Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold133
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: 2564099
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 17052 characters in sequence are not A, C, G, or T
File 2 of 17
Found at i:109895 original size:13 final size:13
Alignment explanation
Indices: 109871--109895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
109861 AATTTATAAT
109871 ATTAATTTGATCA
1 ATTAATTTGATCA
109884 ATTAATTTGATC
1 ATTAATTTGATC
109896 TTATTTATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (13 bp):
ATTAATTTGATCA
Found at i:110430 original size:19 final size:19
Alignment explanation
Indices: 110359--110431 Score: 52
Period size: 19 Copynumber: 4.2 Consensus size: 19
110349 TGAGTTAAAA
110359 TTTAATATAATATATTAAT
1 TTTAATATAATATATTAAT
*
110378 TTT-A-A-CA-ATA--AAT
1 TTTAATATAATATATTAAT
* * * *
110391 TTT-ATCTCATTTATTATT
1 TTTAATATAATATATTAAT
110409 TTTAATATAATATATTAAT
1 TTTAATATAATATATTAAT
110428 TTTA
1 TTTA
110432 TCTTAATATC
Statistics
Matches: 40, Mismatches: 8, Indels: 12
0.67 0.13 0.20
Matches are distributed among these distances:
13 7 0.17
15 5 0.12
16 3 0.08
17 1 0.03
18 6 0.15
19 18 0.45
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTAATATAATATATTAAT
Found at i:110474 original size:19 final size:19
Alignment explanation
Indices: 110402--110474 Score: 58
Period size: 19 Copynumber: 3.6 Consensus size: 19
110392 TTATCTCATT
* *
110402 TATTATTTTTAATATAATA
1 TATTAATTTTATTATAATA
110421 TATTAATTTTATCT-TAATA
1 TATTAATTTTAT-TATAATA
*
110440 TCATTCGTTAAATTTATTATAATA
1 T-A----TTAATTTTATTATAATA
110464 TATTAATTTTA
1 TATTAATTTTA
110475 CTCATTACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
19 24 0.56
20 2 0.05
23 2 0.05
24 15 0.35
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (19 bp):
TATTAATTTTATTATAATA
Found at i:110654 original size:26 final size:27
Alignment explanation
Indices: 110618--110672 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
110608 TTTTCATAAT
* * *
110618 ATTAATTAATAAATATA-TATAGGTTC
1 ATTAATAAATAAATAAATTATAGATTC
*
110644 ATTAATAAATATATAAATTATAGATTC
1 ATTAATAAATAAATAAATTATAGATTC
110671 AT
1 AT
110673 ATATATATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (27 bp):
ATTAATAAATAAATAAATTATAGATTC
Found at i:111447 original size:2 final size:2
Alignment explanation
Indices: 111400--111430 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
111390 TACAAACCTT
111400 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
111431 TATTGACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:113917 original size:6 final size:6
Alignment explanation
Indices: 113906--113930 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
113896 TATTAAGTTC
113906 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
113931 CAAAAAAAGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:116098 original size:21 final size:20
Alignment explanation
Indices: 116055--116107 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
116045 TAGGTTGTTT
*
116055 TAATTTTTAATATTAAATGGA
1 TAATTTTTAA-ATTAAATAGA
*
116076 TAATTTTTAAATGTAAGTAGA
1 TAATTTTTAAAT-TAAATAGA
116097 T-ATTTTTAAAT
1 TAATTTTTAAAT
116108 AATATATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (20 bp):
TAATTTTTAAATTAAATAGA
Found at i:119646 original size:2 final size:2
Alignment explanation
Indices: 119639--119667 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
119629 TGAGTTCAGC
119639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
119668 AAGAAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:119957 original size:20 final size:20
Alignment explanation
Indices: 119932--119972 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
119922 TAACATGAAA
*
119932 TATAAACTAATTTTACACTT
1 TATAAACCAATTTTACACTT
119952 TATAAACCAATTTTACACTT
1 TATAAACCAATTTTACACTT
119972 T
1 T
119973 TTTTTTTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (20 bp):
TATAAACCAATTTTACACTT
Found at i:121257 original size:2 final size:2
Alignment explanation
Indices: 121250--121275 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
121240 AAATTGTATG
121250 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
121276 AGAGGAAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:122388 original size:2 final size:2
Alignment explanation
Indices: 122381--122405 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122371 GATTATGCAA
122381 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
122406 TACTTGTGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:125087 original size:36 final size:36
Alignment explanation
Indices: 125040--125112 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
125030 GTTTATCAAA
125040 TACAACTATGCACTAGATTCAGCAGGTATGTTTGCG
1 TACAACTATGCACTAGATTCAGCAGGTATGTTTGCG
125076 TACAACTATGCACTAGATTCAGCAGGTATGTTTGCG
1 TACAACTATGCACTAGATTCAGCAGGTATGTTTGCG
125112 T
1 T
125113 CCTTTAACGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (36 bp):
TACAACTATGCACTAGATTCAGCAGGTATGTTTGCG
Found at i:131384 original size:16 final size:16
Alignment explanation
Indices: 131365--131403 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
131355 ATAATATGAT
*
131365 TATTTAATTTATTAAA
1 TATTTAATTTATAAAA
131381 TATTTAATTTATAAAA
1 TATTTAATTTATAAAA
131397 TAATTTA
1 T-ATTTA
131404 TTATAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATTTAATTTATAAAA
Found at i:131797 original size:24 final size:25
Alignment explanation
Indices: 131737--131797 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
131727 AAAATAAAAA
131737 ATAATATAAATATATTAAAATTATAT
1 ATAA-ATAAATATATTAAAATTATAT
* * * * *
131763 ATTATTTAATAT-TTTAAATTTTAT
1 ATAAATAAATATATTAAAATTATAT
131787 ATAAATAAATA
1 ATAAATAAATA
131798 ATAATTTAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
24 18 0.67
25 6 0.22
26 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
ATAAATAAATATATTAAAATTATAT
Found at i:132776 original size:31 final size:32
Alignment explanation
Indices: 132724--132808 Score: 91
Period size: 32 Copynumber: 2.6 Consensus size: 32
132714 ACAAAAACTA
* *
132724 ATTAAAATATGATGTAATATAAAAAATT-ATAT
1 ATTAAAAT-TTATATAATATAAAAAATTAATAT
** *
132756 ATTAAAATTTATATAATATAAATTATTAATTT
1 ATTAAAATTTATATAATATAAAAAATTAATAT
*
132788 ATAAAAATTTATATAAATATA
1 ATTAAAATTTATAT-AATATA
132809 TAACCTTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 15 0.33
32 24 0.53
33 6 0.13
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (32 bp):
ATTAAAATTTATATAATATAAAAAATTAATAT
Found at i:133550 original size:16 final size:14
Alignment explanation
Indices: 133536--133577 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 14
133526 TAAATTTATG
133536 TTTATATTTATTTA
1 TTTATATTTATTTA
133550 TTTATATTTAAATTTA
1 TTTATATTT--ATTTA
133566 TTTATATTTATT
1 TTTATATTTATT
133578 AAAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 12 0.46
16 14 0.54
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATATTTATTTA
Found at i:133554 original size:20 final size:20
Alignment explanation
Indices: 133529--133631 Score: 95
Period size: 20 Copynumber: 5.0 Consensus size: 20
133519 GATCGAATAA
* *
133529 ATTTATGTTTATATTTATTT
1 ATTTATATTTAAATTTATTT
133549 ATTTATATTTAAATTTATTT
