Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1896
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: 61902
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:2688 original size:19 final size:16
Alignment explanation
Indices: 2666--2704 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 16
2656 TGAACTATGA
2666 TAATAAATATATTAACAAT
1 TAATAAATA-A-TAA-AAT
2685 TAATAAATAATAAAAT
1 TAATAAATAATAAAAT
2701 TAAT
1 TAAT
2705 GTACAAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 1 0.05
19 9 0.45
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATAAATAATAAAAT
Found at i:3627 original size:40 final size:41
Alignment explanation
Indices: 3566--3661 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 41
3556 TTTTGCAGCG
* * *
3566 TTTTGCTATGAAATGCCACTAAATAATTAAAATTAGTGTGA
1 TTTTACTATGAAATGCCACTAAATAATTAAAATTAATGGGA
*
3607 TTTTA-TATGAAATGCCACTAAATAATTAAATTTAATGGGA
1 TTTTACTATGAAATGCCACTAAATAATTAAAATTAATGGGA
3647 TTTTACTATGAAATG
1 TTTTACTATGAAATG
3662 TGAATAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 37 0.74
41 13 0.26
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.39
Consensus pattern (41 bp):
TTTTACTATGAAATGCCACTAAATAATTAAAATTAATGGGA
Found at i:5771 original size:16 final size:17
Alignment explanation
Indices: 5722--5772 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
5712 TATGTAGCTT
5722 TATTATACT-ATATATA
1 TATTATACTAATATATA
*
5738 TATTAATACAAAGT-TATA
1 TATT-ATACTAA-TATATA
5756 TA-TATACTAATATATA
1 TATTATACTAATATATA
5772 T
1 T
5773 TCTATTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 1 0.03
16 15 0.52
17 5 0.17
18 7 0.24
19 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (17 bp):
TATTATACTAATATATA
Found at i:7710 original size:18 final size:18
Alignment explanation
Indices: 7687--7727 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
7677 AGCACTAAAA
7687 GTTATTATGCTTGTCATT
1 GTTATTATGCTTGTCATT
7705 GTTATTATGCTTGTCATT
1 GTTATTATGCTTGTCATT
7723 GTTAT
1 GTTAT
7728 GCTATGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.56
Consensus pattern (18 bp):
GTTATTATGCTTGTCATT
Found at i:11720 original size:33 final size:33
Alignment explanation
Indices: 11683--11747 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
11673 TAAGTTGGAG
11683 GAAGCAA-AAGAAAAAGAAAAAAAAAGATATGAA
1 GAAGCAAGAA-AAAAAGAAAAAAAAAGATATGAA
* * *
11716 GAAGCAAGAAAAGAAGAAAGAAGAAGATATGA
1 GAAGCAAGAAAAAAAGAAAAAAAAAGATATGA
11748 GGCTCTCCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.68, C:0.03, G:0.23, T:0.06
Consensus pattern (33 bp):
GAAGCAAGAAAAAAAGAAAAAAAAAGATATGAA
Found at i:15067 original size:2 final size:2
Alignment explanation
Indices: 15060--15091 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
15050 ATCAATTACG
15060 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
15092 GTAAATATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16566 original size:23 final size:23
Alignment explanation
Indices: 16517--16567 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
16507 TTAATGAATT
* *
16517 TATTTATAGATATTAAATGATCA
1 TATTTATAAATATTAAATGAGCA
*
16540 TATTTATAAATATATAATTGAGC-
1 TATTTATAAATAT-TAAATGAGCA
16563 TATTT
1 TATTT
16568 CATGACAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (23 bp):
TATTTATAAATATTAAATGAGCA
Found at i:17259 original size:12 final size:12
Alignment explanation
