0.11, G:0.33, T:0.30
Consensus pattern (29 bp):
TGGTGGAAACTTAATGTTGACTCCTGAGG
Found at i:31257170 original size:6 final size:6
Alignment explanation
Indices: 31257159--31257183 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31257149 AATTAATTAC
31257159 ATTTGG ATTTGG ATTTGG ATTTGG A
1 ATTTGG ATTTGG ATTTGG ATTTGG A
31257184 GGAACATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (6 bp):
ATTTGG
Found at i:31269861 original size:30 final size:29
Alignment explanation
Indices: 31269770--31269896 Score: 119
Period size: 30 Copynumber: 4.3 Consensus size: 29
31269760 TAGAGGCCCA
* * * **
31269770 AACCATCCATCTCTTTCCTCAAATCAAAA
1 AACCATCCACCTCTTCCCCCAAATCAAGG
** * * * *
31269799 AACCATTTATCTCTTCTCCCAAAACAATG
1 AACCATCCACCTCTTCCCCCAAATCAAGG
31269828 AACCATCCACCTCTTTCCCCCAAATCAAGG
1 AACCATCCACCTC-TTCCCCCAAATCAAGG
* *
31269858 AACCGTCCACCTCTTCCCCTAAAATCAAGG
1 AACCATCCACCTCTTCCCC-CAAATCAAGG
31269888 AACCATCCA
1 AACCATCCA
31269897 ACTACATGGA
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
29 37 0.47
30 42 0.53
ACGTcount: A:0.34, C:0.38, G:0.05, T:0.24
Consensus pattern (29 bp):
AACCATCCACCTCTTCCCCCAAATCAAGG
Found at i:31273466 original size:17 final size:19
Alignment explanation
Indices: 31273427--31273467 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
31273417 GTTTATAACT
*
31273427 AAATTTGATATATATGAAG
1 AAATTTGATATATATGAAA
*
31273446 AAATTTTATATA-AT-AAA
1 AAATTTGATATATATGAAA
31273463 AAATT
1 AAATT
31273468 GTAGGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 7 0.35
18 2 0.10
19 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (19 bp):
AAATTTGATATATATGAAA
Found at i:31276186 original size:14 final size:15
Alignment explanation
Indices: 31276158--31276186 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31276148 TTGAAAGAGT
31276158 TTTCAAATATATATG
1 TTTCAAATATATATG
31276173 TTTCAAAT-TATATG
1 TTTCAAATATATATG
31276187 CTTTAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TTTCAAATATATATG
Found at i:31276301 original size:16 final size:16
Alignment explanation
Indices: 31276260--31276301 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
31276250 AACTAAAACA
31276260 ATTTCACTCG-ATTCC
1 ATTTCACTCGAATTCC
* * *
31276275 ACTTGACTCGAATTTC
1 ATTTCACTCGAATTCC
31276291 ATTTCACTCGA
1 ATTTCACTCGA
31276302 TTTGATATGA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (16 bp):
ATTTCACTCGAATTCC
Found at i:31289574 original size:10 final size:10
Alignment explanation
Indices: 31289559--31289589 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
31289549 CTGGGGACTG
31289559 GGTCGGGCTA
1 GGTCGGGCTA
31289569 GGTCGGGCTA
1 GGTCGGGCTA
31289579 GGTCGGGCTA
1 GGTCGGGCTA
31289589 G
1 G
31289590 AAATATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.10, C:0.19, G:0.52, T:0.19
Consensus pattern (10 bp):
GGTCGGGCTA
Found at i:31289960 original size:21 final size:21
Alignment explanation
Indices: 31289914--31289977 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
31289904 TATATTAATT
*
31289914 TTAGTTCGAAT-TATTTTGATTA
1 TTAGTTCGATTCTATTTT-A-TA
* *
31289936 TTAGTTCGTTTGTATTTTATA
1 TTAGTTCGATTCTATTTTATA
*
31289957 TTAGTTTGATTCTATTTTATA
1 TTAGTTCGATTCTATTTTATA
31289978 ATCATTCGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 20 0.56
22 10 0.28
23 6 0.17
ACGTcount: A:0.23, C:0.05, G:0.12, T:0.59
Consensus pattern (21 bp):
TTAGTTCGATTCTATTTTATA
Found at i:31293953 original size:4 final size:4
Alignment explanation
Indices: 31293944--31293968 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31293934 TCACCACATT
31293944 CATG CATG CATG CATG CATG CATG C
1 CATG CATG CATG CATG CATG CATG C
31293969 TTATGGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (4 bp):
CATG
Found at i:31314288 original size:3 final size:3
Alignment explanation
Indices: 31314280--31314309 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31314270 TGTTATGCAA
31314280 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31314310 TTCTAAAGGT
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):
AAT
Found at i:31330888 original size:24 final size:24
Alignment explanation
Indices: 31330861--31330910 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
31330851 TTTACCTCCT
31330861 CCATGCTTTCCGTGCTTAAATTTC
1 CCATGCTTTCCGTGCTTAAATTTC
*
31330885 CCATGCTTTCCGTGCTTGAATTTC
1 CCATGCTTTCCGTGCTTAAATTTC
31330909 CC
1 CC
31330911 CCCATGATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.14, C:0.32, G:0.14, T:0.40
Consensus pattern (24 bp):
CCATGCTTTCCGTGCTTAAATTTC
Found at i:31330930 original size:21 final size:22
Alignment explanation
Indices: 31330897--31330955 Score: 57
Period size: 24 Copynumber: 2.6 Consensus size: 22
31330887 ATGCTTTCCG
* *
31330897 TGCTTGAATTTCCCC-CCATGA
1 TGCTTAAACTTCCCCACCATGA
31330918 TGCTTAAACTTCCCACCACCATGA
1 TGCTTAAACTT-CC-CCACCATGA
* *
31330942 TGTTTCAACTTCCC
1 TGCTTAAACTTCCC
31330956 ATGGTGACCA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 9 0.29
22 3 0.10
23 4 0.13
24 15 0.48
ACGTcount: A:0.22, C:0.36, G:0.10, T:0.32
Consensus pattern (22 bp):
TGCTTAAACTTCCCCACCATGA
Found at i:31330992 original size:18 final size:18
Alignment explanation
Indices: 31330969--31331017 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
31330959 GTGACCAAAT
31330969 CCATGAGCACCATAAGCA
1 CCATGAGCACCATAAGCA
*
31330987 CCATGACCACCATAAGCA
1 CCATGAGCACCATAAGCA
* *
31331005 CCGTGAGAACCAT
1 CCATGAGCACCAT
31331018 GAGACACGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.37, C:0.35, G:0.16, T:0.12
Consensus pattern (18 bp):
CCATGAGCACCATAAGCA
Found at i:31331021 original size:9 final size:9
Alignment explanation
Indices: 31330969--31331020 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
31330959 GTGACCAAAT
31330969 CCATGAGCA
1 CCATGAGCA
*
31330978 CCATAAGCA
1 CCATGAGCA
*
31330987 CCATGACCA
1 CCATGAGCA
*
31330996 CCATAAGCA
1 CCATGAGCA
* *
31331005 CCGTGAGAA
1 CCATGAGCA
31331014 CCATGAG
1 CCATGAG
31331021 ACACGTGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.37, C:0.33, G:0.19, T:0.12
Consensus pattern (9 bp):
CCATGAGCA
Found at i:31331232 original size:15 final size:15
Alignment explanation
Indices: 31331212--31331249 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
31331202 GGATGCACCA
31331212 GGATAGCCAGATGGT
1 GGATAGCCAGATGGT
*
31331227 GGATAGCCAGATTGT
1 GGATAGCCAGATGGT
31331242 GGATAGCC
1 GGATAGCC
31331250 GTGAGGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.16, G:0.37, T:0.21
Consensus pattern (15 bp):
GGATAGCCAGATGGT
Found at i:31335286 original size:3 final size:3
Alignment explanation
Indices: 31335278--31335305 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31335268 GACGACATGG
31335278 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT C
31335306 CACTCAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:31345290 original size:57 final size:58
Alignment explanation
Indices: 31345246--31345368 Score: 155
Period size: 58 Copynumber: 2.2 Consensus size: 58
31345236 TAGGATTGTA
* * *
31345246 AAATTAAATA-AA-TTAAAACGAAATTAATTTTAAAAATCAAAATTAATTAAAGAAAT
1 AAATGAAATACAATTTAAAACAAAATTAATTTTAAAAATCAAAATTAAATAAAGAAAT
* * *
31345302 AAATGAATTACAATTTAAAATAAAATTAATTTTAAAAATCAAAATTAAATTTAA-AAAT
1 AAATGAAATACAATTTAAAACAAAATTAATTTTAAAAATCAAAATTAAA-TAAAGAAAT
31345360 AAA-GAAATA
1 AAATGAAATA
31345369 AGTTAATTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
56 8 0.14
57 7 0.12
58 39 0.68
59 3 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (58 bp):
AAATGAAATACAATTTAAAACAAAATTAATTTTAAAAATCAAAATTAAATAAAGAAAT
Found at i:31345295 original size:17 final size:19
Alignment explanation