1 ATTTATATTTAAATTTATTT
*
133569 ATATT-TATTAAAATTT-TTT
1 AT-TTATATTTAAATTTATTT
*
133588 AAAATTATATTTAAATTTATCTT
1 --ATTTATATTTAAATTTAT-TT
*
133611 ATTTAT-TTATAAGTTTATTT
1 ATTTATATT-TAAATTTATTT
133631 A
1 A
133632 AGCTTTATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
19 3 0.04
20 37 0.54
21 26 0.38
22 1 0.01
23 2 0.03
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTATATTTAAATTTATTT
Found at i:133557 original size:10 final size:10
Alignment explanation
Indices: 133536--133631 Score: 72
Period size: 10 Copynumber: 9.4 Consensus size: 10
133526 TAAATTTATG
133536 TTTATATTTA
1 TTTATATTTA
133546 TTTAT-TTATA
1 TTTATATT-TA
*
133556 TTTAAATTTA
1 TTTATATTTA
133566 TTTATATTTA
1 TTTATATTTA
* *
133576 TTAAAATTT-
1 TTTATATTTA
*
133585 TTTAAAATTATA
1 TTT-ATATT-TA
*
133597 TTTAAATTTA
1 TTTATATTTA
*
133607 TCT-TATTTA
1 TTTATATTTA
133616 TTTATAAGTTTA
1 TTTAT-A-TTTA
133628 TTTA
1 TTTA
133632 AGCTTTATTT
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
9 11 0.16
10 39 0.56
11 9 0.13
12 11 0.16
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTATATTTA
Found at i:134066 original size:24 final size:26
Alignment explanation
Indices: 134039--134088 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
134029 TTATTTTATT
* *
134039 TATTTTA-AAAT-TTTATAATTAATA
1 TATTTTATAAATATTTAAAACTAATA
134063 TATTTTATAAATATTTAAAACTAATA
1 TATTTTATAAATATTTAAAACTAATA
134089 AATGCATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 4 0.18
26 11 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTTTATAAATATTTAAAACTAATA
Found at i:134384 original size:55 final size:52
Alignment explanation
Indices: 134267--134385 Score: 116
Period size: 56 Copynumber: 2.2 Consensus size: 52
134257 ATGTAAAATT
** *
134267 TAAT-ATTTTTATTTATAATCAAATAAATATATTTAATGAAATTTTTTAATA
1 TAATAATTTTTATTTATAATCAAATAAATATATTTAATGAAAAATATTAATA
* *
134318 AAATTAAAATTTTTATTTATAAATCAAATAAATAT-TATTAATGATAAAAATATTATTA
1 TAA-T--AATTTTTATTTAT-AATCAAATAAATATAT-TTAATG--AAAAATATTAATA
134376 TAATAATTTT
1 TAATAATTTT
134386 AAAATAGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
51 2 0.04
52 1 0.02
55 19 0.35
56 20 0.37
57 1 0.02
58 11 0.20
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (52 bp):
TAATAATTTTTATTTATAATCAAATAAATATATTTAATGAAAAATATTAATA
Found at i:135079 original size:17 final size:17
Alignment explanation
Indices: 135034--135082 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
135024 AAAAATTAAA
*
135034 AATAAAAATATTAGATAC
1 AATAAAAATA-TAAATAC
** *
135052 AATTTAAATATAAATAT
1 AATAAAAATATAAATAC
135069 AATAAAAATATAAA
1 AATAAAAATATAAA
135083 AATTTATTTA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAAAAATATAAATAC
Found at i:135623 original size:18 final size:19
Alignment explanation
Indices: 135559--135626 Score: 65
Period size: 18 Copynumber: 3.7 Consensus size: 19
135549 AATTAATATG
135559 TTATATTTAATATATATTAT-
1 TTATATTTAATA-AT-TTATA
*
135579 TTATAATTAA-AATTT-TAA
1 TTATATTTAATAATTTAT-A
135597 TT-TATTTAATAATTTATA
1 TTATATTTAATAATTTATA
135615 TTATA-TTAATAA
1 TTATATTTAATAA
135627 AATTATAAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
16 1 0.02
17 8 0.20
18 19 0.46
19 4 0.10
20 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATATTTAATAATTTATA
Found at i:136197 original size:2 final size:2
Alignment explanation
Indices: 136190--136215 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
136180 ATCAATTATT
136190 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
136216 ATAAACGCGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:147202 original size:83 final size:85
Alignment explanation
Indices: 147088--147255 Score: 243
Period size: 83 Copynumber: 2.0 Consensus size: 85
147078 AAGCTAAAAT
* * *
147088 ATTATTAAGATAGATTACCAGCTTAAGATTATCATTCTTTCAACAATAGATAACTTTAATCACAC
1 ATTATTAAGATAGATAACCAGCGTAAGATTATCATCCTTTCAACAATAGATAACTTTAATCACAC
*
147153 -A-ATAACTCATTACTTGCA
66 AAGAGAACTCATTACTTGCA
* *
147171 ATTATTAAGATAGATAACTAGCAGTAA-ATTATCATCCTTTCAACAATAGATAACTTTAATCCCA
1 ATTATTAAGATAGATAACCAGC-GTAAGATTATCATCCTTTCAACAATAGATAACTTTAATCACA
*
147235 CAAGAGAACTCATTATTTGCA
65 CAAGAGAACTCATTACTTGCA
147256 GTTAAAATGA
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
83 56 0.75
84 4 0.05
85 15 0.20
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (85 bp):
ATTATTAAGATAGATAACCAGCGTAAGATTATCATCCTTTCAACAATAGATAACTTTAATCACAC
AAGAGAACTCATTACTTGCA
Found at i:149102 original size:2 final size:2
Alignment explanation
Indices: 149095--149126 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
149085 TGATCAGAAT
149095 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
149127 AATGAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:149483 original size:21 final size:18
Alignment explanation
Indices: 149445--149492 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
149435 ATTTAAAAAA
149445 ATATTAAAATATTATTTTT
1 ATATTAAAATATTA-TTTT
*
149464 ATATTAATATTATATATTTT
1 ATATTAA-AATAT-TATTTT
149484 ATTATTAAA
1 A-TATTAAA
149493 TTTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 7 0.28
20 10 0.40
21 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATATTAAAATATTATTTT
Found at i:149583 original size:21 final size:19
Alignment explanation
Indices: 149559--149624 Score: 55
Period size: 21 Copynumber: 3.3 Consensus size: 19
149549 TTTAAATTCA
149559 TAAAAACTTTATTTTATGATT
1 TAAAAAC-TTATTTTAT-ATT
*
149580 TAAATCACTTATTTTACTCA-T
1 TAAA-AACTTATTTTA-T-ATT
149601 TAATAAA-TTATTTTATATT
1 TAA-AAACTTATTTTATATT
149620 TAAAA
1 TAAAA
149625 TATAATTTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 3 0.08
19 5 0.13
20 8 0.21
21 17 0.45
22 5 0.13
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (19 bp):
TAAAAACTTATTTTATATT
Found at i:149785 original size:17 final size:17
Alignment explanation
Indices: 149753--149816 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 17
149743 CTAAAATAAT
*
149753 TTATAATT-TATGTAT-
1 TTATAATTATATTTATA
*
149768 TTAT-ATTATTTTTATA
1 TTATAATTATATTTATA
149784 TTATAATTATATTTA-A
1 TTATAATTATATTTATA
* *
149800 -TATATTTTTATTTATA
1 TTATAATTATATTTATA
149816 T
1 T
149817 AAATTTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 3 0.08
15 21 0.54
16 6 0.15
17 9 0.23
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATAATTATATTTATA
Found at i:149828 original size:26 final size:28
Alignment explanation
Indices: 149767--149831 Score: 73
Period size: 26 Copynumber: 2.4 Consensus size: 28
149757 AATTTATGTA
*
149767 TTTATATTATTTTTATATTATAATTATAT
1 TTTATA-TATTTTTATATTATAATAATAT
*
149796 TTAATATATTTTTAT-TTAT-ATAA-ATT
1 TTTATATATTTTTATATTATAATAATA-T
149822 TTTATATATT
1 TTTATATATT
149832 AATAAATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 1 0.03
26 13 0.41
27 4 0.12
28 9 0.28
29 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTATATATTTTTATATTATAATAATAT
Found at i:149838 original size:18 final size:18
Alignment explanation
Indices: 149790--149847 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
149780 TATATTATAA
*
149790 TTATAT-TTAATATATTT
1 TTATATATTAATAAATTT
*
149807 TTATTTA-T-ATAAATTT
1 TTATATATTAATAAATTT
149823 TTATATATTAATAAATTT
1 TTATATATTAATAAATTT
149841 TTATATA
1 TTATATA
149848 AATTTTAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 13 0.37