Indices: 17242--17275 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
17232 TGTATCCTAC
17242 TAATTTTATTAT
1 TAATTTTATTAT
17254 TAATTTTATT-T
1 TAATTTTATTAT
17265 T-ATTTTATTAT
1 TAATTTTATTAT
17276 AGGTTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 3 0.14
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TAATTTTATTAT
Found at i:17691 original size:14 final size:15
Alignment explanation
Indices: 17662--17693 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17652 TCTGGAGACT
17662 GAAAAAAAAATGGAA
1 GAAAAAAAAATGGAA
17677 GAAAAAAAAAT-GAA
1 GAAAAAAAAATGGAA
17691 GAA
1 GAA
17694 CCCCTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (15 bp):
GAAAAAAAAATGGAA
Found at i:28563 original size:22 final size:22
Alignment explanation
Indices: 28538--28580 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
28528 ATTTTACAGC
*
28538 TAAACAACTAATAAATATATAA
1 TAAACAACTAATAAAAATATAA
* *
28560 TAAATAATTAATAAAAATATA
1 TAAACAACTAATAAAAATATA
28581 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAACAACTAATAAAAATATAA
Found at i:29176 original size:2 final size:2
Alignment explanation
Indices: 29169--29207 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
29159 GAATACTATT
* * *
29169 TA TA TA TA TT TA TG TA TA TT TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
29208 TTAAACCTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (2 bp):
TA
Found at i:29180 original size:10 final size:10
Alignment explanation
Indices: 29165--29210 Score: 74
Period size: 10 Copynumber: 4.6 Consensus size: 10
29155 CTTCGAATAC
29165 TATTTATATA
1 TATTTATATA
*
29175 TATTTATGTA
1 TATTTATATA
29185 TATTTATATA
1 TATTTATATA
*
29195 TATATATATA
1 TATTTATATA
29205 TATTTA
1 TATTTA
29211 AACCTGCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (10 bp):
TATTTATATA
Found at i:34580 original size:22 final size:22
Alignment explanation
Indices: 34560--34656 Score: 74
Period size: 22 Copynumber: 4.3 Consensus size: 22
34550 ACTGTAATTT
*
34560 TTAAATGTAATTATAAAAATTAA
1 TTAAAT-TAAATATAAAAATTAA
*
34583 TTAAATTAAATATAAAAGTGATAAA
1 TTAAATTAAATATAAAA---ATTAA
* *
34608 ATAAATTTAAATTTAAAAATTAA
1 TTAAA-TTAAATATAAAAATTAA
* *
34631 TT-AA-TAAAT-TTAAATTTAA
1 TTAAATTAAATATAAAAATTAA
34650 TTAAATT
1 TTAAATT
34657 GATTTGATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
19 10 0.17
20 7 0.12
21 1 0.02
22 12 0.20
23 11 0.18
25 8 0.13
26 11 0.18
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TTAAATTAAATATAAAAATTAA
Found at i:34643 original size:13 final size:14
Alignment explanation
Indices: 34607--34656 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
34597 AAAGTGATAA
34607 AATAAATTTAAATTT
1 AATAAATTT-AATTT
34622 AA-AAA-TTAA-TT
1 AATAAATTTAATTT
34633 AATAAATTTAAATTT
1 AATAAATTT-AATTT
34648 AATTAAATT
1 AA-TAAATT
34657 GATTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
11 4 0.13
12 5 0.17
13 4 0.13
14 5 0.17
15 6 0.20
16 6 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATAAATTTAATTT
Found at i:34651 original size:19 final size:20
Alignment explanation
Indices: 34615--34653 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
34605 AAAATAAATT
34615 TAAATTTAAAAATTAATTAA
1 TAAATTTAAAAATTAATTAA
*
34635 TAAATTT-AAATTTAATTAA
1 TAAATTTAAAAATTAATTAA
34654 ATTGATTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TAAATTTAAAAATTAATTAA
Found at i:34695 original size:16 final size:16
Alignment explanation