Indices: 31345266--31345359 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
31345256 AATTAAAACG
*
31345266 AAATTAATTTTAAAAATCA
1 AAATTAAATTTAAAAATCA
* *
31345285 AAATT-AATTAAAGAAATAA
1 AAATTAAATTTAA-AAATCA
31345304 ATGAATTACAATTT-AAAAT-A
1 A--AATTA-AATTTAAAAATCA
*
31345324 AAATTAATTTTAAAAATCA
1 AAATTAAATTTAAAAATCA
31345343 AAATTAAATTTAAAAAT
1 AAATTAAATTTAAAAAT
31345360 AAAGAAATAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
17 4 0.06
18 15 0.24
19 28 0.45
20 2 0.03
21 8 0.13
22 1 0.02
23 4 0.06
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAATTAAATTTAAAAATCA
Found at i:31345405 original size:66 final size:65
Alignment explanation
Indices: 31345293--31345423 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 65
31345283 CAAAATTAAT
* ** *
31345293 TAAAGAAATAAATGAATTACAATTTAAAATAAAATTAAT-TTTAAAAATCAAAATTAAATTTAAA
1 TAAAGAAATAAATGAATTAAAATTTAAAATAAAATTAATATAAAAAAAT--AAATTAAAATTAAA
31345357 AA
64 AA
* * * *
31345359 TAAAGAAATAAGTTAATTAAAATTTAAAATAAATTTTATATAAAAAAATAAATTAAAATTAAAAA
1 TAAAGAAATAAATGAATTAAAATTTAAAATAAAATTAATATAAAAAAATAAATTAAAATTAAAAA
31345424 AACTTGACAT
Statistics
Matches: 56, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
65 15 0.27
66 34 0.61
67 7 0.12
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (65 bp):
TAAAGAAATAAATGAATTAAAATTTAAAATAAAATTAATATAAAAAAATAAATTAAAATTAAAAA
Found at i:31345777 original size:143 final size:143
Alignment explanation
Indices: 31345513--31345794 Score: 377
Period size: 143 Copynumber: 2.0 Consensus size: 143
31345503 TCTGATAAAG
* * * *
31345513 GGGTGTCGATCATCAGTGTGCCATCACTCTCAAATTTTTTTCAAGTACTAGTATAAACGTATACT
1 GGGTGTCGACCATCAGTGTGCCATCACCCTCAAATTTTTTTCAAGTACTAGTATAAACATATACC
* * * * * * *
31345578 AGTATGATACGAGTTGAAAAAAATATAAAAGTGTCGACTATTTAACCCCCAGCACCCAAAAAATT
66 AGCATGATACAAATAGAAAAAAATACAAAAGTGCCGACTATTTAACCCCCAACACCCAAAAAATT
31345643 ATTTTTTTAAAAA
131 ATTTTTTTAAAAA
*
31345656 GGGTGTCGGCCATCAGTGTGCCATCACCCTCAAATTTTTTTCAAGTACT-GATATAAACATATAC
1 GGGTGTCGACCATCAGTGTGCCATCACCCTCAAATTTTTTTCAAGTACTAG-TATAAACATATAC
* ** * * **
31345720 CAGCATGATACAAATAGAAAAAATTACAAGGGTGCCTACTATTTAATCTTCAACACCCAAAAAAT
65 CAGCATGATACAAATAGAAAAAAATACAAAAGTGCCGACTATTTAACCCCCAACACCCAAAAAAT
31345785 TATTTTTTTA
130 TATTTTTTTA
31345795 CCTAATGACA
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
142 1 0.01
143 118 0.99
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (143 bp):
GGGTGTCGACCATCAGTGTGCCATCACCCTCAAATTTTTTTCAAGTACTAGTATAAACATATACC
AGCATGATACAAATAGAAAAAAATACAAAAGTGCCGACTATTTAACCCCCAACACCCAAAAAATT
ATTTTTTTAAAAA
Found at i:31352639 original size:6 final size:6
Alignment explanation
Indices: 31352622--31352659 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
31352612 CTCTGAGCTA
31352622 GGGCAT -GGCAT GGGCAT GGGCAT GGGCAT GGGCAT GGG
1 GGGCAT GGGCAT GGGCAT GGGCAT GGGCAT GGGCAT GGG
31352660 TGTGGAGCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.16, C:0.16, G:0.53, T:0.16
Consensus pattern (6 bp):
GGGCAT
Found at i:31353160 original size:18 final size:20
Alignment explanation
Indices: 31353137--31353174 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
31353127 ACGTGACAGT
31353137 CCAAC-TAGATTTT-AAATG
1 CCAACTTAGATTTTCAAATG
*
31353155 CCAACTTGGATTTTCAAATG
1 CCAACTTAGATTTTCAAATG
31353175 GGATGAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 7 0.41
20 5 0.29
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (20 bp):
CCAACTTAGATTTTCAAATG
Found at i:31355029 original size:18 final size:17
Alignment explanation
Indices: 31355008--31355043 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
31354998 ATAATATTTT
31355008 AATATAAATTAATTTAAA
1 AATATAAATTAA-TTAAA
*
31355026 AATATAATTTAATTAAA
1 AATATAAATTAATTAAA
31355043 A
1 A
31355044 GAGATGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATATAAATTAATTAAA
Found at i:31355761 original size:20 final size:20
Alignment explanation
Indices: 31355736--31355776 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
31355726 AAGTATCATG
31355736 TATTTTAGAATTTAAAATAA
1 TATTTTAGAATTTAAAATAA
* *
31355756 TATTTTATATTTTAAAATAA
1 TATTTTAGAATTTAAAATAA
31355776 T
1 T
31355777 TATTAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TATTTTAGAATTTAAAATAA
Found at i:31355786 original size:19 final size:20
Alignment explanation
Indices: 31355740--31355787 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
31355730 ATCATGTATT
* *
31355740 TTAGAATTTAAAATAATATT
1 TTAGATTTTAAAATAATATA
*
31355760 TTATATTTTAAAATAAT-TA
1 TTAGATTTTAAAATAATATA
31355779 TTAGATTTT
1 TTAGATTTT
31355788 TTTTATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTAGATTTTAAAATAATATA
Found at i:31361605 original size:22 final size:22
Alignment explanation
Indices: 31361580--31361626 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
31361570 AAAGAAAATT
31361580 TCACCAACCAAGGAAAAAAAAG
1 TCACCAACCAAGGAAAAAAAAG
* *
31361602 TCACCAACCTAGGGAAAAAAAG
1 TCACCAACCAAGGAAAAAAAAG
31361624 TCA
1 TCA
31361627 AGAAACGGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.23, G:0.15, T:0.09
Consensus pattern (22 bp):
TCACCAACCAAGGAAAAAAAAG
Found at i:31365378 original size:42 final size:42
Alignment explanation
Indices: 31365328--31365430 Score: 199
Period size: 42 Copynumber: 2.5 Consensus size: 42
31365318 TTGTTTTAAG
31365328 ATTT-GATTGTTTCGGGTTTTGGTTAATTTCAAGTTTAAATT
1 ATTTGGATTGTTTCGGGTTTTGGTTAATTTCAAGTTTAAATT
31365369 ATTTGGATTGTTTCGGGTTTTGGTTAATTTCAAGTTTAAATT
1 ATTTGGATTGTTTCGGGTTTTGGTTAATTTCAAGTTTAAATT
31365411 ATTTGGATTGTTTCGGGTTT
1 ATTTGGATTGTTTCGGGTTT
31365431 AAATAATTTG
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 4 0.07
42 57 0.93
ACGTcount: A:0.19, C:0.05, G:0.22, T:0.53
Consensus pattern (42 bp):
ATTTGGATTGTTTCGGGTTTTGGTTAATTTCAAGTTTAAATT
Found at i:31365424 original size:25 final size:25
Alignment explanation
Indices: 31365396--31365444 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
31365386 TTTTGGTTAA
*
31365396 TTTCAAGTTTAAATTATTTGGATTG
1 TTTCAAGTTTAAATAATTTGGATTG
**
31365421 TTTCGGGTTTAAATAATTTGGATT
1 TTTCAAGTTTAAATAATTTGGATT
31365445 TCAAGTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (25 bp):
TTTCAAGTTTAAATAATTTGGATTG
Found at i:31370015 original size:31 final size:31
Alignment explanation
Indices: 31369965--31370024 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
31369955 AAAGTGATCA
*
31369965 TTAAATTATTCAAAAGTTTTCATTTAAGTAG
1 TTAAACTATTCAAAAGTTTTCATTTAAGTAG
* *
31369996 TTAAACTATTTAAATGTTTTCATTTAAGT
1 TTAAACTATTCAAAAGTTTTCATTTAAGT
31370025 CGATAGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
TTAAACTATTCAAAAGTTTTCATTTAAGTAG
Found at i:31388745 original size:14 final size:14
Alignment explanation
Indices: 31388726--31388752 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31388716 TTTTTTTGCA
31388726 TGTAAAATATTTTT
1 TGTAAAATATTTTT
31388740 TGTAAAATATTTT
1 TGTAAAATATTTT
31388753 CATCATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (14 bp):
TGTAAAATATTTTT
Found at i:31389040 original size:37 final size:36
Alignment explanation
Indices: 31388999--31389079 Score: 83
Period size: 36 Copynumber: 2.2 Consensus size: 36
31388989 ATTTTTTATG
* *
31388999 ATTTAGTCCCT-AAAATCCAAATTTTTACTATTCTACA
1 ATTTAGTCCCTCAAAAACAAAATTTTT--TATTCTACA
* **
31389036 ATTTAATTTCTCAAAAACAAAATTTTTTATTCTACA
1 ATTTAGTCCCTCAAAAACAAAATTTTTTATTCTACA
*
31389072 ATTCAGTC
1 ATTTAGTC
31389080 TTAAACCTCA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
36 14 0.40
37 8 0.23
38 13 0.37
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (36 bp):
ATTTAGTCCCTCAAAAACAAAATTTTTTATTCTACA