17 7 0.20
18 15 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATATTAATAAATTT
Found at i:149847 original size:44 final size:45
Alignment explanation
Indices: 149747--149847 Score: 104
Period size: 44 Copynumber: 2.3 Consensus size: 45
149737 ATTAATCTAA
* *
149747 AATAATTTATA-ATTTATGTATTTATATTATTTTTATATTATAAT
1 AATATTTTATATATTTATGTATTTATATAATTTTTATATTATAAT
* *
149791 TATATTTAATATATTT-T-TATTTATATAAATTTTTATA-TATTAAT
1 AATATTTTATATATTTATGTATTTATAT-AATTTTTATATTA-TAAT
149835 AA-ATTTTTATATA
1 AATA-TTTTATATA
149848 AATTTTAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
43 12 0.26
44 31 0.66
45 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (45 bp):
AATATTTTATATATTTATGTATTTATATAATTTTTATATTATAAT
Found at i:150177 original size:22 final size:21
Alignment explanation
Indices: 150139--150182 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
150129 ATATTTTATT
150139 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
150160 TAAATATTAATGTA-AAAATATA
1 TAAAT-TTAAT-TATAAAATATA
150182 T
1 T
150183 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 14 0.67
23 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:151380 original size:20 final size:21
Alignment explanation
Indices: 151357--151397 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
151347 TTTAATATAT
*
151357 ATTAAA-AAAATTAATAAAAA
1 ATTAAATAAAACTAATAAAAA
*
151377 ATTAAATTAAACTAATAAAAA
1 ATTAAATAAAACTAATAAAAA
151398 TATATTTCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
ATTAAATAAAACTAATAAAAA
Found at i:151835 original size:2 final size:2
Alignment explanation
Indices: 151823--151866 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
151813 TTGAAAAAGT
151823 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
151864 TA T
1 TA T
151867 TTCATGCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:156065 original size:20 final size:21
Alignment explanation
Indices: 156027--156065 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
156017 ATCAATGATG
156027 TTTTGAATATTTAAAAAATAA
1 TTTTGAATATTTAAAAAATAA
156048 TTTT-AATA-TTAAATAAAT
1 TTTTGAATATTTAAA-AAAT
156066 GTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTTGAATATTTAAAAAATAA
Found at i:158013 original size:2 final size:2
Alignment explanation
Indices: 157959--157997 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
157949 TAAATACCTG
157959 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
157998 GCTAATCTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:160968 original size:3 final size:3
Alignment explanation
Indices: 160954--160988 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
160944 CTCAATCTCT
*
160954 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
160989 CCTAATATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:161841 original size:2 final size:2
Alignment explanation
Indices: 161834--161877 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
161824 CTTCATGATT
161834 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
161876 TA
1 TA
161878 AAATTAGGTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:163430 original size:31 final size:30
Alignment explanation
Indices: 163384--163441 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
163374 ATTGTTTACG
*
163384 TAAATATAAATTATTAAATATGTTAAAATT
1 TAAATATAAATTATTAAATATATTAAAATT
*
163414 TAAATATATAATTATTATATATATTAAA
1 TAAATATA-AATTATTAAATATATTAAA
163442 TGTGTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (30 bp):
TAAATATAAATTATTAAATATATTAAAATT
Found at i:164191 original size:16 final size:15
Alignment explanation
Indices: 164152--164193 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
164142 TCCCAAGTTG
*
164152 TGATATATAAATATA
1 TGATATATATATATA
164167 TG-TATATATATATA
1 TGATATATATATATA
164181 TGATATA-ATATAT
1 TGATATATATATAT
164194 TGCAATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (15 bp):
TGATATATATATATA
Found at i:165196 original size:2 final size:2
Alignment explanation
Indices: 165189--165213 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
165179 ACCATGACTA
165189 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
165214 ATACAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:165989 original size:19 final size:19
Alignment explanation
Indices: 165950--165989 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
165940 TGTTAAAATT
*
165950 AAATTAAAAAATAATTTAA
1 AAATTAAAAAATAATTGAA
165969 AAATTAAAAAAATAA-TGAA
1 AAATT-AAAAAATAATTGAA
165988 AA
1 AA
165990 GAGAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAATTAAAAAATAATTGAA
Found at i:166807 original size:3 final size:3
Alignment explanation
Indices: 166799--166831 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
166789 CTGTTATTTA
166799 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
166832 ATAATTAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:167144 original size:23 final size:24
Alignment explanation
Indices: 167117--167176 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 24
167107 TCATCATTAA
**
167117 ATAATATTT-TTATTTTTTATTTT
1 ATAATATTTATTATAATTTATTTT
167140 ATAAT-TTTATTATAATTTATTTT
1 ATAATATTTATTATAATTTATTTT
167163 AT-ATATTTAATTAT
1 ATAATATTT-ATTAT
167177 TTAACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 5 0.16
23 22 0.69
24 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATAATATTTATTATAATTTATTTT
Found at i:167202 original size:9 final size:9
Alignment explanation
Indices: 167145--167209 Score: 60
Period size: 9 Copynumber: 7.1 Consensus size: 9
167135 ATTTTATAAT
167145 TTTATTATAA
1 TTTATT-TAA
*
167155 TTTATTTTA
1 TTTATTTAA
*
167164 TATATTTAA
1 TTTATTTAA
167173 -TTATTTAA
1 TTTATTTAA
* * *
167181 CTAATTGAA
1 TTTATTTAA
167190 TTTATTTAA
1 TTTATTTAA
167199 TTTAATTTAA
1 TTT-ATTTAA
167209 T
1 T
167210 GATATCAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
8 7 0.16
9 24 0.55
10 13 0.30
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TTTATTTAA
Found at i:168840 original size:2 final size:2
Alignment explanation
Indices: 168833--168872 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
168823 AAGCTGAAGA
**
168833 AT AT AT AT AT AT AT AT AT AT GC AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
168873 GAAGGTGCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:169826 original size:15 final size:14
Alignment explanation
Indices: 169788--169834 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
169778 ATATTTTTAC
169788 TATATATT-AAATA
1 TATATATTAAAATA
* *
169801 TATACACTAAAATCA
1 TATATATTAAAAT-A
169816 TATATATTAAAAT-
1 TATATATTAAAATA
169829 TATATA
1 TATATA
169835 CATATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.43
14 4 0.14
15 12 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (14 bp):
TATATATTAAAATA
Found at i:169865 original size:21 final size:23
Alignment explanation
Indices: 169824--169866 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
169814 CATATATATT
*
169824 AAAATTATATACATATTAATTAA
1 AAAATTATATACATATAAATTAA
169847 AAAATTATATAC-TA-AAATTA
1 AAAATTATATACATATAAATTA
169867 TGTTAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 2 0.11
23 12 0.63
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (23 bp):
