Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3512
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: 115983
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3354 original size:57 final size:56
Alignment explanation
Indices: 3268--3387 Score: 206
Period size: 57 Copynumber: 2.1 Consensus size: 56
3258 TTCCAGACTC
3268 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTAGGAAAATTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGT-GG-AAATTT
*
3326 TTTTTTTTTA-GGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTGGCAATTT
1 TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTGGAAATTT
3381 TTTTTTT
1 TTTTTTT
3388 ATTTTTTTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
55 12 0.20
56 2 0.03
57 37 0.61
58 10 0.16
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (56 bp):
TTTTTTTTTACGGATCTTTCACGTTCTTTTCGTCCGCGCCTAGACCGTGGAAATTT
Found at i:4007 original size:45 final size:45
Alignment explanation
Indices: 3958--4190 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
3948 TCGGCCATGG
* * * *
3958 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
4003 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
4048 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
4093 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* *
4138 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
4183 TGCTTCCT
1 TGCTTCCT
4191 TAATTTCATG
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 180 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:11712 original size:23 final size:23
Alignment explanation
Indices: 11668--11712 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
11658 TGAAATCGAC
11668 ACAAGCAGAAAATTAAAAAGATTG
1 ACAAGCAGAAAA-TAAAAAGATTG
11692 ACAAGCAAGAAAA-AAAAAGAT
1 ACAAGC-AGAAAATAAAAAGAT
11713 AAAGTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 6 0.30
25 6 0.30
ACGTcount: A:0.64, C:0.09, G:0.16, T:0.11
Consensus pattern (23 bp):
ACAAGCAGAAAATAAAAAGATTG
Found at i:22188 original size:17 final size:18
Alignment explanation
Indices: 22166--22206 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
22156 CGTTTCTTTT
22166 TCTTTTGAATCACTC-TC
1 TCTTTTGAATCACTCATC
**
22183 TCTTTTTTATCACTCATC
1 TCTTTTGAATCACTCATC
22201 T-TTTTG
1 TCTTTTG
22207 TTTTTCTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.15, C:0.24, G:0.05, T:0.56
Consensus pattern (18 bp):
TCTTTTGAATCACTCATC
Found at i:22190 original size:24 final size:25
Alignment explanation
Indices: 22137--22190 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
22127 AACAAATTCT
* *
22137 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
22162 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
22185 TTTTTT
1 TTTTTT
22191 ATCACTCATC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:29355 original size:499 final size:499
Alignment explanation
Indices: 28417--29415 Score: 1989
Period size: 499 Copynumber: 2.0 Consensus size: 499
28407 GACACTTTGG
28417 TAGTTTCGGTTCATACACTTTCTAATTGTTGATATAGACTCTACTAAAGAACTCACAAGACTGAA
1 TAGTTTCGGTTCATACACTTTCTAATTGTTGATATAGACTCTACTAAAGAACTCACAAGACTGAA
28482 TTCTACCTCATTGAGAATTTGATTTTTCTTTTTGAGTGACTAACGGTGAGGTTTGCTAATTTTTC
66 TTCTACCTCATTGAGAATTTGATTTTTCTTTTTGAGTGACTAACGGTGAGGTTTGCTAATTTTTC