Found at i:31390186 original size:17 final size:16
Alignment explanation
Indices: 31390166--31390199 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
31390156 ACATATTAAA
*
31390166 TTAAAAATAATATATAT
1 TTAAAAAAAATA-ATAT
31390183 TTAAAAAAAATAATAT
1 TTAAAAAAAATAATAT
31390199 T
1 T
31390200 AGATTACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAAAAAATAATAT
Found at i:31413007 original size:15 final size:15
Alignment explanation
Indices: 31412983--31413028 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
31412973 ATCACCCCTG
*
31412983 CCTCTGCTTCACTC-T
1 CCTCTTCTTC-CTCTT
31412998 CCTCTTCTTCCTCTT
1 CCTCTTCTTCCTCTT
*
31413013 CCTCTTCTTCTTCTT
1 CCTCTTCTTCCTCTT
31413028 C
1 C
31413029 ATTGTCATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 3 0.11
15 25 0.89
ACGTcount: A:0.02, C:0.46, G:0.02, T:0.50
Consensus pattern (15 bp):
CCTCTTCTTCCTCTT
Found at i:31415841 original size:23 final size:24
Alignment explanation
Indices: 31415810--31415863 Score: 101
Period size: 23 Copynumber: 2.3 Consensus size: 24
31415800 TTTAGCCCAC
31415810 ATGAGCCCAGAATGGTTAGCTCTT
1 ATGAGCCCAGAATGGTTAGCTCTT
31415834 A-GAGCCCAGAATGGTTAGCTCTT
1 ATGAGCCCAGAATGGTTAGCTCTT
31415857 ATGAGCC
1 ATGAGCC
31415864 GAGACAGAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.26
Consensus pattern (24 bp):
ATGAGCCCAGAATGGTTAGCTCTT
Found at i:31417329 original size:14 final size:15
Alignment explanation
Indices: 31417312--31417344 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
31417302 ACTAAATTTT
31417312 AATTCAGT-AATTAA
1 AATTCAGTCAATTAA
31417326 AATT-AGTCAATTAA
1 AATTCAGTCAATTAA
31417340 AATTC
1 AATTC
31417345 CATATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.09, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTCAGTCAATTAA
Found at i:31420757 original size:3 final size:3
Alignment explanation
Indices: 31420749--31420776 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31420739 AATGGGTTTT
31420749 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
31420777 GACTGCTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:31429778 original size:18 final size:18
Alignment explanation
Indices: 31429748--31429795 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
31429738 TACAGTTTTT
*
31429748 TAATTTAAAATTTTAAATA
1 TAATTT-AAATTTCAAATA
31429767 TAATTTAAATTTCAAATA
1 TAATTTAAATTTCAAATA
*
31429785 TTATTATAAAT
1 TAATT-TAAAT
31429796 ATCTCAAATG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATTTAAATTTCAAATA
Found at i:31429804 original size:21 final size:20
Alignment explanation
Indices: 31429762--31429818 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
31429752 TTAAAATTTT
*
31429762 AAATATAATT-TAAAT-TTC
1 AAATATTATTATAAATATTC
31429780 AAATATTATTATAAATATCTC
1 AAATATTATTATAAATAT-TC
**
31429801 AAATGCTATTATAAATAT
1 AAATATTATTATAAATAT
31429819 ACAACAATCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.27
19 5 0.15
20 1 0.03
21 18 0.55
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (20 bp):
AAATATTATTATAAATATTC
Found at i:31436396 original size:3 final size:3
Alignment explanation
Indices: 31436381--31436460 Score: 115
Period size: 3 Copynumber: 26.7 Consensus size: 3
31436371 TTAACCGAGT
* * * **
31436381 TCA TCA TCT TCA TCA TCA TTA TCA ACA TTG TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
31436429 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
31436461 TGAGTTTATA
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.31, C:0.31, G:0.01, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:31448468 original size:31 final size:31
Alignment explanation
Indices: 31448411--31448469 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
31448401 TGTATAATTA
* *
31448411 TATACTTAAAATTTTTATTATAATTTAAATG
1 TATACATAAAATTTTAATTATAATTTAAATG
* *
31448442 TATACATAAAATTTTAATTTTGATTTAA
1 TATACATAAAATTTTAATTATAATTTAA
31448470 TTTTACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.51
Consensus pattern (31 bp):
TATACATAAAATTTTAATTATAATTTAAATG
Found at i:31448897 original size:20 final size:20
Alignment explanation
Indices: 31448874--31448991 Score: 56
Period size: 20 Copynumber: 6.3 Consensus size: 20
31448864 ATTTAAATGT
31448874 ATATAAAACAAAGTAAAATA
1 ATATAAAACAAAGTAAAATA
*
31448894 ATAT--AAC---GTAAAACA
1 ATATAAAACAAAGTAAAATA
* * * * *
31448909 AGACAATATAAAGTAAAGTA
1 ATATAAAACAAAGTAAAATA
* * **
31448929 ATATAAAGCAAAGCAAAGCA
1 ATATAAAACAAAGTAAAATA
* *
31448949 ATATAAAGCAAA--ACAAT-
1 ATATAAAACAAAGTAAAATA
*
31448966 ATA-AAAACAAAGCAAAATA
1 ATATAAAACAAAGTAAAATA
31448985 ATATAAA
1 ATATAAA
31448992 GTAAAGCAAA
Statistics
Matches: 70, Mismatches: 19, Indels: 18
0.65 0.18 0.17
Matches are distributed among these distances:
15 9 0.13
16 7 0.10
17 4 0.06
18 9 0.13
19 3 0.04
20 38 0.54
ACGTcount: A:0.65, C:0.09, G:0.08, T:0.17
Consensus pattern (20 bp):
ATATAAAACAAAGTAAAATA
Found at i:31448931 original size:35 final size:35
Alignment explanation
Indices: 31448883--31449381 Score: 129
Period size: 35 Copynumber: 14.7 Consensus size: 35
31448873 TATATAAAAC
* *
31448883 AAAGTAAAATAATATAACGTAAAAC-AAGACAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAG-CAATAT
* *
31448918 AAAGTAAAGTAATATAAAGCAAAGCAAAGCAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
* * * * **
31448953 AAAGCAAAACAATATAAAAACAAAGCAAAATAATAT
1 AAAGTAAAATAATAT-AAAGCAAAACAAAGCAATAT
** * * * * * *
31448989 AAAGTAAAGCAA-AGCAAAACAATATAAAACAA-AGC
1 AAAGTAAAATAATA-TAAAGCAAAACAAAGCAATA-T
** * * *
31449024 AAA-TCAAAGCAATACAAAGCATAGCAAAGCAATAT
1 AAAGT-AAAATAATATAAAGCAAAACAAAGCAATAT
* * *
31449059 AAAGTAAAGTAA-AGTAAAGTAATAA-AAAGCAA-AGC
1 AAAGTAAAATAATA-TAAAGCAA-AACAAAGCAATA-T
* * ** *
31449094 AAAG--CAAT-ATA-AAA-TAAAGTAAAGTAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
* * * *
31449124 AAAATAAAACAATAAAAAGCAAAGCAAAGCAAAACAATAT
1 AAAGTAAAATAATATAAAGC--A--AAA-CAAAGCAATAT
** * * *
31449164 AAAACAAAATAATACAAAGCAAAGCAATA-CAAAAT
1 AAAGTAAAATAATATAAAGCAAAACAA-AGCAATAT
* * * *
31449199 ATAA-CAAAACAATATAAAACAAAACAAAGTAATAT
1 A-AAGTAAAATAATATAAAGCAAAACAAAGCAATAT
** * * * *
31449234 AAAACAAAGTAATATAAAACAAAAGAAAGTAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
** * *
31449269 AAAGT--AA-AGCA-AAA-CAAAATAAAGTAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
*
31449299 AAAG--------TA-AAA-CAAAACAAAGTAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
* * *
31449324 AAAGCAAAATAATAAAAAGCATAACAAAGCAATAT
1 AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
*
31449359 AAAGTAAAATAATACAAAGCAAA
1 AAAGTAAAATAATATAAAGCAAA
31449382 GCAATATAAA
Statistics
Matches: 355, Mismatches: 71, Indels: 76
0.71 0.14 0.15
Matches are distributed among these distances:
25 23 0.06
29 1 0.00
30 31 0.09
31 7 0.02
32 5 0.01
33 9 0.03
34 13 0.04
35 198 0.56
36 39 0.11
37 1 0.00
38 1 0.00
39 2 0.01
40 25 0.07
ACGTcount: A:0.66, C:0.10, G:0.09, T:0.15
Consensus pattern (35 bp):
AAAGTAAAATAATATAAAGCAAAACAAAGCAATAT
Found at i:31448982 original size:10 final size:10
Alignment explanation
Indices: 31448933--31449055 Score: 59
Period size: 10 Copynumber: 11.7 Consensus size: 10
31448923 AAAGTAATAT
*
31448933 AAAGCAAAGC
1 AAAGCAAAAC
* *
31448943 AAAGCAATAT
1 AAAGCAAAAC
31448953 AAAGCAAAAC
1 AAAGCAAAAC
**
31448963 AATATAAAAAC
1 AA-AGCAAAAC
*
31448974 AAAGCAAAATAATAT
1 AAAGC---A-AA-AC
* *
31448989 AAAGTAAAGC
1 AAAGCAAAAC
31448999 AAAGCAAAAC
1 AAAGCAAAAC
*
31449009 AATA-TAAAAC
1 AA-AGCAAAAC
*
31449019 AAAGCAAATC
1 AAAGCAAAAC
*
31449029 AAAGCAATAC
1 AAAGCAAAAC
* *
31449039 AAAGCATAGC
1 AAAGCAAAAC
31449049 AAAGCAA
1 AAAGCAA
31449056 TATAAAGTAA
Statistics
Matches: 81, Mismatches: 24, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