Indices: 34675--34731 Score: 62
Period size: 16 Copynumber: 3.6 Consensus size: 16
34665 AAAAAATTAA
*
34675 AAATTTAAATTGTTTC
1 AAATTTAAAATGTTTC
* *
34691 GAATTTAAAATGTTTT
1 AAATTTAAAATGTTTC
* *
34707 AAATTTAAAATATCT-
1 AAATTTAAAATGTTTC
34722 AAATTTAAAA
1 AAATTTAAAA
34732 AATTTAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
15 10 0.29
16 25 0.71
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (16 bp):
AAATTTAAAATGTTTC
Found at i:34726 original size:15 final size:15
Alignment explanation
Indices: 34692--34746 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
34682 AATTGTTTCG
*
34692 AATTTAAAATGTTTTA
1 AATTTAAAAT-ATTTA
*
34708 AATTTAAAATATCTA
1 AATTTAAAATATTTA
*
34723 AATTTAAAAAATTTA
1 AATTTAAAATATTTA
*
34738 AATTCAAAA
1 AATTTAAAA
34747 AAATATTAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 24 0.71
16 10 0.29
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTTAAAATATTTA
Found at i:34747 original size:15 final size:15
Alignment explanation
Indices: 34704--34759 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
34694 TTTAAAATGT
*
34704 TTTAAATTTAAAATA
1 TTTAAATTTAAAAAA
*
34719 TCTAAATTTAAAAAA
1 TTTAAATTTAAAAAA
*
34734 TTTAAATTCAAAAAAA
1 TTTAAATT-TAAAAAA
34750 TATTAAATTT
1 T-TTAAATTT
34760 GAACTTAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 20 0.59
16 7 0.21
17 7 0.21
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAATTTAAAAAA
Found at i:38118 original size:23 final size:23
Alignment explanation
Indices: 38088--38133 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
38078 GGGTCATGTG
38088 ATCTCTGGCGCTAGCATAACTAT
1 ATCTCTGGCGCTAGCATAACTAT
38111 ATCTCTGGCGCTAGCATAACTAT
1 ATCTCTGGCGCTAGCATAACTAT
38134 GGATTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
ATCTCTGGCGCTAGCATAACTAT
Found at i:42278 original size:2 final size:2
Alignment explanation
Indices: 42271--42299 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
42261 ATATAATAAT
42271 AG AG 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 AG AG A
42300 TAATATGGGT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44954 original size:2 final size:2
Alignment explanation
Indices: 44947--45035 Score: 80
Period size: 2 Copynumber: 46.0 Consensus size: 2
44937 CTTTTTCTTT
** *
44947 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GGG T- TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
* *
44989 -A T- TCC T- TA AA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
45028 TA TA TA TA
1 TA TA TA TA
45036 GGGTTAGAAT
Statistics
Matches: 74, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
1 5 0.07
2 68 0.92
3 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:45923 original size:26 final size:27
Alignment explanation
Indices: 45888--45939 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
45878 TTTTCATCCA
* *
45888 TATTTAATTTTATATTATTTT-TATAT
1 TATTCAATTTCATATTATTTTGTATAT
*
45914 TATTCAATTTCATTTTATTTTGTATA
1 TATTCAATTTCATATTATTTTGTATA
45940 CATATATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 18 0.82
27 4 0.18
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTCAATTTCATATTATTTTGTATAT
Found at i:52372 original size:20 final size:16
Alignment explanation
Indices: 52330--52380 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 16
52320 AATGTTTATA
52330 TAAATATAAAATATTT
1 TAAATATAAAATATTT
52346 TAAATATAATAATAATTCT
1 TAAATATAA-AAT-ATT-T