28547 TTTTGAGTGTTGAGTATTTGTTTTACAGGTATTTCAAAAAAAAGAGAAAAAAAATAAGATGGTAG
131 TTTTGAGTGTTGAGTATTTGTTTTACAGGTATTTCAAAAAAAAGAGAAAAAAAATAAGATGGTAG
28612 TCTGCCGCACCCTTAACATCCAAATGAGAGACGATTGTGATAACCAAAGGACCAATATTTTCCAT
196 TCTGCCGCACCCTTAACATCCAAATGAGAGACGATTGTGATAACCAAAGGACCAATATTTTCCAT
*
28677 TCTAGATGTTTTATAAAAGGTAACTTATGTTCACTTATTATTGATAGTGGGAGTTGTTCGAATGT
261 TCTAGATGTTTTATAAAAGGTAACTTATGTTCACTTATTATTGATAGTGGGAGTTGTTCGAATAT
28742 AGTTAGCAGCTATTTGGTGGATTCCTTAAAGTTACCTTGTATCAAGCACCCTAAGCCGTATCACC
326 AGTTAGCAGCTATTTGGTGGATTCCTTAAAGTTACCTTGTATCAAGCACCCTAAGCCGTATCACC
28807 TTCAGTGGCTTAATGAATGCTTGGAAGTTAAAGTTACAAAAAAGTCCTTGATCACTTTTAAGCTT
391 TTCAGTGGCTTAATGAATGCTTGGAAGTTAAAGTTACAAAAAAGTCCTTGATCACTTTTAAGCTT
28872 GAGAATTACGAGGATGACGTATGGTGTGATGTGGTCCCAATGCA
456 GAGAATTACGAGGATGACGTATGGTGTGATGTGGTCCCAATGCA
28916 TAGTTTCGGTTCATACACTTTCTAATTGTTGATATAGACTCTACTAAAGAACTCACAAGACTGAA
1 TAGTTTCGGTTCATACACTTTCTAATTGTTGATATAGACTCTACTAAAGAACTCACAAGACTGAA
28981 TTCTACCTCATTGAGAATTTGATTTTTCTTTTTGAGTGACTAACGGTGAGGTTTGCTAATTTTTC
66 TTCTACCTCATTGAGAATTTGATTTTTCTTTTTGAGTGACTAACGGTGAGGTTTGCTAATTTTTC
29046 TTTTGAGTGTTGAGTATTTGTTTTACAGGTATTTCAAAAAAAAGAGAAAAAAAATAAGATGGTAG
131 TTTTGAGTGTTGAGTATTTGTTTTACAGGTATTTCAAAAAAAAGAGAAAAAAAATAAGATGGTAG
29111 TCTGCCGCACCCTTAACATCCAAATGAGAGACGATTGTGATAACCAAAGGACCAATATTTTCCAT
196 TCTGCCGCACCCTTAACATCCAAATGAGAGACGATTGTGATAACCAAAGGACCAATATTTTCCAT
29176 TCTAGATGTTTTATAAAAGGTAACTTATGTTCACTTATTATTGATAGTGGGAGTTGTTCGAATAT
261 TCTAGATGTTTTATAAAAGGTAACTTATGTTCACTTATTATTGATAGTGGGAGTTGTTCGAATAT
29241 AGTTAGCAGCTATTTGGTGGATTCCTTAAAGTTACCTTGTATCAAGCACCCTAAGCCGTATCACC
326 AGTTAGCAGCTATTTGGTGGATTCCTTAAAGTTACCTTGTATCAAGCACCCTAAGCCGTATCACC
29306 TTCAGTGGCTTAATGAATGCTTGGAAGTTAAAGTTACAAAAAAGTCCTTGATCACTTTTAAGCTT
391 TTCAGTGGCTTAATGAATGCTTGGAAGTTAAAGTTACAAAAAAGTCCTTGATCACTTTTAAGCTT
29371 GAGAATTACGAGGATGACGTATGGTGTGATGTGGTCCCAATGCA
456 GAGAATTACGAGGATGACGTATGGTGTGATGTGGTCCCAATGCA
29415 T
1 T
29416 GCGACACACT
Statistics
Matches: 499, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
499 499 1.00
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (499 bp):
TAGTTTCGGTTCATACACTTTCTAATTGTTGATATAGACTCTACTAAAGAACTCACAAGACTGAA
TTCTACCTCATTGAGAATTTGATTTTTCTTTTTGAGTGACTAACGGTGAGGTTTGCTAATTTTTC
TTTTGAGTGTTGAGTATTTGTTTTACAGGTATTTCAAAAAAAAGAGAAAAAAAATAAGATGGTAG
TCTGCCGCACCCTTAACATCCAAATGAGAGACGATTGTGATAACCAAAGGACCAATATTTTCCAT
TCTAGATGTTTTATAAAAGGTAACTTATGTTCACTTATTATTGATAGTGGGAGTTGTTCGAATAT
AGTTAGCAGCTATTTGGTGGATTCCTTAAAGTTACCTTGTATCAAGCACCCTAAGCCGTATCACC
TTCAGTGGCTTAATGAATGCTTGGAAGTTAAAGTTACAAAAAAGTCCTTGATCACTTTTAAGCTT
GAGAATTACGAGGATGACGTATGGTGTGATGTGGTCCCAATGCA
Found at i:37627 original size:29 final size:27
Alignment explanation
Indices: 37594--37648 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
37584 GTGATTAAAT
37594 AAAATCGACA-CAAGCAGAATTTAAAAGAA
1 AAAATCGACAGCAAG-A-AA-TTAAAAGAA
*
37623 AAAATTGACAGCAAGAAATTAAAAGA
1 AAAATCGACAGCAAGAAATTAAAAGA
37649 TAAGTCCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 10 0.42
30 4 0.17
ACGTcount: A:0.60, C:0.11, G:0.15, T:0.15
Consensus pattern (27 bp):
AAAATCGACAGCAAGAAATTAAAAGAA
Found at i:40881 original size:23 final size:22
Alignment explanation