9 1 0.01
10 60 0.74
11 11 0.14
12 1 0.01
13 1 0.01
14 2 0.02
15 5 0.06
ACGTcount: A:0.64, C:0.15, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAGCAAAAC
Found at i:31448999 original size:20 final size:20
Alignment explanation
Indices: 31448927--31450125 Score: 172
Period size: 20 Copynumber: 60.1 Consensus size: 20
31448917 TAAAGTAAAG
*
31448927 TAATATAAAGCAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
* * *
31448947 CAATATAAAGCAAAACAATA
1 TAATATAAAGCAAAGCAAAA
* * ** *
31448967 TAAAAACAAAGCAAAATAATA
1 T-AATATAAAGCAAAGCAAAA
31448988 TAA-AGTAAAGCAAAGCAAAA
1 TAATA-TAAAGCAAAGCAAAA
* *
31449008 CAATATAAAACAAAGCAAATCAAA
1 TAATATAAAGCAAAGC--A--AAA
* * *
31449032 GCAATACAAAGCATAGCAAAGCAA
1 -TAATATAAAGCAAAGC-AA--AA
* * * *
31449056 TATAAAGTAAAGTAAAGTAAAG
1 TA-ATA-TAAAGCAAAGCAAAA
* *
31449078 TAATAAAAAGCAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
* ** * *
31449098 CAATATAAAATAAAGTAAAG
1 TAATATAAAGCAAAGCAAAA
** *
31449118 TAATATAAAATAAAACAATAA
1 TAATATAAAGCAAAGCAA-AA
*
31449139 -AA-AGCAAAGCAAAGCAAAA
1 TAATA-TAAAGCAAAGCAAAA
*
31449158 CAATAT--A--AAA-CAAAA
1 TAATATAAAGCAAAGCAAAA
*
31449173 TAATACAAAGCAAAGCAATACA
1 TAATATAAAGCAAAGCAA-A-A
* *
31449195 AAATAT-AA-CAAA--ACAA
1 TAATATAAAGCAAAGCAAAA
* *
31449211 T-ATA-AAA-CAAAACAAAG
1 TAATATAAAGCAAAGCAAAA
* * *
31449228 TAATATAAAACAAAGTAATA
1 TAATATAAAGCAAAGCAAAA
* * * *
31449248 TAAAACAAAAG-AAAGTAATA
1 TAATA-TAAAGCAAAGCAAAA
*
31449268 TAA-AGTAAAGCAAAACAAAATAAA
1 TAATA-TAAAGCAAAGC---A-AAA
* *
31449292 GTAATATAAAGTAAAACAAAA
1 -TAATATAAAGCAAAGCAAAA
* *
31449313 CAA-AGTAATA-TAAAGCAAAA
1 TAATA-TAA-AGCAAAGCAAAA
* *
31449333 TAATAAAAAGCATAA-CAAAG
1 TAATATAAAGCA-AAGCAAAA
* *
31449353 CAATAT-----AAAGTAAAA
1 TAATATAAAGCAAAGCAAAA
*
31449368 TAATACAAAGCAAAGC--AA
1 TAATATAAAGCAAAGCAAAA
*
31449386 T-ATA-AAA-CAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
*
31449403 TAATATAAAGTAAAG-----
1 TAATATAAAGCAAAGCAAAA
* *
31449418 TAATATAAAACAAAGCAATA
1 TAATATAAAGCAAAGCAAAA
*
31449438 TAATATAAAGCAAAGTAAAA
1 TAATATAAAGCAAAGCAAAA
* *
31449458 CAATATAAAACAAAGCAATATAAAACA
1 TAATATAAAGCAAAGC------AAA-A
*
31449485 AAGATATAAAGCAAAGCAAAA
1 TA-ATATAAAGCAAAGCAAAA
** *
31449506 CGATATAAAGCAAAACAAAA
1 TAATATAAAGCAAAGCAAAA
* * *
31449526 GAATATACAA-TAAAGCAATA
1 TAATATA-AAGCAAAGCAAAA
* *
31449546 TAA-ATTAAAGCAAACCAATA
1 TAATA-TAAAGCAAAGCAAAA
* * * *
31449566 TAAAACAAAGCAAAACAATA
1 TAATATAAAGCAAAGCAAAA
* *
31449586 CAATATAAAGCAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
*
31449606 TAATATAAAGTAAAGCAAAACAAA
1 TAATATAAAGCAAAGC---A-AAA
* *
31449630 GCAATATAAAACAAAGC-AAA
1 -TAATATAAAGCAAAGCAAAA
* * * *
31449650 TCAAAGCAATGCAAAACATAGCAAAG
1 T--AA--TAT--AAAGCAAAGCAAAA
* * *
31449676 CAATATAAAGTAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
* *
31449696 TAATAAAAAGCAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
* *
31449716 CAATAT--A--AAA-TAAAA
1 TAATATAAAGCAAAGCAAAA
*
31449731 CAATATAAAGCAAAGCAAAA
1 TAATATAAAGCAAAGCAAAA
*
31449751 CAATATAAA-CAAAG-----
1 TAATATAAAGCAAAGCAAAA
*
31449765 TAATACAAAGCAAAGC--AA
1 TAATATAAAGCAAAGCAAAA
*
31449783 T-ACA-AAA-CATAA-CAAAA
1 TAATATAAAGCA-AAGCAAAA
* * *
31449800 CAATATAAAGCAAAACAAAG
1 TAATATAAAGCAAAGCAAAA
* *
31449820 TAATATAAAACAAAGCAATA
1 TAATATAAAGCAAAGCAAAA
* * * * *
31449840 TAAAACAAAGTAATA-TAAAG
1 TAATATAAAGCAA-AGCAAAA
* * * * *
31449860 CAAAAGAAAGCAATA-TAAAG
1 TAATATAAAGCAA-AGCAAAA
* *
31449880 TAA-ATCAAAACAAAGTAAAA
1 TAATAT-AAAGCAAAGCAAAA
31449900 TAATATAAAGCAAAGCAAAACAAAA
1 TAATATAAAGCAAAG-----CAAAA
* * *
31449925 AAATATAAAGCAAAGTAAAG
1 TAATATAAAGCAAAGCAAAA
* * *
31449945 TAATAAAAAGCATAA-TAAAG
1 TAATATAAAGCA-AAGCAAAA
* *** *
31449965 CAATATAAAGCAATTTAAAG
1 TAATATAAAGCAAAGCAAAA
*
31449985 TAA-AGTAATA-CAAAGCAAAG
1 TAATA-TAA-AGCAAAGCAAAA
*
31450005 TAATATAAAGCAAAGCAAAG
1 TAATATAAAGCAAAGCAAAA
* *
31450025 CAATATAAAGTAAAG-----
1 TAATATAAAGCAAAGCAAAA
* *
31450040 TAATATAAAACAAAGCAATA
1 TAATATAAAGCAAAGCAAAA
* *
31450060 TAATATAAAGCAAAGTAAAG
1 TAATATAAAGCAAAGCAAAA
* * * **
31450080 CAAAACAAAGCAATATAAAACA
1 TAATATAAAGCAA-AGCAAA-A
*
31450102 AATATATAAAGCAAAGCAAAA
1 TA-ATATAAAGCAAAGCAAAA
31450123 TAA
1 TAA
31450126 AGGAATATAC
Statistics
Matches: 868, Mismatches: 190, Indels: 242
0.67 0.15 0.19
Matches are distributed among these distances:
14 9 0.01
15 74 0.09
16 15 0.02
17 15 0.02
18 15 0.02
19 41 0.05
20 499 0.57
21 54 0.06
22 21 0.02
23 14 0.02
24 17 0.02
25 73 0.08
26 6 0.01
27 2 0.00
28 13 0.01
ACGTcount: A:0.65, C:0.11, G:0.10, T:0.15
Consensus pattern (20 bp):
TAATATAAAGCAAAGCAAAA
Found at i:31449003 original size:5 final size:5
Alignment explanation
Indices: 31448989--31449100 Score: 52
Period size: 5 Copynumber: 22.4 Consensus size: 5
31448979 AAAATAATAT
* * * * *
31448989 AAAGT AAAGC AAAGC AAAAC AATA-T AAAAC AAAGC AAATC AAAGC AATA-C
1 AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC
* * * * * * *
31449039 AAAGC ATAGC AAAGC AATA-T AAAGT AAAGT AAAGT AAAGT AATA-A AAAGC
1 AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC
31449089 AAAGC AAAGC AA
1 AAAGC AAAGC AA
31449101 TATAAAATAA
Statistics
Matches: 87, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
4 4 0.05
5 79 0.91
6 4 0.05
ACGTcount: A:0.62, C:0.12, G:0.13, T:0.12
Consensus pattern (5 bp):
AAAGC
Found at i:31449043 original size:45 final size:44
Alignment explanation
Indices: 31448953--31449112 Score: 162
Period size: 45 Copynumber: 3.5 Consensus size: 44
31448943 AAAGCAATAT
*
31448953 AAAGCAAAACAATATAAAAACAAAGCAAAATAATA-TAA-AGTAAAGC
1 AAAGCAAAACAATAT-AAAACAAAGC-AAATAA-AGTAATA-AAAAGC
* *
31448999 AAAGCAAAACAATATAAAACAAAGCAAATCAAAGCAATACAAAGC
1 AAAGCAAAACAATATAAAACAAAGCAAAT-AAAGTAATAAAAAGC
* * ** *
31449044 ATAGCAAAGCAATATAAAGTAAAGTAAAGTAAAGTAATAAAAAGC
1 AAAGCAAAACAATATAAAACAAAGCAAA-TAAAGTAATAAAAAGC
* *
31449089 AAAGCAAAGCAATATAAAATAAAG
1 AAAGCAAAACAATATAAAACAAAG
31449113 TAAAGTAATA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
44 5 0.05
45 77 0.78
46 17 0.17
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.13
Consensus pattern (44 bp):
AAAGCAAAACAATATAAAACAAAGCAAATAAAGTAATAAAAAGC
Found at i:31449113 original size:45 final size:45
Alignment explanation
Indices: 31448994--31449120 Score: 175
Period size: 45 Copynumber: 2.8 Consensus size: 45
31448984 AATATAAAGT
* * * *
31448994 AAAGCAAAGCAAAACAATATAAAACAAAGCAAA-TCAAAGCAATAC
1 AAAGCAAAGCAAAGCAATATAAAATAAAGTAAAGT-AAAGCAATAA
* * *
31449039 AAAGCATAGCAAAGCAATATAAAGTAAAGTAAAGTAAAGTAATAA
1 AAAGCAAAGCAAAGCAATATAAAATAAAGTAAAGTAAAGCAATAA
31449084 AAAGCAAAGCAAAGCAATATAAAATAAAGTAAAGTAA
1 AAAGCAAAGCAAAGCAATATAAAATAAAGTAAAGTAA
31449121 TATAAAATAA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 71 0.99
46 1 0.01
ACGTcount: A:0.63, C:0.11, G:0.13, T:0.13
Consensus pattern (45 bp):
AAAGCAAAGCAAAGCAATATAAAATAAAGTAAAGTAAAGCAATAA
Found at i:31449143 original size:45 final size:45
Alignment explanation
Indices: 31448998--31449145 Score: 126
Period size: 45 Copynumber: 3.3 Consensus size: 45
31448988 TAAAGTAAAG
* * * * *
31448998 CAAAGCAAAA-CAATATAAAACAAAGCAAA-TCAAAGCAATACAAAG
1 CAAAG-AAAAGCAATATAAAATAAAGTAAAGT-AAAGTAATAAAAAA
* * * *
31449043 CATAGCAAAGCAATATAAAGTAAAGTAAAGTAAAGTAATAAAAAG
1 CAAAGAAAAGCAATATAAAATAAAGTAAAGTAAAGTAATAAAAAA
*
31449088 CAAAGCAAAGCAATATAAAATAAAGTAAAGTAATA-TAA-AATAAAA
1 CAAAGAAAAGCAATATAAAATAAAGTAAAGTAA-AGTAATAA-AAAA
31449133 CAATA-AAAAGCAA
1 CAA-AGAAAAGCAA
31449146 AGCAAAGCAA
Statistics
Matches: 87, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
44 5 0.06
45 79 0.91
46 3 0.03
ACGTcount: A:0.64, C:0.11, G:0.11, T:0.14