52365 TAAAATATATAAATAT
1 T-AAATATA-AAATAT
52381 AATAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 3 0.10
19 4 0.13
20 10 0.33
21 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:53716 original size:113 final size:115
Alignment explanation
Indices: 53527--53750 Score: 301
Period size: 113 Copynumber: 1.9 Consensus size: 115
53517 ATTTTTACTC
* * *
53527 TGTGTAAATAATTAATTATTTGCAATAATTTAAAGAACAATTTATCAAATAGTCAAAAATCTTTG
1 TGTGTAAATAATTAATTATTTGC-ATAA-TTAAAGAACAACTAATCAAATAGGCAAAAATCTTTG
* * *
53592 TAATGAATTTTTTTAAGTATATTTAATTTGTAATATTTTGAAATTTGCTAGG
64 GAATGAATTTTTTTAAGTATATTTAATTTGCAAAATTTTGAAATTTGCTAGG
* * *
53644 TGTGTAAATAATTAATTATTTTC-TAA-T-AATAACAACTAATCAAATTAGGCAAGAATCTTTGG
1 TGTGTAAATAATTAATTATTTGCATAATTAAAGAACAACTAATCAAA-TAGGCAAAAATCTTTGG
* *
53706 AATGAGTTTTTTTAAGTGTATTTAATTTGCAAAATTTTGAAATTT
65 AATGAATTTTTTTAAGTATATTTAATTTGCAAAATTTTGAAATTT
53751 ACTACGAGAA
Statistics
Matches: 95, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
112 14 0.15
113 56 0.59
115 3 0.03
117 22 0.23
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.44
Consensus pattern (115 bp):
TGTGTAAATAATTAATTATTTGCATAATTAAAGAACAACTAATCAAATAGGCAAAAATCTTTGGA
ATGAATTTTTTTAAGTATATTTAATTTGCAAAATTTTGAAATTTGCTAGG
Found at i:54904 original size:2 final size:2
Alignment explanation
Indices: 54897--54930 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54887 ACACAGAATC
54897 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
54931 AAAGTCCGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56478 original size:14 final size:14
Alignment explanation
Indices: 56459--56531 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
56449 GCTTATACTT
56459 TTATATTCTATTTA
1 TTATATTCTATTTA
**
56473 TTATATTAAATGTTA
1 TTATATTCTAT-TTA
56488 -TATATTCTA-TTA
1 TTATATTCTATTTA
* *
56500 GTATATTTTATTTA
1 TTATATTCTATTTA
* * *
56514 GTATATTTTATATA
1 TTATATTCTATTTA
56528 TTAT
1 TTAT
56532 TATAAAGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
12 3 0.06
13 8 0.16
14 35 0.71
15 3 0.06
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (14 bp):
TTATATTCTATTTA
Found at i:56506 original size:13 final size:14
Alignment explanation
Indices: 56460--56520 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
56450 CTTATACTTT
*
56460 TATATTCTATTTAT
1 TATATTCTATTTAG
**
56474 TATATTAAATGTTA-
1 TATATTCTAT-TTAG
56488 TATATTCTA-TTAG
1 TATATTCTATTTAG
*
56501 TATATTTTATTTAG
1 TATATTCTATTTAG
56515 TATATT
1 TATATT
56521 TTATATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
12 3 0.08
13 8 0.21
14 25 0.64
15 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (14 bp):
TATATTCTATTTAG
Found at i:57997 original size:17 final size:17
Alignment explanation
Indices: 57975--58007 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57965 ATCTTCTCTG
*
57975 ATTTTTATTATTTTTTT
1 ATTTTTATAATTTTTTT
57992 ATTTTTATAATTTTTT
1 ATTTTTATAATTTTTT
58008 GAATTATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTATAATTTTTTT
Found at i:58827 original size:16 final size:16
Alignment explanation
Indices: 58801--58862 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
58791 TTTCTTCAAT
*
58801 TTTTTATTTTTTATT-
1 TTTTAATTTTTTATTA
*
58816 TTTATAATTTTTAAATTA
1 TTT-TAATTTTT-TATTA
58834 TATTTAA-TTTTTATTA
1 T-TTTAATTTTTTATTA
58850 TTTTTAATTTTTT
1 -TTTTAATTTTTT
58863 TATAATTGAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