Indices: 40829--40881 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40819 TCCACGTCTT
*
40829 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40851 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40874 TTTCTTTT
1 TTTCTTTT
40882 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:47017 original size:19 final size:17
Alignment explanation
Indices: 46981--47019 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
46971 TCAGTTGCTG
46981 ATTAGTTAAATAAATTA
1 ATTAGTTAAATAAATTA
*
46998 ATTAGCTTAAGATTAATTA
1 ATTAG-TTAA-ATAAATTA
47017 ATT
1 ATT
47020 TAATAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTAGTTAAATAAATTA
Found at i:49300 original size:18 final size:18
Alignment explanation
Indices: 49262--49301 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
49252 AAACAAAAAC
* *
49262 AAAGAAAAAGAAATTGTA
1 AAAGAAAAAGAAATCGAA
49280 AAAGAAAAAGAAATCGAA
1 AAAGAAAAAGAAATCGAA
49298 AAAG
1 AAAG
49302 TGAGAGAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.70, C:0.03, G:0.17, T:0.10
Consensus pattern (18 bp):
AAAGAAAAAGAAATCGAA
Found at i:56783 original size:26 final size:26
Alignment explanation
Indices: 56741--56793 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
56731 GAATATTTAC
*
56741 ATAAAAATTAAACTAAGTAAAAATAA
1 ATAAAAAATAAACTAAGTAAAAATAA
56767 ATAAATAAATAAA-TAAGTAAAAATAA
1 ATAAA-AAATAAACTAAGTAAAAATAA
56793 A
1 A
56794 AATAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (26 bp):
ATAAAAAATAAACTAAGTAAAAATAA
Found at i:56799 original size:12 final size:13
Alignment explanation
Indices: 56741--56800 Score: 61
Period size: 12 Copynumber: 4.5 Consensus size: 13
56731 GAATATTTAC
56741 ATAAAAATTAAACTA
1 ATAAAAA-TAAA-TA
56756 AGTAAAAATAAATA
1 A-TAAAAATAAATA
*
56770 A-ATAAATAAATA
1 ATAAAAATAAATA
56782 AGTAAAAATAAA-A
1 A-TAAAAATAAATA
56795 ATAAAA
1 ATAAAA
56801 CTTTACAACT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
12 16 0.40
13 2 0.05
14 11 0.28
15 5 0.12
16 6 0.15
ACGTcount: A:0.73, C:0.02, G:0.03, T:0.22
Consensus pattern (13 bp):
ATAAAAATAAATA
Found at i:59036 original size:56 final size:56
Alignment explanation
Indices: 58931--59037 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
58921 ATTAATGTCG
* * * * *
58931 TCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCCCTTTAAATGCCGT
1 TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
58987 TCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCACATTAAAT
1 TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCACATTAAAT
59038 CAGCAAGCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 21 0.47
56 24 0.53
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCACATTAAATGCCGT
Found at i:59686 original size:20 final size:20
Alignment explanation
Indices: 59661--59715 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
59651 ACGAGTTAAA
* *
59661 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
59681 TTGAGCACGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
59701 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
59716 TTGAACCACA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:61887 original size:18 final size:19
Alignment explanation
Indices: 61842--61890 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