Consensus pattern (45 bp):
CAAAGAAAAGCAATATAAAATAAAGTAAAGTAAAGTAATAAAAAA
Found at i:31449177 original size:15 final size:15
Alignment explanation
Indices: 31449153--31449341 Score: 62
Period size: 15 Copynumber: 12.0 Consensus size: 15
31449143 CAAAGCAAAG
*
31449153 CAAAACAATATAAAA
1 CAAAATAATATAAAA
* *
31449168 CAAAATAATACAAAG
1 CAAAATAATATAAAA
* *
31449183 CAAAGCAATACAAAATATAA
1 C-AA--AAT--AATATAAAA
*
31449203 CAAAACAATATAAAA
1 CAAAATAATATAAAA
31449218 CAAAACAAAGTAATATAAAA
1 C---A-AAA-TAATATAAAA
*
31449238 CAAAGTAATATAAAA
1 CAAAATAATATAAAA
* *
31449253 CAAAAGAA-AGTAATA
1 CAAAATAATA-TAAAA
* * *
31449268 TAAAGTAA-AGCAAAA
1 CAAAATAATA-TAAAA
*
31449283 CAAAATAA-AGTAATA
1 CAAAATAATA-TAAAA
* * * *
31449298 TAAAGTAAAACAAAA
1 CAAAATAATATAAAA
* *
31449313 CAAAGTAATATAAAG
1 CAAAATAATATAAAA
31449328 CAAAATAATA-AAAA
1 CAAAATAATATAAAA
31449342 GCATAACAAA
Statistics
Matches: 128, Mismatches: 34, Indels: 25
0.68 0.18 0.13
Matches are distributed among these distances:
14 4 0.03
15 91 0.71
16 5 0.04
17 3 0.02
18 4 0.03
19 5 0.04
20 16 0.12
ACGTcount: A:0.69, C:0.10, G:0.06, T:0.15
Consensus pattern (15 bp):
CAAAATAATATAAAA
Found at i:31449181 original size:25 final size:25
Alignment explanation
Indices: 31449153--31449222 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
31449143 CAAAGCAAAG
31449153 CAAAACAATATAAAACAAAATA-ATA
1 CAAAACAATATAAAACAAAATATA-A
* * *
31449178 CAAAGCAA-AGCAATACAAAATATAA
1 CAAAACAATA-TAAAACAAAATATAA
31449203 CAAAACAATATAAAACAAAA
1 CAAAACAATATAAAACAAAA
31449223 CAAAGTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.70, C:0.14, G:0.03, T:0.13
Consensus pattern (25 bp):
CAAAACAATATAAAACAAAATATAA
Found at i:31449238 original size:30 final size:30
Alignment explanation
Indices: 31449204--31449395 Score: 108
Period size: 30 Copynumber: 6.2 Consensus size: 30
31449194 AAAATATAAC
31449204 AAAACAATATAAAACAAAACAAAGTAATAT
1 AAAACAATATAAAACAAAACAAAGTAATAT
*
31449234 AAAACAAAGTAATATAAAACAAAAGAAAGTAATAT
1 AAAAC-----AATATAAAACAAAACAAAGTAATAT
** * *
31449269 AAAGTAA-AGCAAAACAAAATAAAGTAATAT
1 AAAACAATA-TAAAACAAAACAAAGTAATAT
*
31449299 ---A-AA-GTAAAACAAAACAAAGTAATAT
1 AAAACAATATAAAACAAAACAAAGTAATAT
* * *
31449324 AAAGCAAAATAATAAAAAGCATAACAAAGCAATAT
1 AAA--ACAAT-AT-AAAA-CAAAACAAAGTAATAT
** * * * *
31449359 AAAGTAAAATAATACAAAGCAAAGCAATAT
1 AAAACAATATAAAACAAAACAAAGTAATAT
31449389 AAAACAA
1 AAAACAA
31449396 AGCAAAGTAA
Statistics
Matches: 126, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
25 19 0.15
26 2 0.02
29 1 0.01
30 46 0.37
31 5 0.04
32 2 0.02
33 3 0.02
34 4 0.03
35 44 0.35
ACGTcount: A:0.68, C:0.09, G:0.08, T:0.16
Consensus pattern (30 bp):
AAAACAATATAAAACAAAACAAAGTAATAT
Found at i:31449268 original size:55 final size:55
Alignment explanation
Indices: 31449074--31449487 Score: 164
Period size: 55 Copynumber: 7.7 Consensus size: 55
31449064 AAAGTAAAGT
* * *
31449074 AAAGTAATA-AAAAGC-AAAGCAAAGCAATATAAAATAAAGTAAAGTAATATAAAAT
1 AAAGTAATACAAAA-CAAAAG-AAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
** * * * * * * * *
31449129 AAAACAATA-AAAAGC-AAAGCAAAGCAAAACAATATAAAACAAAATAATACAAAGC
1 AAAGTAATACAAAA-CAAAAG-AAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
* * * * * *
31449184 AAAGCAATACAAAATATAACAAAACAATATAAAACAAAACAAAGTAATATAAAAC
1 AAAGTAATACAAAACAAAAGAAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
* * ** * *
31449239 AAAGTAATATAAAACAAAAGAAAGTAATATAAAGTAAAGC--A--AA-ACAAAAT
1 AAAGTAATACAAAACAAAAGAAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
* ** * * * * *
31449289 AAAGTAATATAAAGTAAAACAAAACAA-AGTAATATAAAGCAAAATAATA-AAAAGC
1 AAAGTAATACAAAACAAAAGAAAGCAATA-TAAAACAAAGCAAAGTAATATAAAA-C
* * * * * * *
31449344 --A-T-A-ACAAAGCAATATAAAGTAAAATAATACAAAGCAAAGCAATATAAAAC
1 AAAGTAATACAAAACAAAAGAAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
* * * * * *
31449394 AAAGCAA-AGTAATA-TAAAGTAAAGTAATATAAAACAAAGCAATA-TAATATAAAGC
1 AAAGTAATA-CAAAACAAAAG-AAAGCAATATAAAACAAAGCAA-AGTAATATAAAAC
* * * *
31449449 AAAGTAAAACAATATAAAACAAAGCAATATAAAACAAAG
1 AAAGTAATACAAAACAAAAGAAAGCAATATAAAACAAAG
31449488 ATATAAAGCA
Statistics
Matches: 271, Mismatches: 68, Indels: 40
0.72 0.18 0.11
Matches are distributed among these distances:
49 1 0.00
50 67 0.25
51 8 0.03
52 3 0.01
53 2 0.01
54 10 0.04
55 169 0.62
56 11 0.04
ACGTcount: A:0.67, C:0.09, G:0.08, T:0.15
Consensus pattern (55 bp):
AAAGTAATACAAAACAAAAGAAAGCAATATAAAACAAAGCAAAGTAATATAAAAC
Found at i:31449342 original size:25 final size:25
Alignment explanation
Indices: 31449234--31449938 Score: 116
Period size: 25 Copynumber: 28.9 Consensus size: 25
31449224 AAAGTAATAT
* *
31449234 AAAACAAAGTAATATAAAACAAAAG
1 AAAACAAAGTAATATAAAGCAAAAC
**
31449259 AAAGTAATA-TAA-AGTAAAGCAAAAC
1 AAAACAA-AGTAATA-TAAAGCAAAAC
* *
31449284 AAAATAAAGTAATATAAAGTAAAAC
1 AAAACAAAGTAATATAAAGCAAAAC
*
31449309 AAAACAAAGTAATATAAAGCAAAAT
1 AAAACAAAGTAATATAAAGCAAAAC
* *
31449334 AATAA-AAAG---CAT-AA-CAAAGC
1 AA-AACAAAGTAATATAAAGCAAAAC
* * * *
31449354 AATATAAAGTAAAATAATA-CAAAGC
1 AAAACAAAGTAATATAA-AGCAAAAC
* * * **
31449379 AAAGCAATA-TAAAACAAAGCAAAGT
1 AAAACAA-AGTAATATAAAGCAAAAC
* * *
31449404 AATATAAAGTAA-AGTAATA-TAAAAC
1 AAAACAAAGTAATA-TAA-AGCAAAAC
* **
31449429 AAAGCAATA-TAATATAAAGCAAAGT
1 AAAACAA-AGTAATATAAAGCAAAAC
* * * *
31449454 AAAACAATA-TAAAACAAAGCAATAT
1 AAAACAA-AGTAATATAAAGCAAAAC
*
31449479 AAAACAAAG--ATATAAAGCAAAGC
1 AAAACAAAGTAATATAAAGCAAAAC
31449502 AAAAC---G--ATATAAAGCAAAAC
1 AAAACAAAGTAATATAAAGCAAAAC
* *
31449522 AAAAGAATA-TACA-ATAAAGCAATATAA
1 AAAACAA-AGTA-ATATAAAGCAA-A-AC
** * *
31449549 ATTAAAGCAAACCAATATAAAACAAAGC
1 A--AAA-CAAAGTAATATAAAGCAAAAC
*
31449577 AAAACAATA-CAATATAAAG-----C
1 AAAACAA-AGTAATATAAAGCAAAAC
* * *
31449597 AAAGCAAAGTAATATAAAGTAAAGC
1 AAAACAAAGTAATATAAAGCAAAAC
* * *
31449622 AAAACAAAGCAATATAAAACAAAGC
1 AAAACAAAGTAATATAAAGCAAAAC
* *
31449647 AAATCAAAG-CA-AT---GCAAAAC
1 AAAACAAAGTAATATAAAGCAAAAC
* * * *
31449667 ATAGCAAAGCAATATAAAG-----T
1 AAAACAAAGTAATATAAAGCAAAAC
* * *
31449687 AAAGCAAAGTAATAAAAAGCAAAGC
1 AAAACAAAGTAATATAAAGCAAAAC
* * *
31449712 AAAGCAATA-TAAAATAAAACAATATAAAGC
1 AAAACAA-AGTAATATAAAGC---A-AAA-C
* ** **
31449742 AAAGCAAAACAATATAAA-CAAAGT
1 AAAACAAAGTAATATAAAGCAAAAC
* * *
31449766 AATACAAAGCAA-AGCAATA-CAAAAC
1 AAAACAAAGTAATA-TAA-AGCAAAAC
* **
31449791 ATAACAAAACAATATAAAGCAAAAC
1 AAAACAAAGTAATATAAAGCAAAAC
** * * * *
31449816 AAAGTAATA-TAAAACAAAGCAATAT
1 AAAACAA-AGTAATATAAAGCAAAAC
*
31449841 AAAACAAAGTAATATAAAGCAAAAG
1 AAAACAAAGTAATATAAAGCAAAAC
* *
31449866 AAAGCAATA-TAA-AGTAAATCAAAAC
1 AAAACAA-AGTAATA-TAAAGCAAAAC
** * *
31449891 AAAGTAAAATAATATAAAGCAAAGC
1 AAAACAAAGTAATATAAAGCAAAAC
**
31449916 AAAACAAAAAAATATAAAGCAAA
1 AAAACAAAGTAATATAAAGCAAA
31449939 GTAAAGTAAT
Statistics
Matches: 502, Mismatches: 110, Indels: 136
0.67 0.15 0.18
Matches are distributed among these distances:
19 2 0.00
20 72 0.14
21 3 0.01
22 4 0.01
23 19 0.04
24 24 0.05
25 318 0.63
26 20 0.04
27 2 0.00
28 2 0.00
29 10 0.02
30 26 0.05
ACGTcount: A:0.65, C:0.11, G:0.09, T:0.14
Consensus pattern (25 bp):
AAAACAAAGTAATATAAAGCAAAAC
Found at i:31449372 original size:50 final size:50
Alignment explanation
Indices: 31449318--31449849 Score: 161
Period size: 55 Copynumber: 10.6 Consensus size: 50
31449308 CAAAACAAAG
*
31449318 TAATATAAAGCAAAATAATA-AAAAGCATAA-CAAAGCAATATAAAGTAAAA
1 TAATATAAAGCAAAACAATATAAAA-CA-AAGCAAAGCAATATAAAGTAAAA
* * * *
31449368 TAATACAAAGCAAAGCAATATAAAACAAAGCAAAGTAATATAAAGTAAAG
1 TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
* * * * ** *
31449418 TAATATAAAACAAAGCAATATAATATAAAGCAAAGTAAAACAATATAAAACAAAG
1 TAATATAAAGCAAAAC-A-AT-ATA-AAA-CAAAGCAAAGCAATATAAAGTAAAA