AAAATTATATACATATAAATTAA
Found at i:170170 original size:2 final size:2
Alignment explanation
Indices: 170163--170188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170153 TAATTTGATT
170163 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
170189 AAAGATAAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:171665 original size:2 final size:2
Alignment explanation
Indices: 171658--171693 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
171648 TAAGTATGTA
171658 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
171694 TTTTGATAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:172191 original size:25 final size:25
Alignment explanation
Indices: 172154--172201 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
172144 TAATTTATTT
*
172154 TTTTATTTATTAAATTAAAATTATA
1 TTTTATTTATTAAAATAAAATTATA
*
172179 TTTTA-TTATTTAAAATAATATTA
1 TTTTATTTA-TTAAAATAAAATTA
172202 AAAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTTATTTATTAAAATAAAATTATA
Found at i:172215 original size:30 final size:30
Alignment explanation
Indices: 172166--172241 Score: 100
Period size: 31 Copynumber: 2.4 Consensus size: 30
172156 TTATTTATTA
*
172166 AATTAAAATTATATTTTATTATTTAAAATAAT
1 AATTAAAAATAT-TTTTATTATTT-AAATAAT
172198 -ATTAAAAATATTTTTATTATTTAAATAAT
1 AATTAAAAATATTTTTATTATTTAAATAAT
172227 AATTTAAATAATATT
1 AA-TTAAA-AATATT
172242 AAGTCAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 7 0.17
30 12 0.30
31 15 0.38
32 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
AATTAAAAATATTTTTATTATTTAAATAAT
Found at i:177717 original size:24 final size:25
Alignment explanation
Indices: 177653--177722 Score: 61
Period size: 25 Copynumber: 2.8 Consensus size: 25
177643 AAATTTAAAC
* * *
177653 TTATGTTTTAATTAAAATATATATT
1 TTATTTTTTATTTAAAATATATATA
* * *
177678 TTAATTTTGATATTAATATAT-TATA
1 TTATTTTTTAT-TTAAAATATATATA
177703 TTATTTTTTATTTAAGAATA
1 TTATTTTTTATTTAA-AATA
177723 AATTAGTTAC
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
24 4 0.12
25 22 0.65
26 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (25 bp):
TTATTTTTTATTTAAAATATATATA
Found at i:178437 original size:32 final size:34
Alignment explanation
Indices: 178397--178461 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 34
178387 ATATTTATAT
**
178397 ATAAATTTTATTATAT-TAA-TAAATCATATTAA
1 ATAAATTTTAAAATATATAATTAAATCATATTAA
*
178429 ATAAATTTTAAAATATATAATTATATCATATTA
1 ATAAATTTTAAAATATATAATTAAATCATATTA
178462 TATATTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 14 0.50
33 3 0.11
34 11 0.39
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (34 bp):
ATAAATTTTAAAATATATAATTAAATCATATTAA
Found at i:178465 original size:2 final size:2
Alignment explanation
Indices: 178441--178525 Score: 106
Period size: 2 Copynumber: 43.5 Consensus size: 2
178431 AAATTTTAAA
*
178441 AT AT AT A- AT -T AT AT CAT AT -T AT AT AT TT A- AT AT CAT AT AT
1 AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT -AT AT AT
*
178481 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
178523 AT A
1 AT A
178526 ATTATATTTA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
1 4 0.05
2 65 0.89
3 4 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178537 original size:18 final size:18
Alignment explanation
Indices: 178439--178542 Score: 84
Period size: 20 Copynumber: 5.4 Consensus size: 18
178429 ATAAATTTTA
178439 AAATATATAATTATATCAT
1 AAATATATAATTATAT-AT
* *
178458 -ATTATATATTTAATATCAT
1 AAATATATAATT-ATAT-AT
*
178477 ATATATATATATATATATAT
1 AAATATATA-AT-TATATAT
*
178497 ATATATATATATATATATAT
1 AAATATATA-AT-TATATAT
*
178517 AAATATATAATTATATTT
1 AAATATATAATTATATAT
*
178535 AAAAATAT
1 AAATATAT
178543 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
18 22 0.30
19 9 0.12
20 36 0.49
21 5 0.07
22 1 0.01
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATATATAATTATATAT
Found at i:188369 original size:75 final size:76
Alignment explanation
Indices: 188246--188391 Score: 206
Period size: 75 Copynumber: 1.9 Consensus size: 76
188236 GGGACTGTCC
* * * *
188246 GAGCATTAGTTGATTACATAGTCAAAGGTATTGCAATTTTTATTGAA-TTTTTGGCCACCCAATT
1 GAGCATTAGATAATTACATAGTCAAAGGTAATGCAAATTTTATTGAATTTTTTGGCCACCCAATT
*
188310 AGCTTCGGTCG
66 AACTTCGGTCG
* *
188321 GAGCATTAGATAATTACCTAGTCAAAGGTAATG-AGAATTTTATTGAATTTTTTGGCCACCCCAT
1 GAGCATTAGATAATTACATAGTCAAAGGTAATGCA-AATTTTATTGAATTTTTTGGCCACCCAAT
188385 TAACTTC
65 TAACTTC
188392 AGTGCATGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
74 1 0.02
75 40 0.65
76 21 0.34
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (76 bp):
GAGCATTAGATAATTACATAGTCAAAGGTAATGCAAATTTTATTGAATTTTTTGGCCACCCAATT
AACTTCGGTCG
Found at i:188523 original size:48 final size:50
Alignment explanation
Indices: 188468--188579 Score: 131
Period size: 48 Copynumber: 2.3 Consensus size: 50
188458 TTTGAGATTG
* *
188468 AATTTTAATATTTA-TAATTTTTTTAAATA-TTTAAAAAAATAATA-TTAA
1 AATTTTAAT-TTTATTAATTTATATAAATATTTTAAAAAAATAATATTTAA
* * * *
188516 AATTTTAATTTAATTAATTTATATAATTATTTTTAAAATATAATATTTTAA
1 AATTTTAATTTTATTAATTTATATAAATATTTTAAAAAAATAATA-TTTAA
188567 AATTTTAATTTTA
1 AATTTTAATTTTA
188580 ATTTTAATGT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
47 3 0.06
48 21 0.40
49 13 0.25
51 16 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (50 bp):
AATTTTAATTTTATTAATTTATATAAATATTTTAAAAAAATAATATTTAA
Found at i:188566 original size:15 final size:17
Alignment explanation
Indices: 188536--188569 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
188526 TAATTAATTT
188536 ATATAATTATTTTTAAA
1 ATATAATTATTTTTAAA
188553 ATATAA-TA-TTTTAAA
1 ATATAATTATTTTTAAA
188568 AT
1 AT
188570 TTTAATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 2 0.12
17 6 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATAATTATTTTTAAA
Found at i:189872 original size:27 final size:29
Alignment explanation
Indices: 189840--189949 Score: 111
Period size: 27 Copynumber: 3.8 Consensus size: 29
189830 TAATATGATA
189840 TTAATATCAAAATATTATATTAA-AATA-
1 TTAATATCAAAATATTATATTAACAATAT
* * *
189867 TTAATATTTTAAATAATATTATTTTAATAATAT
1 TTAATA---TCAA-AATATTATATTAACAATAT
* *
189900 TTAATAT--TAATATTATTTTAACAATAT
1 TTAATATCAAAATATTATATTAACAATAT
189927 TTAATATCAAAATATTATATTAA
1 TTAATATCAAAATATTATATTAA
189950 TATTAAATTA
Statistics
Matches: 69, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
27 31 0.45
29 12 0.17
30 4 0.06
31 12 0.17
32 4 0.06
33 6 0.09
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TTAATATCAAAATATTATATTAACAATAT
Found at i:189874 original size:19 final size:19
Alignment explanation
Indices: 189819--189874 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
189809 TTTAAAATAT
*
189819 TATTAAAATATTAATATGA
1 TATTAAAATATTAATATTA
* *
189838 TATTAATATCA-AAATATTA
1 TATTAAAAT-ATTAATATTA
189857 TATTAAAATATTAATATT
1 TATTAAAATATTAATATT
189875 TTAAATAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.03
19 28 0.93
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAAAATATTAATATTA
Found at i:189886 original size:18 final size:17
Alignment explanation
Indices: 189859--189907 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
189849 AAATATTATA
189859 TTAA-AATATTAATATT
1 TTAATAATATTAATATT