61832 GAATATTTAC
*
61842 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
61862 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
61880 ATAAAAATAAA
1 ATAAAAATAAA
61891 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:65341 original size:16 final size:16
Alignment explanation
Indices: 65306--65338 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
65296 ATGAATCCAA
*
65306 CCATTCATGTATTCAT
1 CCATTCATGTATTAAT
65322 CCATTCATGTA-TAAT
1 CCATTCATGTATTAAT
65337 CC
1 CC
65339 CATACGTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.39
Consensus pattern (16 bp):
CCATTCATGTATTAAT
Found at i:68642 original size:13 final size:13
Alignment explanation
Indices: 68624--68657 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
68614 ATACTTCAAA
68624 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
68637 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
68650 TTTTTTTT
1 TTTTTTTT
68658 CAAATTTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:68663 original size:13 final size:13
Alignment explanation
Indices: 68618--68664 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
68608 TTTTTTATAC
68618 TTCAAATTTTTTT
1 TTCAAATTTTTTT
*
68631 TT-GAATTTTTTT
1 TTCAAATTTTTTT
**
68643 TTTGAATTTTTTT
1 TTCAAATTTTTTT
68656 TTCAAATTT
1 TTCAAATTT
68665 CCTCTTCTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.70
Consensus pattern (13 bp):
TTCAAATTTTTTT
Found at i:76260 original size:23 final size:23
Alignment explanation
Indices: 76230--76295 Score: 114
Period size: 23 Copynumber: 2.9 Consensus size: 23
76220 CTTTTTGAAC
*
76230 CATTTCCATTTCGAACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
76253 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
*
76276 CATTACCATTTCGTACCAAA
1 CATTTCCATTTCGTACCAAA
76296 CCCAAACCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (23 bp):
CATTTCCATTTCGTACCAAATTA
Found at i:81492 original size:23 final size:22
Alignment explanation
Indices: 81441--81492 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
81431 CCTCGTCTTT
*
81441 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
81463 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
81486 TTCTTTT
1 TTCTTTT
81493 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:86344 original size:23 final size:23
Alignment explanation
Indices: 86312--86400 Score: 151
Period size: 23 Copynumber: 3.9 Consensus size: 23
86302 CTTTTTGAAC
* *
86312 CATTTGCATTTCGAACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
86335 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
86358 CATTTCCATTTCGTACCAAATTA
1 CATTTCCATTTCGTACCAAATTA
*
86381 CATTACCATTTCGTACCAAA
1 CATTTCCATTTCGTACCAAA
86401 CCCAAACTGA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 63 1.00
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.36
Consensus pattern (23 bp):
CATTTCCATTTCGTACCAAATTA
Found at i:86552 original size:4 final size:4
Alignment explanation
Indices: 86539--86568 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
86529 GTTGTAAAGT
86539 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
86569 TACTTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:88975 original size:24 final size:23