* * * * * * *
31449473 CAATATAAAAC-AAA-GATATAAAGCAAAGCAAAACGATATAAAGCAAAA
1 TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
* * * * ** * *
31449521 CAAAAGAATATACAATAAAGCAATATAAATTAAAGCAAACCAATATAAA--ACAA
1 TAATATAA-A-GC-A-AAA-CAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
** * * *
31449574 -AGCA-AAA-CAATACAATATAAAGCAAAGCAAAGTAATATAAAGT--AA
1 TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
** * * ** **
31449619 -AGCA-AAA-CAAAGCAATATAAAACAAAGCAAATCAA-AGCAA-TGCAA
1 TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
* * ** * * *
31449664 -AACAT--AGCAAAGCAATATAAAGTAAAGCAAAGTAATAAAAAGCAAAGCAAA
1 TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAG--TA--AAA
* ** * * * *
31449715 GCAATATAAAATAAAACAATATAAAGCAAAGCAAAACAATATAAA-CAAAG
1 -TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
* * * * *
31449765 TAATACAAAGCAAAGCAATACAAAACATAA-CAAAACAATATAAAGCAAAACAAA
1 TAATATAAAGCAAAACAATATAAAACA-AAGCAAAGCAATATAAAG---TA-AAA
* *
31449819 GTAATATAAAACAAAGCAATATAAAACAAAG
1 -TAATATAAAGCAAAACAATATAAAACAAAG
31449850 TAATATAAAG
Statistics
Matches: 370, Mismatches: 74, Indels: 71
0.72 0.14 0.14
Matches are distributed among these distances:
43 1 0.00
44 4 0.01
45 86 0.23
46 5 0.01
47 1 0.00
48 28 0.08
49 39 0.11
50 61 0.16
51 11 0.03
52 5 0.01
53 14 0.04
54 9 0.02
55 106 0.29
ACGTcount: A:0.64, C:0.12, G:0.09, T:0.14
Consensus pattern (50 bp):
TAATATAAAGCAAAACAATATAAAACAAAGCAAAGCAATATAAAGTAAAA
Found at i:31449387 original size:15 final size:15
Alignment explanation
Indices: 31449348--31450180 Score: 133
Period size: 15 Copynumber: 55.5 Consensus size: 15
31449338 AAAAGCATAA
31449348 CAAAGCAATATAAAG
1 CAAAGCAATATAAAG
* ** *
31449363 TAAAATAATACAAAG
1 CAAAGCAATATAAAG
31449378 CAAAGCAATATAAAACAAAG
1 CAAAGCAATAT-----AAAG
*
31449398 CAAAGTAATATAAAG
1 CAAAGCAATATAAAG
* * *
31449413 TAAAGTAATATAAAA
1 CAAAGCAATATAAAG
31449428 CAAAGCAATATAATA-
1 CAAAGCAATATAA-AG
*
31449443 TAAAGCAA-AGT--A-
1 CAAAGCAATA-TAAAG
*
31449455 -AAA-CAATATAAAA
1 CAAAGCAATATAAAG
*
31449468 CAAAGCAATATAAAA
1 CAAAGCAATATAAAG
31449483 CAAAG--ATATAAAG
1 CAAAGCAATATAAAG
31449496 CAAAGCAAAACGATATAAAG
1 CAAAGC---A--ATATAAAG
*
31449516 CAAAACAA-A-AGAA-
1 CAAAGCAATATA-AAG
* *
31449529 TATA-C-A-ATAAAG
1 CAAAGCAATATAAAG
**
31449541 CAATATAAAT-TAAAG
1 CAA-AGCAATATAAAG
* *
31449556 CAAACCAATATAAAA
1 CAAAGCAATATAAAG
31449571 CAAAGC---A-AAA-
1 CAAAGCAATATAAAG
31449581 CAATA-CAATATAAAG
1 CAA-AGCAATATAAAG
31449596 CAAAGCAA-AGTAATA-
1 CAAAGCAATA-TAA-AG
* * * *
31449611 TAAAGTAA-AGCAAAA
1 CAAAGCAATA-TAAAG
*
31449626 CAAAGCAATATAAAA
1 CAAAGCAATATAAAG
31449641 CAAAGCAA-ATCAAAG
1 CAAAGCAATAT-AAAG
* * * *
31449656 CAATGCAAAACATAG
1 CAAAGCAATATAAAG
31449671 CAAAGCAATATAAAG
1 CAAAGCAATATAAAG
*
31449686 TAAAGCAA-AGTAATA-
1 CAAAGCAATA-TAA-AG
*
31449701 AAAAGC-----AAAG
1 CAAAGCAATATAAAG
*
31449711 CAAAGCAATATAAAA
1 CAAAGCAATATAAAG
* *
31449726 TAAAACAATATAAAG
1 CAAAGCAATATAAAG
31449741 CAAAGCAAAACAATATAAA-
1 CAAAG-----CAATATAAAG
* *
31449760 CAAAGTAATACAAAG
1 CAAAGCAATATAAAG
* *
31449775 CAAAGCAATACAAAA
1 CAAAGCAATATAAAG
* *
31449790 CATAA-CAAAACAATA-
1 CA-AAGCAATATAA-AG
*
31449805 TAAAGC---A-AAA-
1 CAAAGCAATATAAAG
* *
31449815 CAAAGTAATATAAAA
1 CAAAGCAATATAAAG
*
31449830 CAAAGCAATATAAAA
1 CAAAGCAATATAAAG
*
31449845 CAAAGTAATATAAAG
1 CAAAGCAATATAAAG
31449860 CAAAAGAAAGCAATATAAAG
1 C-----AAAGCAATATAAAG
* * * *
31449880 TAAATCAAAACAAAG
1 CAAAGCAATATAAAG
* **
31449895 TAAAATAATATAAAG
1 CAAAGCAATATAAAG
31449910 CAAAGCAA-A-ACAA-
1 CAAAGCAATATA-AAG
31449923 -AAA--AATATAAAG
1 CAAAGCAATATAAAG
*
31449935 CAAAGTAA-AGTAATA-
1 CAAAGCAATA-TAA-AG
*
31449950 AAAAGC-ATAATAAAG
1 CAAAGCAAT-ATAAAG
*
31449965 CAATATAAAGCAATTTAAAG
1 C-----AAAGCAATATAAAG
* * *
31449985 TAAAGTAATACAAAG
1 CAAAGCAATATAAAG
*
31450000 CAAAGTAATATAAAGCAAAG
1 CAAAGCAATAT-----AAAG
31450020 CAAAGCAATATAAAG
1 CAAAGCAATATAAAG
* * *
31450035 TAAAGTAATATAAAA
1 CAAAGCAATATAAAG
31450050 CAAAGCAATATAATA-
1 CAAAGCAATATAA-AG
*
31450065 TAAAGCAA-AGTAAAG
1 CAAAGCAATA-TAAAG
*
31450080 CAAAACAAAGCAATATAAAA
1 -----CAAAGCAATATAAAG
*
31450100 CAAA--TATATAAAG
1 CAAAGCAATATAAAG
*
31450113 CAAAGCAAAATAAAG
1 CAAAGCAATATAAAG
* *
31450128 GAATA-TACA-ATAAAG
1 CAA-AGCA-ATATAAAG
**
31450143 CAATATAAAT-TAAAG
1 CAA-AGCAATATAAAG
*
31450158 CAAAGCAATATAAAA
1 CAAAGCAATATAAAG
31450173 CAAAGCAA
1 CAAAGCAA
31450181 AACAATACAA
Statistics
Matches: 610, Mismatches: 101, Indels: 214
0.66 0.11 0.23
Matches are distributed among these distances:
9 1 0.00
10 22 0.04
11 17 0.03
12 11 0.02
13 33 0.05
14 44 0.07
15 375 0.61
16 14 0.02
17 1 0.00
19 5 0.01
20 84 0.14
21 3 0.00
ACGTcount: A:0.64, C:0.11, G:0.10, T:0.15
Consensus pattern (15 bp):
CAAAGCAATATAAAG
Found at i:31449407 original size:35 final size:35
Alignment explanation
Indices: 31449088--31450092 Score: 239
Period size: 35 Copynumber: 28.8 Consensus size: 35
31449078 TAATAAAAAG
* *
31449088 CAAAGCAAAGCAATATAAAATAAAGTAAAGTAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* ** * * *
31449123 TAAAATAAAACAATA-AAAAGCAAAGCAAAGCAAAA
1 CAAAGCAAAGCAATATAAAA-CAAAGCAAAGTAATA
* * * * *
31449158 CAATA-TAAAACAAAATAATACAAAGCAAAGCAATA
1 CAA-AGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31449193 CAAAATATAACAAAACAATATAAAACAAAACAAAGTAATA
1 C---A-A-AGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31449233 TAAAACAAAGTAATATAAAACAAAAG-AAAGTAATA
1 CAAAGCAAAGCAATATAAAAC-AAAGCAAAGTAATA
* * * * * *
31449268 TAAAGTAAAGCAAAACAAAATAAAGTAATA-TAAAGTA
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGT-AA-TA
* * * *
31449305 -AAA-CAAAACAA-AGTAATATAAAGCAAAATAATA
1 CAAAGCAAAGCAATA-TAAAACAAAGCAAAGTAATA
* * * * * *
31449338 AAAAGCATAA-CAA-AGCAATATAAAGTAAAATAATA
1 CAAAGCA-AAGCAATA-TAAAACAAAGCAAAGTAATA
31449373 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31449408 TAAAGTAAAGTAATATAAAACAAAGCAATA-TAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGTAATA
*
31449443 TAAAGCAAAGTAAAACAATATAAAACAAAGC-AA-T-ATA
1 CAAAGCAAAG-----CAATATAAAACAAAGCAAAGTAATA
* *
31449480 -AAA-CAAAG--ATATAAAGCAAAGCAAAACGATATAAA
1 CAAAGCAAAGCAATATAAAACAAAGC-AAA-G-TA-ATA
* * *
31449515 GCAAAACAAAAG-AATATACAATAAAGCAATA-TAA-A
1 -CAAAGC-AAAGCAATATAAAACAAAGCAA-AGTAATA
* * **
31449550 TTAAAGCAAACCAATATAAAACAAAGCAAAACAATA
1 -CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * ** *
31449586 CAATA-TAAAGCAA-AGCAAAGTAATA-TAAAGTAA-A
1 CAA-AGCAAAGCAATA-TAAAACAA-AGCAAAGTAATA
*
31449620 GCAAAACAAAGCAATATAAAACAAAGC--A--AAT-
1 -CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * * * *
31449651 CAAAGCAATGCAAAACATAGCAAAGCAATA-TAA-A
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGTAATA
* * *
31449685 GTAAAGCAAAGTAATA-AAAAGCAAAGCAAAGCAATA
1 -CAAAGCAAAGCAATATAAAA-CAAAGCAAAGTAATA
* ** * * **
31449721 TAAAATAAAACAATATAAAGCAAAGCAAAACAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * * * * *
31449756 TAAA-CAAAGTAATACAAAGCAAAGCAATA-CAAAA
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGTAATA
* * *
31449790 CATAA-CAAAACAATATAAAGCAAAACAAAGTAATA
1 CA-AAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31449825 TAAAACAAAGCAATATAAAACAAAGTAATA-TAA-A
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGTAATA
** *
31449859 GCAAAAG-AAAGCAATATAAAGTAAATC--A--AA-A
1 -C-AAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* ** *
31449890 CAAAGTAAAATAATATAAAGCAAAGC-AA---A-A
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* *
31449920 C-AA--AAA--AATATAAAGCAAAGTAAAGTAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31449950 AAAAGCATAATAAAGCAATATAAAGCAATTTAAAGTAAAGTAATA
1 CAAAGC-----AAAGCAATAT-AA--AA--CAAAGCAAAGTAATA