15 3 0.08
16 16 0.42
17 13 0.34
18 4 0.11
19 2 0.05
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTAATTTTTTATTA
Found at i:58843 original size:27 final size:27
Alignment explanation
Indices: 58804--58856 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
58794 CTTCAATTTT
* *
58804 TTATTTTTTATTTTTATAATTTTTAAA
1 TTATATTTAATTTTTATAATTTTTAAA
*
58831 TTATATTTAATTTTTATTATTTTTAA
1 TTATATTTAATTTTTATAATTTTTAA
58857 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATATTTAATTTTTATAATTTTTAAA
Found at i:58882 original size:9 final size:9
Alignment explanation
Indices: 58871--58901 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
58861 TTTATAATTG
*
58871 AATCAATCG
1 AATCAATCA
58880 AATCAATCA
1 AATCAATCA
58889 AATCAATCA
1 AATCAATCA
58898 AATC
1 AATC
58902 GAAAACTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.52, C:0.23, G:0.03, T:0.23
Consensus pattern (9 bp):
AATCAATCA
Found at i:58964 original size:2 final size:2
Alignment explanation
Indices: 58957--58988 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
58947 TTCCTTGCTG
58957 AT AT AT AT -T AT A- 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
58989 TAAATAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58974 original size:12 final size:12
Alignment explanation
Indices: 58957--58994 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
58947 TTCCTTGCTG
58957 ATATATATTATA
1 ATATATATTATA
58969 ATATATA-TATA
1 ATATATATTATA
58980 TATATATATTA-A
1 -ATATATATTATA
58992 ATA
1 ATA
58995 GTAGAGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 15 0.62
13 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATTATA
Found at i:60487 original size:216 final size:215
Alignment explanation
Indices: 60113--60593 Score: 804
Period size: 216 Copynumber: 2.2 Consensus size: 215
60103 ATAAGACCGA
*
60113 TAGATCATAAAGTTAAGAAGAAATAAGAACTTTTGTTTTTTAGATCATTAAACGAAGAATGAAAG
1 TAGATCATAAAGTTAAGACGAAATAAGAACTTTTGTTTTTTAGATCATTAAACGAAGAATGAAAG
60178 ATAAAAGAAAGAACGTTCATTTTTTTTTCAATCATTGAAGGAAGAAGAAAATAGAAGAACTTGGT
66 ATAAAAGAAAGAACGTTCATTTTTTTTTCAATCATTGAAGGAAGAAGAAAATAGAAGAACTTGGT
* * *
60243 TTTCTTTCTTTGTCATTCAAGGAAGAAAGAAAGGTAAGTTTTTTCCTTGGTTTTAATGAAAAAAA
131 TTTCTTTCTTTCTCATTCAAAGAAGAAAGAAAGATAAGTTTTTT-CTTGGTTTTAATGAAAAAAA
*
60308 -AAGTTAGAGAACTTTGTTTTT
195 GAAGTTAGAAAAC-TTGTTTTT
60329 TAGATCATAAAGTTAAGACGAAATAAGAACTTTTGTTTTTTAGATCATTAAACGAAGAATGAAAG
1 TAGATCATAAAGTTAAGACGAAATAAGAACTTTTGTTTTTTAGATCATTAAACGAAGAATGAAAG
* * * * * *
60394 ATAAATGAATGAACTTTTA-TTTTTTTTCAGTCATTGAAGGAAGAAGAAAATATAAGAACTTTGG
66 ATAAAAGAAAGAACGTTCATTTTTTTTTCAATCATTGAAGGAAGAAGAAAATAGAAGAAC-TTGG
60458 TTTTCTTTCTTTCTCATTCAAAGAAGAAAGAAAGATAAGTTTTTTCTTGGTTTTAATGAAAAAAA
130 TTTTCTTTCTTTCTCATTCAAAGAAGAAAGAAAGATAAGTTTTTTCTTGGTTTTAATGAAAAAAA
60523 GGAAGTTAGAAAACTTGTTTTT
195 -GAAGTTAGAAAACTTGTTTTT
*
60545 TAGATCATAAAGTTAAGACGAAATAAGAACTTTTATTTTTTAGATCATT
1 TAGATCATAAAGTTAAGACGAAATAAGAACTTTTGTTTTTTAGATCATT
60594 GTCGCAACGT
Statistics
Matches: 250, Mismatches: 12, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
215 58 0.23
216 181 0.72
217 11 0.04
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (215 bp):
TAGATCATAAAGTTAAGACGAAATAAGAACTTTTGTTTTTTAGATCATTAAACGAAGAATGAAAG
ATAAAAGAAAGAACGTTCATTTTTTTTTCAATCATTGAAGGAAGAAGAAAATAGAAGAACTTGGT
TTTCTTTCTTTCTCATTCAAAGAAGAAAGAAAGATAAGTTTTTTCTTGGTTTTAATGAAAAAAAG
AAGTTAGAAAACTTGTTTTT
Done.