189875 TTAAATAATA-T--TATT
1 TT-AATAATATTAATATT
189890 TTAATAATATTTAATATT
1 TTAATAATA-TTAATATT
189908 AATATTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 3 0.11
17 3 0.11
18 8 0.30
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATAATATTAATATT
Found at i:189889 original size:15 final size:15
Alignment explanation
Indices: 189850--189900 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
189840 TTAATATCAA
*
189850 AATATTATATTAAAAT
1 AATATTAT-TTTAAAT
* *
189866 ATTAATATTTTAAAT
1 AATATTATTTTAAAT
189881 AATATTATTTT-AAT
1 AATATTATTTTAAAT
189895 AATATT
1 AATATT
189901 TAATATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
14 9 0.30
15 15 0.50
16 6 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
AATATTATTTTAAAT
Found at i:189954 original size:11 final size:11
Alignment explanation
Indices: 189826--189914 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
189816 TATTATTAAA
*
189826 ATATTAATATG
1 ATATTAATATT
*
189837 ATATTAATATC
1 ATATTAATATT
189848 A-A--AATATT
1 ATATTAATATT
189856 ATATTAA-A--
1 ATATTAATATT
189864 ATATTAATATT
1 ATATTAATATT
* *
189875 TTAAATAATATT
1 AT-ATTAATATT
* *
189887 ATTTTAATAAT
1 ATATTAATATT
189898 AT-TTAATATT
1 ATATTAATATT
189908 AATATTA
1 -ATATTA
189915 TTTTAACAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
8 13 0.22
9 2 0.03
10 9 0.15
11 24 0.40
12 12 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (11 bp):
ATATTAATATT
Found at i:190286 original size:24 final size:24
Alignment explanation
Indices: 190259--190305 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
190249 TATTTATATT
190259 TTAAAAT-TTAATAAAATAAATTTA
1 TTAAAATATTAA-AAAATAAATTTA
* *
190283 TTAAATTATTAAAAATTAAATTT
1 TTAAAATATTAAAAAATAAATTT
190306 TAAAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAAAATATTAAAAAATAAATTTA
Found at i:190307 original size:25 final size:23
Alignment explanation
Indices: 190271--190317 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
190261 AAAATTTAAT
**
190271 AAAATAAATTTATTAAATTATTA
1 AAAATAAATTTAAAAAATTATTA
190294 AAAATTAAATTTTAAAAAATTATT
1 AAAA-TAAA-TTTAAAAAATTATT
190318 TTTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 4 0.20
25 12 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATAAATTTAAAAAATTATTA
Found at i:190310 original size:14 final size:14
Alignment explanation
Indices: 190282--190334 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
190272 AAATAAATTT
190282 ATTAAATTATTAAAA
1 ATTAAATT-TTAAAA
190297 ATTAAATTTTAAAAA
1 ATTAAATTTT-AAAA
**
190312 ATTATTTTTATAAAA
1 ATTAAATTT-TAAAA
190327 ATTAAATT
1 ATTAAATT
190335 AAAAATATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 2 0.06
15 29 0.91
16 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTAAATTTTAAAA
Found at i:197371 original size:31 final size:32
Alignment explanation
Indices: 197297--197375 Score: 115
Period size: 32 Copynumber: 2.5 Consensus size: 32
197287 TATCTTTTAG
* ** *
197297 CCATTTAATCAACAATGGTAGTATTTTTGCAT
1 CCATTTAGTCAACAATGGTAGTACCTTTGCAC
197329 CCATTTAGTCAACAATGGTAGTACCTTTGCAC
1 CCATTTAGTCAACAATGGTAGTACCTTTGCAC
197361 CCA-TTAGTCAACAAT
1 CCATTTAGTCAACAAT
197376 TCTCTTACTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 12 0.28
32 31 0.72
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (32 bp):
CCATTTAGTCAACAATGGTAGTACCTTTGCAC
Found at i:202452 original size:32 final size:33
Alignment explanation
Indices: 202372--202453 Score: 85
Period size: 32 Copynumber: 2.5 Consensus size: 33
202362 AAGTGGAAGA
* *
202372 ATTGTTGATTAAGTGGGCCCGCAAAGGTGCTGCT
1 ATTGTTGATTAAATGGG-CCGCAAAGGTGCTGCC
* ** * *
202406 ATTATTGACCAAATGGG-TGCAAAGGTGTTGCC
1 ATTGTTGATTAAATGGGCCGCAAAGGTGCTGCC
202438 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
202454 CTAAAAGACA
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
32 25 0.66
34 13 0.34
ACGTcount: A:0.26, C:0.13, G:0.29, T:0.32
Consensus pattern (33 bp):
ATTGTTGATTAAATGGGCCGCAAAGGTGCTGCC
Found at i:204935 original size:13 final size:13
Alignment explanation
Indices: 204917--204973 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
204907 TTCAACGATT
204917 TGTATCGATACAA
1 TGTATCGATACAA
*
204930 TGTATCGATGCATAA
1 TGTATCGAT--ACAA
204945 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
204962 TGTATCGATACA
1 TGTATCGATACA
204974 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 21 0.58
15 3 0.08
17 3 0.08
19 9 0.25
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:204957 original size:32 final size:32
Alignment explanation
Indices: 204916--205000 Score: 143
Period size: 32 Copynumber: 2.7 Consensus size: 32
204906 TTTCAACGAT
*
204916 TTGTATCGATACAATGTATCGATGCATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
204948 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
204980 TTGTGTCGATACAATGTATCG
1 TTGTATCGATACAATGTATCG
205001 CTACGAAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:205042 original size:13 final size:13
Alignment explanation
Indices: 205024--205048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
205014 GCCAAGAAAA
205024 TGTATCGATACAT
1 TGTATCGATACAT
205037 TGTATCGATACA
1 TGTATCGATACA
205049 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:205096 original size:52 final size:52
Alignment explanation
Indices: 205057--205185 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
205047 CACTGATCTT
* *
205057 TGTATCGATACATGCAGGCCAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
205109 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
* * *
205161 TGTATCGATATATGCAGGTAAATTT
1 TGTATCGATACATACAGGCAAATTT
205186 TCATATTTCG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
Found at i:208828 original size:18 final size:19
Alignment explanation
Indices: 208805--208845 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
208795 ACAACTCAGC
208805 TTTATTTTCTC-CACTCTT
1 TTTATTTTCTCACACTCTT
*
208823 TTTATTTTTTCAACACTCTT
1 TTTATTTTCTC-ACACTCTT
208843 TTT
1 TTT
208846 TAATGTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.15, C:0.22, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTTTCTCACACTCTT
Found at i:212202 original size:19 final size:19
Alignment explanation
Indices: 212178--212216 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
212168 ATTAGTTTTT
212178 ACGATATAATATATAATAA
1 ACGATATAATATATAATAA
* *
212197 ACGATATGATATCTAATAA
1 ACGATATAATATATAATAA
212216 A
1 A
212217 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (19 bp):
ACGATATAATATATAATAA
Found at i:217552 original size:26 final size:29
Alignment explanation
Indices: 217491--217554 Score: 71
Period size: 30 Copynumber: 2.3 Consensus size: 29
217481 AAGTTCATTT
*
217491 AATTTAAATAAACGAACATGAACACACTTA
1 AATTTAAATAAACAAACATGAACACAC-TA
* *
217521 ATTTTAAATAAATAAACAT-AA-ACA-TA
1 AATTTAAATAAACAAACATGAACACACTA
217547 AATTTAAA
1 AATTTAAA
217555 CTTTTTAACG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 9 0.30
28 3 0.10
29 2 0.07
30 16 0.53
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (29 bp):
AATTTAAATAAACAAACATGAACACACTA
Found at i:218492 original size:18 final size:17
Alignment explanation
Indices: 218471--218572 Score: 54
Period size: 18 Copynumber: 6.0 Consensus size: 17
218461 CACGATATTG