* * *
31449995 CAAAGCAAAGTAATATAAAGCAAAGCAAAGCAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
* * *
31450030 TAAAGTAAAGTAATATAAAACAAAGCAATA-TAATA
1 CAAAGCAAAGCAATATAAAACAAAGCAA-AGTAATA
* * *
31450065 TAAAGCAAAGTAA-AGCAAAACAAAGCAA
1 CAAAGCAAAGCAATA-TAAAACAAAGCAA
31450093 TATAAAACAA
Statistics
Matches: 746, Mismatches: 133, Indels: 182
0.70 0.13 0.17
Matches are distributed among these distances:
25 14 0.02
26 2 0.00
27 3 0.00
28 13 0.02
29 7 0.01
30 43 0.06
31 8 0.01
32 1 0.00
33 5 0.01
34 59 0.08
35 437 0.59
36 35 0.05
37 12 0.02
38 7 0.01
39 12 0.02
40 66 0.09
41 2 0.00
43 1 0.00
45 19 0.03
ACGTcount: A:0.65, C:0.11, G:0.09, T:0.15
Consensus pattern (35 bp):
CAAAGCAAAGCAATATAAAACAAAGCAAAGTAATA
Found at i:31449600 original size:5 final size:5
Alignment explanation
Indices: 31449592--31449718 Score: 64
Period size: 5 Copynumber: 25.4 Consensus size: 5
31449582 AATACAATAT
* * * * * *
31449592 AAAGC AAAGC AAAGT AATA-T AAAGT AAAGC AAAAC AAAGC AATA-T AAAAC
1 AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC
* * * * * *
31449642 AAAGC AAATC AAAGC AATGC AAAAC ATAGC AAAGC AATA-T AAAGT AAAGC
1 AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AAAGC AA-AGC AAAGC AAAGC
* *
31449692 AAAGT AATA-A AAAGC AAAGC AAAGC AA
1 AAAGC AA-AGC AAAGC AAAGC AAAGC AA
31449719 TATAAAATAA
Statistics
Matches: 94, Mismatches: 20, Indels: 16
0.72 0.15 0.12
Matches are distributed among these distances:
4 4 0.04
5 86 0.91
6 4 0.04
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (5 bp):
AAAGC
Found at i:31449952 original size:25 final size:25
Alignment explanation
Indices: 31449851--31450082 Score: 93
Period size: 25 Copynumber: 8.9 Consensus size: 25
31449841 AAAACAAAGT
31449851 AATATAAAGCAAAAG-AAAGCAATATA
1 AATATAAAGC-AAAGCAAAGCAATA-A
* * * *
31449877 AA-GTAAATCAAAACAAAGTAA-AA
1 AATATAAAGCAAAGCAAAGCAATAA
* *
31449900 TAATATAAAGCAAAGCAAAACAAAAA
1 -AATATAAAGCAAAGCAAAGCAATAA
* *
31449926 AATATAAAGCAAAGTAAAGTAATAAAA
1 AATATAAAGCAAAGCAAAGCAAT--AA
* *
31449953 AGCATAATAAAGCAATA-TAAAGCAATTTA
1 A--AT-ATAAAGCAA-AGCAAAGCAA-TAA
* * *
31449982 AA-GTAAAGTAATA-CAAAGCAA-AGT
1 AATATAAAGCAA-AGCAAAGCAATA-A
31450006 AATATAAAGCAAAGCAAAGCAATATA
1 AATATAAAGCAAAGCAAAGCAATA-A
* * *
31450032 AAGTAAAGTAATA-TAAAACAAAGCAATAT
1 AA-T--A-TAA-AGCAAAGCAAAGCAATAA
*
31450061 AATATAAAGCAAAGTAAAGCAA
1 AATATAAAGCAAAGCAAAGCAA
31450083 AACAAAGCAA
Statistics
Matches: 155, Mismatches: 30, Indels: 43
0.68 0.13 0.19
Matches are distributed among these distances:
23 1 0.01
24 10 0.06
25 88 0.57
26 8 0.05
27 5 0.03
28 1 0.01
29 7 0.05
30 32 0.21
31 3 0.02
ACGTcount: A:0.63, C:0.09, G:0.11, T:0.17
Consensus pattern (25 bp):
AATATAAAGCAAAGCAAAGCAATAA
Found at i:31450093 original size:35 final size:35
Alignment explanation
Indices: 31449905--31450181 Score: 121
Period size: 35 Copynumber: 8.0 Consensus size: 35
31449895 TAAAATAATA
* * * *
31449905 TAAAGCAAAGCAAAACAAAAAAATATAAAGCAAAG
1 TAAAGCAAAACAAAGCAATATAATATAAAGCAAAG
*
31449940 TAAAGTAATAA-AAAGC---AT-A-ATAAAGCAATA-
1 TAAAGCAA-AACAAAGCAATATAATATAAAGCAA-AG
*** * *
31449970 TAAAGCAATTTAAAGTAA-AGTAATACAAAGCAAAG
1 TAAAGCAAAACAAAGCAATA-TAATATAAAGCAAAG
* * * *
31450005 TAATA-TAAAGCAAAGCAA-AGCAATATAAAGTAAAG
1 TAA-AGCAAAACAAAGCAATA-TAATATAAAGCAAAG
*
31450040 TAATA-TAAAACAAAGCAATATAATATAAAGCAAAG
1 TAA-AGCAAAACAAAGCAATATAATATAAAGCAAAG
* * **
31450075 TAAAGCAAAACAAAGCAATATAAAACAAATATATAAAG
1 TAAAGCAAAACAAAGCAATATAATA-TAA-A-GCAAAG
* * *
31450113 CAAAGCAAAATAAAGGAATATACA-ATAAAGCAATA-
1 TAAAGCAAAACAAAGCAATATA-ATATAAAGCAA-AG
** * * *
31450148 TAAATTAAAGCAAAGCAATATAAAACAAAGCAAA
1 TAAAGCAAAACAAAGCAATATAATATAAAGCAAA
31450182 ACAATACAAT
Statistics
Matches: 186, Mismatches: 38, Indels: 37
0.71 0.15 0.14
Matches are distributed among these distances:
30 20 0.11
31 2 0.01
32 2 0.01
33 1 0.01
34 5 0.03
35 121 0.65
36 7 0.04
37 3 0.02
38 24 0.13
39 1 0.01
ACGTcount: A:0.63, C:0.10, G:0.11, T:0.16
Consensus pattern (35 bp):
TAAAGCAAAACAAAGCAATATAATATAAAGCAAAG
Found at i:31450164 original size:20 final size:20
Alignment explanation
Indices: 31450139--31450187 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
31450129 AATATACAAT
**
31450139 AAAGCAATATAAATTAAAGC
1 AAAGCAATATAAAACAAAGC
31450159 AAAGCAATATAAAACAAAGC
1 AAAGCAATATAAAACAAAGC
*
31450179 AAAACAATA
1 AAAGCAATA
31450188 CAATATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.65, C:0.12, G:0.08, T:0.14
Consensus pattern (20 bp):
AAAGCAATATAAAACAAAGC
Found at i:31450217 original size:25 final size:25
Alignment explanation
Indices: 31450153--31450226 Score: 96
Period size: 25 Copynumber: 3.0 Consensus size: 25
31450143 CAATATAAAT
31450153 TAAAGCAAAGCAATATAAAACAAAG
1 TAAAGCAAAGCAATATAAAACAAAG
* *
31450178 CAAAACAATA-CAATATAAAACAAAG
1 TAAAGCAA-AGCAATATAAAACAAAG
* *
31450203 TAAAGTAAAGTAATATAAAACAAA
1 TAAAGCAAAGCAATATAAAACAAA
31450227 TCGATATAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
24 1 0.02
25 39 0.95
26 1 0.02
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.15
Consensus pattern (25 bp):
TAAAGCAAAGCAATATAAAACAAAG
Found at i:31451089 original size:19 final size:20
Alignment explanation
Indices: 31451048--31451091 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
31451038 CTTCTAAAAC
* * *
31451048 CCCCAAAACTTTTTATTTTT
1 CCCCTAAACTTTTTACTTCT
31451068 CCCCTAAAC-TTTTACTTCT
1 CCCCTAAACTTTTTACTTCT
31451087 CCCCT
1 CCCCT
31451092 TTTACCCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.43
Consensus pattern (20 bp):
CCCCTAAACTTTTTACTTCT
Found at i:31454172 original size:17 final size:18
Alignment explanation
Indices: 31454142--31454175 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31454132 AAAAATATAT
31454142 ATACAAAATCTAAAAATA
1 ATACAAAATCTAAAAATA
*
31454160 ATAC-AAATGTAAAAAT
1 ATACAAAATCTAAAAAT
31454176 TTATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.65, C:0.09, G:0.03, T:0.24
Consensus pattern (18 bp):
ATACAAAATCTAAAAATA
Found at i:31454929 original size:28 final size:27
Alignment explanation
Indices: 31454896--31454966 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
31454886 ATTTTACAAA
31454896 ATTTTAATTTAATAAATAATAAAATTAT
1 ATTTTAATTTAATAAATAAT-AAATTAT
* * * *
31454924 ATTTTAACTTAAAAAATGATAAATTTT
1 ATTTTAATTTAATAAATAATAAATTAT
* *
31454951 AATTTAATTTTATAAA
1 ATTTTAATTTAATAAA
31454967 AACTATAAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 18 0.51
28 17 0.49
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (27 bp):
ATTTTAATTTAATAAATAATAAATTAT
Found at i:31470061 original size:22 final size:21
Alignment explanation
Indices: 31470027--31470071 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
31470017 ATTTACTCCT
**
31470027 TTTTAAATGTTGAGGGTTAAA
1 TTTTAAATGTTGAGAATTAAA
31470048 TTTTAAATGTTTGAGAATTAAA
1 TTTTAAATG-TTGAGAATTAAA
31470070 TT
1 TT
31470072 GTTAGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.47
Consensus pattern (21 bp):
TTTTAAATGTTGAGAATTAAA
Found at i:31473637 original size:79 final size:79
Alignment explanation
Indices: 31473506--31473666 Score: 304
Period size: 79 Copynumber: 2.0 Consensus size: 79
31473496 TATTAAATAT
*
31473506 ACTCCAAACATATGAGATTGTAGTTTGGCGTAGCAGGTAAGAGGCAACCTGTTCATTTTCGAATA
1 ACTCCAAACATATGAGACTGTAGTTTGGCGTAGCAGGTAAGAGGCAACCTGTTCATTTTCGAATA
31473571 AAATAATTGAATCC
66 AAATAATTGAATCC
*
31473585 ACTCCAAATATATGAGACTGTAGTTTGGCGTAGCAGGTAAGAGGCAACCTGTTCATTTTCGAATA
1 ACTCCAAACATATGAGACTGTAGTTTGGCGTAGCAGGTAAGAGGCAACCTGTTCATTTTCGAATA
31473650 AAATAATTGAATCC
66 AAATAATTGAATCC
31473664 ACT
1 ACT
31473667 GTTTTCAGCT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (79 bp):