218471 AAAATAATTAAAATATAT
1 AAAATAA-TAAAATATAT
218489 AAAA-AAT---ATA-AT
1 AAAATAATAAAATATAT
* * *
218501 ATAATATTAAAATTTAT
1 AAAATAATAAAATATAT
*
218518 ATAAAT-ATAAAATATTTT
1 A-AAATAATAAAATA-TAT
* *
218536 AAATATAATTATAATAAAT
1 AAA-ATAA-TAAAATATAT
218555 AAAATAATATAAATATAT
1 AAAATAATA-AAATATAT
218573 TTTCAGATAG
Statistics
Matches: 61, Mismatches: 12, Indels: 22
0.64 0.13 0.23
Matches are distributed among these distances:
12 5 0.08
13 5 0.08
16 3 0.05
17 15 0.25
18 22 0.36
19 5 0.08
20 6 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAATAATAAAATATAT
Found at i:218509 original size:29 final size:28
Alignment explanation
Indices: 218477--218572 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 28
218467 ATTGAAAATA
*
218477 ATTAAAATATATAAAAAATATAATATAAT
1 ATTAAAATATATAATAAATATAA-ATAAT
*
218506 ATTAAAATTTAT-ATAAATATAAA-ATAT
1 ATTAAAATATATAATAAATATAAATA-AT
*
218533 TTTAAATATAATTATAATAAATA-AAATAAT
1 ATTAAA-AT-A-TATAATAAATATAAATAAT
218563 A-T-AAATATAT
1 ATTAAAATATAT
218573 TTTCAGATAG
Statistics
Matches: 56, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
25 3 0.05
26 2 0.04
27 10 0.18
28 13 0.23
29 12 0.21
30 8 0.14
31 8 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTAAAATATATAATAAATATAAATAAT
Found at i:222610 original size:11 final size:11
Alignment explanation
Indices: 222578--222631 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
222568 GTGTAATAGG
222578 ATTATATAATATT
1 ATTATATAA-A-T
*
222591 AATATATAAAT
1 ATTATATAAAT
*
222602 ATTACATAAAT
1 ATTATATAAAT
222613 A--ATATAAAT
1 ATTATATAAAT
222622 ATTATATAAA
1 ATTATATAAA
222632 AATAAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 8 0.23
11 18 0.51
12 1 0.03
13 8 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTATATAAAT
Found at i:222619 original size:20 final size:19
Alignment explanation
Indices: 222594--222641 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
222584 TAATATTAAT
222594 ATATAAATATTACATAAATA
1 ATATAAATATTACATAAA-A
*
222614 ATATAAATATTATATAAAA
1 ATATAAATATTACATAAAA
*
222633 ATAAAAATA
1 ATATAAATA
222642 ATATAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATATAAATATTACATAAAA
Found at i:222655 original size:28 final size:32
Alignment explanation
Indices: 222581--222655 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 32
222571 TAATAGGATT
*
222581 ATATAATATTAATATATAAATATTACATAAATA
1 ATATAATA-TAATATATAAATAATACATAAATA
*
222614 ATATAA-ATATTATATAAA-AATA-A-AAATA
1 ATATAATATAATATATAAATAATACATAAATA
222642 ATATAATA-AATATA
1 ATATAATATAATATA
222656 ATAGATTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 16 0.42
29 2 0.05
30 3 0.08
31 10 0.26
32 1 0.03
33 6 0.16
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (32 bp):
ATATAATATAATATATAAATAATACATAAATA
Found at i:222718 original size:23 final size:24
Alignment explanation
Indices: 222687--222752 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 24
222677 ATGATATTAT
222687 AATATATTATATTATAATTAA-AA
1 AATATATTATATTATAATTAATAA
* *
222710 AATTTATTATATTTAATAATTAATAT
1 AATATATTATA-TT-ATAATTAATAA
222736 AATAT-TTATATTATAAT
1 AATATATTATATTATAAT
222753 ATTAATATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
23 15 0.41
24 4 0.11
25 13 0.35
26 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATATATTATATTATAATTAATAA
Found at i:222744 original size:25 final size:26
Alignment explanation
Indices: 222684--222765 Score: 93
Period size: 25 Copynumber: 3.3 Consensus size: 26
222674 AATATGATAT
222684 TATAATATATTATA-TT-ATAATTAA
1 TATAATATATTATATTTAATAATTAA
* *
222708 -AAAATTTATTATATTTAATAATTAA
1 TATAATATATTATATTTAATAATTAA
222733 TATAATAT-TTATATTATAAT-ATTAA
1 TATAATATATTATATT-TAATAATTAA
222758 TATTAATA
1 TA-TAATA
222766 AGTTTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 11 0.22
24 2 0.04
25 22 0.45
26 14 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATAATATATTATATTTAATAATTAA
Found at i:222750 original size:14 final size:14
Alignment explanation
Indices: 222716--222762 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
222706 AAAAAATTTA
*
222716 TTATATT-TAATAA
1 TTATATTATAATAT
222729 TTA-A-TATAATAT
1 TTATATTATAATAT
222741 TTATATTATAATAT
1 TTATATTATAATAT
*
222755 TAATATTA
1 TTATATTA
222763 ATAAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 1 0.03
12 9 0.31
13 4 0.14
14 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTATATTATAATAT
Found at i:223361 original size:17 final size:16
Alignment explanation
Indices: 223339--223388 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 16
223329 CTCTAAATCC
223339 AATAATATATGATAAAT
1 AATAATATAT-ATAAAT
*
223356 AATAATAAATATTAAAT
1 AATAATATATA-TAAAT
223373 -ATAAATATATATAAAT
1 AAT-AATATATATAAAT
223389 TTATTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (16 bp):
AATAATATATATAAAT
Found at i:223947 original size:12 final size:12
Alignment explanation
Indices: 223823--223947 Score: 58
Period size: 12 Copynumber: 10.1 Consensus size: 12
223813 TATATTATTT
*
223823 ATATTTTTTTAA
1 ATATATTTTTAA
* *
223835 ATTTAATTTTAA
1 ATATATTTTTAA
* *
223847 ATAAAATTTTAA
1 ATATATTTTTAA
*
223859 ATTTTATTTATTTAA
1 A-TATA-TT-TTTAA
*
223874 TTATATTTATT-A
1 ATATATTT-TTAA
* *
223886 ATAAATAATTTAA
1 ATATAT-TTTTAA
*
223899 GTATATTTTTATA
1 ATATATTTTTA-A
* *
223912 TTTTATATTTTAA
1 ATATAT-TTTTAA
223925 AT-T-TTTTTAA
1 ATATATTTTTAA
223935 ATATATTTTTAA
1 ATATATTTTTAA
223947 A
1 A
223948 ATTTAATTTT
Statistics
Matches: 84, Mismatches: 19, Indels: 20
0.68 0.15 0.16
Matches are distributed among these distances:
10 8 0.10
11 2 0.02
12 41 0.49
13 19 0.23
14 9 0.11
15 5 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (12 bp):
ATATATTTTTAA
Found at i:223958 original size:15 final size:15
Alignment explanation
Indices: 223939--223969 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
223929 TTTTAAATAT
223939 ATTTTTAA-AATTTA
1 ATTTTTAATAATTTA
223953 ATTTTTAATAATTTA
1 ATTTTTAATAATTTA
223968 AT
1 AT
223970 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTTTTAATAATTTA
Found at i:224035 original size:20 final size:20
Alignment explanation
Indices: 223997--224038 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
223987 TAATAGATGA
*
223997 TATATTTTTAATATTTATAT
1 TATATTTTTAATATATATAT
224017 TATATTTTT-ATACTATATAT
1 TATATTTTTAATA-TATATAT
224037 TA
1 TA
224039 CATAATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATATTTTTAATATATATAT
Found at i:224059 original size:26 final size:26
Alignment explanation
Indices: 224030--224083 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
224020 ATTTTTATAC
*
224030 TATATATTACATAA-TATATAAATAAA
1 TATATATTACATAATTA-AAAAATAAA
*
224056 TATATATTATATAATTAAAAAATAAA
1 TATATATTACATAATTAAAAAATAAA
224082 TA
1 TA
224084 AAAAAAGAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
TATATATTACATAATTAAAAAATAAA
Found at i:224148 original size:18 final size:17
Alignment explanation
Indices: 224125--224184 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
224115 TAATATTTAG
224125 ATTATTTTTTAATCAAAT
1 ATTATTTTTTAAT-AAAT
224143 ATTATTTTTTACATAAAT
1 ATTATTTTTTA-ATAAAT
* *
224161 -TTATATTTTAA-AATT
1 ATTATTTTTTAATAAAT
*
224176 AATATTTTT
1 ATTATTTTT
224185 ATTTAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 3 0.08
16 7 0.19
17 9 0.25
18 15 0.42
19 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATTTTTTAATAAAT
Found at i:224167 original size:19 final size:18
Alignment explanation
Indices: 224125--224171 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
224115 TAATATTTAG
224125 ATTATTTTTTAATCAAAT
1 ATTATTTTTTAATCAAAT
224143 ATTATTTTTTACAT-AAAT
1 ATTATTTTTTA-ATCAAAT
*
224161 -TTATATTTTAA
1 ATTATTTTTTAA
224172 AATTAATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 1 0.04
17 9 0.33
18 15 0.56
19 2 0.07
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTTTTAATCAAAT
Found at i:231384 original size:26 final size:27
Alignment explanation
Indices: 231354--231405 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
231344 AATATATATT
231354 TATTTCGAATATATTT-AATTTTTTTA
1 TATTTCGAATATATTTAAATTTTTTTA
***
231380 TATTTTTTATATATTTAAATTTTTTT
1 TATTTCGAATATATTTAAATTTTTTT
231406 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TATTTCGAATATATTTAAATTTTTTTA
Found at i:231465 original size:13 final size:13
Alignment explanation
Indices: 231447--231483 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
231437 TATCCATCAG
231447 ATATAAATATTAA
1 ATATAAATATTAA
231460 ATATAAATATTAA
1 ATATAAATATTAA
231473 A-A-AAATATTAA
1 ATATAAATATTAA
231484 CGTAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 14 0.58
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
ATATAAATATTAA
Found at i:235745 original size:12 final size:11
Alignment explanation
Indices: 235726--235776 Score: 66
Period size: 12 Copynumber: 4.4 Consensus size: 11
235716 ATTTTAAAAG
235726 TTTTTTTCTTT
1 TTTTTTTCTTT
235737 TTTTCTTTCTCTT
1 TTTT-TTTCT-TT
235750 TTTTTTTCATTT
1 TTTTTTTC-TTT
*
235762 TTTTTTCCTTT
1 TTTTTTTCTTT
235773 TTTT
1 TTTT
235777 CCTTTTTCTT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
11 11 0.31
12 18 0.50
13 7 0.19
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:235756 original size:24 final size:22
Alignment explanation
Indices: 235726--235776 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 22
235716 ATTTTAAAAG
*
235726 TTTTTTTCTTTTTTTCTTTCTCTT
1 TTTTTTTCATTTTTT-TTTC-CTT
235750 TTTTTTTCATTTTTTTTTCCTT
1 TTTTTTTCATTTTTTTTTCCTT
235772 TTTTT
1 TTTTT
235777 CCTTTTTCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.31
23 4 0.15
24 14 0.54
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTCATTTTTTTTTCCTT
Found at i:235788 original size:12 final size:11
Alignment explanation
Indices: 235726--235788 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
235716 ATTTTAAAAG
*
235726 TTTTTTTCTTT
1 TTTTTTTCCTT
235737 TTTTCTTTCTCTT
1 TTTT-TTTC-CTT
*
235750 TTTTTTTCATT
1 TTTTTTTCCTT
235761 TTTTTTTCC--
1 TTTTTTTCCTT
235770 TTTTTTTCCTT
1 TTTTTTTCCTT
235781 TTTCTTTT
1 TTT-TTTT
235789 AAAAAAAATG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.20
11 17 0.39
12 12 0.27
13 6 0.14
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTCCTT
Found at i:244349 original size:21 final size:19
Alignment explanation
Indices: 244289--244364 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 19
244279 TATCATCAAA
**
244289 TTAAAAATTTTTTAAATTT
1 TTAAAAATAATTTAAATTT
* * *
244308 ATAAAAATAATTAAAAATT
1 TTAAAAATAATTTAAATTT
244327 TTAAAAATTAAATTTAAATTTTT
1 TTAAAAA-T-AATTTAAA--TTT
244350 TTAATAAATAATTTA
1 TTAA-AAATAATTTA
244365 TTATATATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
19 20 0.45
20 1 0.02
21 7 0.16
22 6 0.14
23 7 0.16
24 3 0.07
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAAAAATAATTTAAATTT
Found at i:244432 original size:20 final size:20
Alignment explanation
Indices: 244407--244448 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
244397 TTAAATATAT
244407 ATTAAAAATCATA-TTATTTA
1 ATTAAAAAT-ATATTTATTTA
*
244427 ATTAAATATATATTTATTTA
1 ATTAAAAATATATTTATTTA
244447 AT
1 AT
244449 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAAAATATATTTATTTA
Found at i:245131 original size:35 final size:36
Alignment explanation
Indices: 245092--245159 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 36
245082 ATTAAAATTA
245092 TTTATAAGTCAGATCA-TTTATTTAAAAATAAACTT
1 TTTATAAGTCAGATCACTTTATTTAAAAATAAACTT
* ** *
245127 TTTATAATTTGGATCACTTTATTTAATAATAAA
1 TTTATAAGTCAGATCACTTTATTTAAAAATAAA
245160 AATATATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 13 0.46
36 15 0.54
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (36 bp):
TTTATAAGTCAGATCACTTTATTTAAAAATAAACTT
Found at i:246948 original size:19 final size:20
Alignment explanation
Indices: 246915--246953 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
246905 TCTTTCTACG
* *
246915 TATATTTAAATAATATTAAA
1 TATATTTAAAAAATAATAAA
246935 TATA-TTAAAAAATAATAAA
1 TATATTTAAAAAATAATAAA
246954 CTGAATCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATTTAAAAAATAATAAA
Found at i:248243 original size:20 final size:20
Alignment explanation
Indices: 248204--248245 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
248194 ATTTTTTATA
* **
248204 TTTTATTAGTTTAACTAATT
1 TTTTATTAATTTAAAAAATT
248224 TTTTATTAATTTAAAAAATT
1 TTTTATTAATTTAAAAAATT
248244 TT
1 TT
248246 AATTTTACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTATTAATTTAAAAAATT
Found at i:249070 original size:20 final size:20
Alignment explanation
Indices: 249032--249070 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
249022 AAATTTTAAG
*
249032 TATTATAATTATATTTAAAA
1 TATTATAATTATATATAAAA
*
249052 TATTATAATTTTATATAAA
1 TATTATAATTATATATAAA
249071 TTTTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTATAATTATATATAAAA
Found at i:250904 original size:15 final size:17
Alignment explanation
Indices: 250870--250910 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
250860 TTTACATATT
250870 TTATATATTAGAATTAA
1 TTATATATTAGAATTAA
*
250887 TTATATTTTA-AATT-A
1 TTATATATTAGAATTAA
250902 TTATATATT
1 TTATATATT
250911 TTATATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TTATATATTAGAATTAA
Found at i:250911 original size:17 final size:17
Alignment explanation
Indices: 250869--250913 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
250859 ATTTACATAT
*
250869 TTTATATATTAGAATTA
1 TTTATATTTTAGAATTA
*
250886 ATTATATTTTA-AATTA
1 TTTATATTTTAGAATTA
250902 TTATATATTTTA
1 TT-TATATTTTA
250914 TATAAATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTATATTTTAGAATTA
Found at i:250963 original size:22 final size:21
Alignment explanation
Indices: 250920--250969 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
250910 TTTATATAAA
*
250920 TATTAATATATTTATTTATTTT
1 TATT-ATAAATTTATTTATTTT
*
250942 TATTATAAATTTATTATTTTTT
1 TATTATAAATTTATT-TATTTT
250964 TATTAT
1 TATTAT
250970 TTTTATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTATAAATTTATTTATTTT
Found at i:250965 original size:11 final size:11
Alignment explanation
Indices: 250951--250980 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
250941 TTATTATAAA
250951 TTTATTATTTT
1 TTTATTATTTT
250962 TTTATTATTTT
1 TTTATTATTTT
*
250973 TATATTAT
1 TTTATTAT
250981 ATTATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTATTATTTT
Found at i:250970 original size:31 final size:31
Alignment explanation
Indices: 250899--250975 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