ACTCCAAACATATGAGACTGTAGTTTGGCGTAGCAGGTAAGAGGCAACCTGTTCATTTTCGAATA
AAATAATTGAATCC
Found at i:31474039 original size:17 final size:18
Alignment explanation
Indices: 31473996--31474041 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
31473986 TAAGTTTTTC
*
31473996 TAAAATTTAAACTTAATAA
1 TAAAA-TTAAATTTAATAA
*
31474015 -AAATTTAAATTTAA-AA
1 TAAAATTAAATTTAATAA
31474031 TAAAATTAAAT
1 TAAAATTAAAT
31474042 GCCCAGATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 2 0.09
17 18 0.78
18 3 0.13
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
TAAAATTAAATTTAATAA
Found at i:31474464 original size:24 final size:25
Alignment explanation
Indices: 31474432--31474514 Score: 105
Period size: 26 Copynumber: 3.3 Consensus size: 25
31474422 TGTAAAGGGT
31474432 TACAAACCCTATTC-TGAAAATCAA
1 TACAAACCCTATTCTTGAAAATCAA
* *
31474456 TACAAACCCTGTTCTTGAAATTCGAA
1 TACAAACCCTATTCTTGAAAATC-AA
* *
31474482 TACAAACCCAACTCTTGAAGAATCAA
1 TACAAACCCTATTCTTGAA-AATCAA
31474508 TACAAAC
1 TACAAAC
31474515 AGATTTGTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.26
25 7 0.14
26 27 0.54
27 3 0.06
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.24
Consensus pattern (25 bp):
TACAAACCCTATTCTTGAAAATCAA
Found at i:31474831 original size:21 final size:20
Alignment explanation
Indices: 31474807--31474858 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
31474797 AAAGGCAGTT
*
31474807 ATAATGATAATTGCTTTAATA
1 ATAAT-ATAATTGCATTAATA
*
31474828 ATAATATTAAATGCATTAATA
1 ATAATA-TAATTGCATTAATA
31474849 ATAATATAAT
1 ATAATATAAT
31474859 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
ATAATATAATTGCATTAATA
Found at i:31474866 original size:21 final size:21
Alignment explanation
Indices: 31474822--31474869 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
31474812 GATAATTGCT
* *
31474822 TTAATAATAATATTAAATGCA
1 TTAATAATAATATAAAATGAA
31474843 TTAATAATAATATAATAAT-AA
1 TTAATAATAATATAA-AATGAA
31474864 TTAATA
1 TTAATA
31474870 GTGTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
TTAATAATAATATAAAATGAA
Found at i:31476080 original size:58 final size:59
Alignment explanation
Indices: 31475809--31476124 Score: 439
Period size: 59 Copynumber: 5.4 Consensus size: 59
31475799 CCTAGACTAT
* *
31475809 CCAAAAATTACCATTTTACCCCTAAACTTT-CTAAAATCCCATTTTAAAACCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAA-TTTCCTAAAATCCCATTTTTAACCCCGATTTCA
* * *
31475868 CCAAAAATTACCCTTTTACCCCTGAACTTTCC-AAAATCCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-AAATTTCCTAAAATCCCATTTTTAACCCCGATTTCA
* * *
31475927 CCAAAAATTACCATTTTACGCCCGAACTTTCCT-AAATCCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTAC-CCCTAAATTTCCTAAAATCCCATTTTTAACCCCGATTTCA
*
31475986 TCAAAAATTACCATTTTA-CCCTCAAACTTTCC-AAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCT-AAA-TTTCCTAAAATCCCATTTTTAACCCCGATTTCA
*
31476045 CC-AAAATTACCATTTTACCCCTAAATTTCCTAAAATCCCATTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTAAATTTCCTAAAATCCCATTTTTAACCCCGATTTCA
31476103 CCAAAAATTA-CATTTTTACCCC
1 CCAAAAATTACCA-TTTTACCCC
31476125 CGAAAGTCAA
Statistics
Matches: 231, Mismatches: 15, Indels: 22
0.86 0.06 0.08
Matches are distributed among these distances:
57 8 0.03
58 50 0.22
59 167 0.72
60 6 0.03
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTAAATTTCCTAAAATCCCATTTTTAACCCCGATTTCA
Found at i:31476108 original size:29 final size:28
Alignment explanation
Indices: 31475841--31476124 Score: 133
Period size: 30 Copynumber: 9.7 Consensus size: 28
31475831 TAAACTTTCT
* *
31475841 AAAATCCCATTTTAAAACCCGATTTCACC
1 AAAATCCCATTTT-TACCCCGATTTCACC
31475870 AAAAATTACCC--TTTTACCCCTGAACTTT--CC
1 -AAAA-T-CCCATTTTTACCCC-G-A-TTTCACC
*
31475900 AAAATCCCATTTTTAACCTCGATTTCACC
1 AAAATCCCATTTTT-ACCCCGATTTCACC
*
31475929 AAAAATTACCA-TTTTACGCCCGAACTTT--CC
1 -AAAA-TCCCATTTTTAC-CCCG-A-TTTCACC
* * *
31475959 TAAATCCCATTTTTAACCCTGATTTCATCA
1 AAAATCCCATTTTT-ACCCCGATTTCA-CC
* *
31475989 AAAATTACCA-TTTTACCCTCAAACTTT--CC
1 AAAA-TCCCATTTTTACCC-C-GA-TTTCACC
31476018 AAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATCCCATTTTT-ACCCCGATTTCACC
* * *
31476047 AAAATTACCA-TTTTACCCCTAAATTTC-CT
1 AAAA-TCCCATTTTTACCCC--GATTTCACC
31476076 AAAATCCCATTTTTGACCCCGATTTCACC
1 AAAATCCCATTTTT-ACCCCGATTTCACC
**
31476105 AAAAATTACATTTTTACCCC
1 -AAAATCCCATTTTTACCCC
31476125 CGAAAGTCAA
Statistics
Matches: 195, Mismatches: 24, Indels: 71
0.67 0.08 0.24
Matches are distributed among these distances:
27 12 0.06
28 26 0.13
29 66 0.34
30 67 0.34
31 12 0.06
32 12 0.06
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (28 bp):
AAAATCCCATTTTTACCCCGATTTCACC
Found at i:31484319 original size:7 final size:7
Alignment explanation
Indices: 31484307--31484338 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
31484297 TATGCATGTA
31484307 AGAGATG
1 AGAGATG
31484314 AGAGATG
1 AGAGATG
31484321 AGAGATG
1 AGAGATG
*
31484328 AGAGACG
1 AGAGATG
31484335 AGAG
1 AGAG
31484339 GACTGATGTG
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:0.44, C:0.03, G:0.44, T:0.09
Consensus pattern (7 bp):
AGAGATG
Found at i:31485789 original size:23 final size:24
Alignment explanation
Indices: 31485762--31485814 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
31485752 TTGGTGTTTT
*
31485762 TTTTTTTTACTATTTTAGTTGCTG
1 TTTTTTTTACTATTTTAGGTGCTG
* *
31485786 TTTTTTTTATTATTTT-GGTGTTG
1 TTTTTTTTACTATTTTAGGTGCTG
31485809 TTTTTT
1 TTTTTT
31485815 ACTGTTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.09, C:0.04, G:0.13, T:0.74
Consensus pattern (24 bp):
TTTTTTTTACTATTTTAGGTGCTG
Found at i:31485822 original size:21 final size:20
Alignment explanation
Indices: 31485762--31485822 Score: 59
Period size: 24 Copynumber: 2.8 Consensus size: 20
31485752 TTGGTGTTTT
31485762 TTTTTTTTACTATTTTAGTTGCTG
1 TTTTTTTTACTATTTT-G--G-TG
*
31485786 TTTTTTTTATTATTTTGGTG
1 TTTTTTTTACTATTTTGGTG
*
31485806 TTGTTTTTTACTGTTTT
1 TT-TTTTTTACTATTTT
31485823 AATGCTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
23 1 0.03
24 15 0.45
ACGTcount: A:0.10, C:0.05, G:0.13, T:0.72
Consensus pattern (20 bp):
TTTTTTTTACTATTTTGGTG
Found at i:31485866 original size:33 final size:35
Alignment explanation
Indices: 31485828--31485921 Score: 113
Period size: 33 Copynumber: 2.7 Consensus size: 35
31485818 GTTTTAATGC
31485828 TTTTTTACTGTTTTAATTGTTATTTTAG-TGCTA-
1 TTTTTTACTGTTTTAATTGTTATTTTAGCTGCTAT
* * *
31485861 TTTTTTACTGTTTTGA-TGTTATTTTTGCTGTTAT
1 TTTTTTACTGTTTTAATTGTTATTTTAGCTGCTAT
**
31485895 TTTTATTACTGTTTTTGTTGTTATTTT
1 TTTT-TTACTGTTTTAATTGTTATTTT
31485922 TACTATTATT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
32 10 0.19
33 19 0.37
34 4 0.08
35 10 0.19
36 9 0.17
ACGTcount: A:0.14, C:0.05, G:0.13, T:0.68
Consensus pattern (35 bp):
TTTTTTACTGTTTTAATTGTTATTTTAGCTGCTAT
Found at i:31485892 original size:12 final size:12
Alignment explanation
Indices: 31485871--31485986 Score: 74
Period size: 12 Copynumber: 9.8 Consensus size: 12
31485861 TTTTTTACTG
*
31485871 TTTTGATGTTAT
1 TTTTGTTGTTAT
*
31485883 TTTTGCTGTTAT
1 TTTTGTTGTTAT
* ** *
31485895 TTTTATTACTGT
1 TTTTGTTGTTAT
31485907 TTTTGTTGTTAT
1 TTTTGTTGTTAT
** *
31485919 TTTTACTATTA-
1 TTTTGTTGTTAT
* *
31485930 TTTTATTGTT-G
1 TTTTGTTGTTAT
31485941 TTTTGTTGTTAT
1 TTTTGTTGTTAT
** *
31485953 TTTTACTGTTGT
1 TTTTGTTGTTAT
*
31485965 TTTGGTTGTTAT
1 TTTTGTTGTTAT
*
31485977 TTTGGTTGTT
1 TTTTGTTGTT
31485987 TGGATATTAT
Statistics
Matches: 78, Mismatches: 24, Indels: 4
0.74 0.23 0.04
Matches are distributed among these distances:
11 17 0.22
12 61 0.78
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.69
Consensus pattern (12 bp):
TTTTGTTGTTAT
Done.