250889 ATATTTTAAA
250899 TTATTATATATTTTA-TATAAATATTAATATAT
1 TTATT-TAT-TTTTATTATAAATATTAATATAT
* *
250931 TTATTTATTTTTATTATAAAT-TTATTATTT
1 TTATTTATTTTTATTATAAATATTAATATAT
*
250961 TTTTATTATTTTTAT
1 TTAT-TTATTTTTAT
250976 ATTATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 15 0.38
31 20 0.50
32 5 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TTATTTATTTTTATTATAAATATTAATATAT
Found at i:250996 original size:29 final size:29
Alignment explanation
Indices: 250919--251012 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
250909 TTTTATATAA
250919 ATATTA-A-TATATTTATTTATT-TTTATT
1 ATATTATATTATATTTATTTATTATTT-TT
250946 ATAAATT-TATTAT-TTT-TTTATTATTTTT
1 AT--ATTATATTATATTTATTTATTATTTTT
* * *
250974 ATATTATATTATATTTAATTATTAATTTA
1 ATATTATATTATATTTATTTATTATTTTT
251003 ATATTATATT
1 ATATTATATT
251013 TATGTCAGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
26 3 0.05
27 8 0.14
28 13 0.23
29 29 0.52
30 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (29 bp):
ATATTATATTATATTTATTTATTATTTTT
Found at i:251014 original size:12 final size:12
Alignment explanation
Indices: 250979--251014 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
250969 TTTTTATATT
250979 ATATTATATTTA
1 ATATTATATTTA
250991 ATTATTA-ATTTA
1 A-TATTATATTTA
251003 ATATTATATTTA
1 ATATTATATTTA
251015 TGTCAGAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.23
12 12 0.55
13 5 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:251282 original size:14 final size:14
Alignment explanation
Indices: 251265--251295 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
251255 TATAATCTTA
251265 TTATTATTTAAATT
1 TTATTATTTAAATT
*
251279 TTATTTTTTAAATT
1 TTATTATTTAAATT
251293 TTA
1 TTA
251296 ATTTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTTAAATT
Found at i:251300 original size:14 final size:14
Alignment explanation
Indices: 251271--251300 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
251261 CTTATTATTA
*
251271 TTTAAATTTTATTT
1 TTTAAATTTTAATT
251285 TTTAAATTTTAATT
1 TTTAAATTTTAATT
251299 TT
1 TT
251301 AATTAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTAAATTTTAATT
Found at i:251343 original size:17 final size:17
Alignment explanation
Indices: 251230--251351 Score: 60
Period size: 17 Copynumber: 7.2 Consensus size: 17
251220 ATATTTGGTT
*
251230 AATTTATATAATATTTA
1 AATTTATTTAATATTTA
251247 AATTTATTT-ATAATCTT-
1 AATTTATTTAAT-AT-TTA
*
251264 ATTATTATTTAA-ATTT-
1 AAT-TTATTTAATATTTA
*
251280 TATTT-TTTAA-ATTTTA
1 AATTTATTTAATA-TTTA
* * *
251296 ATTTTAATTAA-ATAATA
1 AATTTATTTAATAT-TTA
** *
251313 ATATCAATTCAATATTTA
1 A-ATTTATTTAATATTTA
251331 AATTTATTTAATATTTA
1 AATTTATTTAATATTTA
251348 AATT
1 AATT
251352 GTGATAATAA
Statistics
Matches: 78, Mismatches: 17, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
14 6 0.08
15 5 0.06
16 9 0.12
17 39 0.50
18 16 0.21
19 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:252128 original size:26 final size:26
Alignment explanation
Indices: 252068--252118 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
252058 TCCAGTGAGT
252068 AAATTTTTCTGGTACGTGAGAAATTA
1 AAATTTTTCTGGTACGTGAGAAATTA
* *
252094 AAATTTTTCTTGTAGGTGAGAAATT
1 AAATTTTTCTGGTACGTGAGAAATT
252119 TCTAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.20, T:0.41
Consensus pattern (26 bp):
AAATTTTTCTGGTACGTGAGAAATTA
Found at i:253149 original size:16 final size:16
Alignment explanation
Indices: 253125--253167 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
253115 TAGGTTGAAA
253125 TTTTATTTATTATTTT
1 TTTTATTTATTATTTT
*
253141 TTTTGTTTATTA-TTT
1 TTTTATTTATTATTTT
*
253156 TTTAATTTATTA
1 TTTTATTTATTA
253168 ACGATCCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTATTTT
Found at i:254685 original size:16 final size:17
Alignment explanation
Indices: 254666--254698 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
254656 TACTCATATT
*
254666 ATAT-TTTTTATTTTAA
1 ATATGTTTTTAATTTAA
254682 ATATGTTTTTAATTTAA
1 ATATGTTTTTAATTTAA
254699 TTTTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
ATATGTTTTTAATTTAA
Found at i:254848 original size:22 final size:21
Alignment explanation
Indices: 254807--254876 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 21
254797 AATAATTAAT
254807 AAAATAAAATTATTATTATAA
1 AAAATAAAATTATTATTATAA
254828 AAAATATATAATTA-TATTATAA
1 AAAATA-A-AATTATTATTATAA
* * * *
254850 AATATAAATTTTATAATTAAAA
1 AAAATAAA-ATTATTATTATAA
254872 AAAAT
1 AAAAT
254877 CTTATTTGGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.03
21 10 0.25
22 24 0.60
23 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATAAAATTATTATTATAA
Found at i:256055 original size:20 final size:20
Alignment explanation
Indices: 256032--256069 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
256022 TTTATATTTA
256032 TTTTAAT-AATTTATTTAAAT
1 TTTTAATAAATTT-TTTAAAT
*
256052 TTTTTATAAATTTTTTAA
1 TTTTAATAAATTTTTTAA
256070 TTGAATTAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATAAATTTTTTAAAT
Found at i:256753 original size:5 final size:5
Alignment explanation
Indices: 256691--256879 Score: 55
Period size: 5 Copynumber: 39.2 Consensus size: 5
256681 GAAGATATAT
* * * *
256691 TATTA -ATT- TATTA TTATTA TAGTTA TTTTG TATAA T-TTAA TAATA
1 TATTA TATTA TATTA -TATTA TA-TTA TATTA TATTA TATT-A TATTA
* ** * *
256736 TATGTA T-TTA TATTA TATTT TA-TA -ATTA TATT- TAAAA TATTT TAATTT
1 TAT-TA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA
* * * * * *
256784 TATTA AATTT TATTA TATTA AATAA T-TTA TATTA TATAA T-TTT TAATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA T-ATTA
** *
256833 TATT- TATTA -ATTTA TATTA TA-TA -ATTA TAACA TATTA -AATA TATTA
1 TATTA TATTA TA-TTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
256879 T
1 T
256880 TAGATGTAAT
Statistics
Matches: 129, Mismatches: 34, Indels: 42
0.63 0.17 0.20
Matches are distributed among these distances:
3 2 0.02
4 32 0.25
5 73 0.57
6 22 0.17
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:256802 original size:15 final size:16
Alignment explanation
Indices: 256774--256836 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 16
256764 TATTTAAAAT
*
256774 ATTTTAATTTTATTAA
1 ATTTTAATTATATTAA
256790 ATTTT-ATTATATTAA
1 ATTTTAATTATATTAA
256805 ATAATTTATATTATA-TAA
1 AT--TTTA-ATTATATTAA
*
256823 TTTTTAATTATATT
1 ATTTTAATTATATT
256837 TATTAATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
15 17 0.43
16 10 0.25
17 3 0.08
18 4 0.10
19 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTTTAATTATATTAA
Found at i:256802 original size:48 final size:47
Alignment explanation
Indices: 256741--256861 Score: 129
Period size: 48 Copynumber: 2.5 Consensus size: 47
256731 TAATATATGT
* *
256741 ATTTATATTATATTTTATAATTATATT-TAAAATATTTTAATTTTATTAA
1 ATTT-TATTATATTATATAATTATATTATAAAAT-TTTTAATTATATT-A
* * *
256790 ATTTTATTATATTAAATAATTTATATTATATAATTTTTAATTATATTT
1 ATTTTATTATATTATATAA-TTATATTATAAAATTTTTAATTATATTA
*
256838 A-TTAATTTATATTATATAATTATA
1 ATTTTA-TTATATTATATAATTATA
256862 ACATATTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
47 8 0.13
48 26 0.42
49 23 0.37
50 5 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (47 bp):
ATTTTATTATATTATATAATTATATTATAAAATTTTTAATTATATTA
Done.