Alignment explanation
Indices: 88943--88987 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 23
88933 GATTGAGAGT
88943 GAAAAAGAAATT-GAAGAAAGAAGA
1 GAAAAAG-AATTAGAA-AAAGAAGA
88967 GAAAAAGAATTAGAAAAAGAA
1 GAAAAAGAATTAGAAAAAGAA
88988 ACAAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.69, C:0.00, G:0.22, T:0.09
Consensus pattern (23 bp):
GAAAAAGAATTAGAAAAAGAAGA
Found at i:101211 original size:18 final size:18
Alignment explanation
Indices: 101190--101248 Score: 73
Period size: 18 Copynumber: 3.2 Consensus size: 18
101180 GACCTCACTC
*
101190 TCTTTTTTGATTTCTTTT
1 TCTTTTTTAATTTCTTTT
* *
101208 TCTTTTTCAATCTCTTTT
1 TCTTTTTTAATTTCTTTT
101226 TCTTTTTTTCAATTTCTTTT
1 TC-TTTTTT-AATTTCTTTT
101246 TCT
1 TCT
101249 CGCTCGCACT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 17 0.50
19 6 0.18
20 11 0.32
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.73
Consensus pattern (18 bp):
TCTTTTTTAATTTCTTTT
Found at i:101235 original size:20 final size:19
Alignment explanation
Indices: 101202--101248 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
101192 TTTTTTGATT
101202 TCTTTTTC-TTTTTCAATC
1 TCTTTTTCTTTTTTCAATC
*
101220 TCTTTTTCTTTTTTTCAATT
1 TCTTTTTC-TTTTTTCAATC
101240 TCTTTTTCT
1 TCTTTTTCT
101249 CGCTCGCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 8 0.31
19 1 0.04
20 17 0.65
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (19 bp):
TCTTTTTCTTTTTTCAATC
Found at i:102210 original size:17 final size:17
Alignment explanation
Indices: 102190--102247 Score: 91
Period size: 17 Copynumber: 3.5 Consensus size: 17
102180 TATACTTCGA
102190 TTTTTTTTAAAATTTTC
1 TTTTTTTTAAAATTTTC
*
102207 TTTTTTTTAAAAATTT-
1 TTTTTTTTAAAATTTTC
*
102223 TTTTTTTTCAAATTTTC
1 TTTTTTTTAAAATTTTC
102240 TTTTTTTT
1 TTTTTTTT
102248 TTTCGATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTTAAAATTTTC
Found at i:102211 original size:33 final size:33
Alignment explanation
Indices: 102173--102260 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
102163 AGACTTTTCA
*
102173 CTTTTTTTATACTTCGATTTTTTTTAAAATTTT
1 CTTTTTTTATAATTCGATTTTTTTTAAAATTTT
* * *
102206 CTTTTTTTTAAAAATT--TTTTTTTTTCAAATTTT
1 C-TTTTTTT-ATAATTCGATTTTTTTTAAAATTTT
*
102239 CTTTTTTT-T-TTTCGATTTTTTT
1 CTTTTTTTATAATTCGATTTTTTT
102261 ATTTTTTTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
29 2 0.05
31 7 0.16
32 7 0.16
33 17 0.39
34 7 0.16
35 4 0.09
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.72
Consensus pattern (33 bp):
CTTTTTTTATAATTCGATTTTTTTTAAAATTTT
Found at i:102256 original size:19 final size:19
Alignment explanation
Indices: 102220--102271 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
102210 TTTTTAAAAA
102220 TTTTTTTTTTTCAAATTTT
1 TTTTTTTTTTTCAAATTTT
*
102239 CTTTTTTTTTTTC-GATTTT
1 -TTTTTTTTTTTCAAATTTT
*
102258 TTTATTTTTTTCAA
1 TTTTTTTTTTTCAA
102272 TTACAATATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
19 5 0.18
20 12 0.43
ACGTcount: A:0.13, C:0.08, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTTTTTTTCAAATTTT
Found at i:107217 original size:106 final size:106
Alignment explanation
Indices: 107032--107245 Score: 410
Period size: 106 Copynumber: 2.0 Consensus size: 106
107022 TGTTTGAAGC
*
107032 CATTATCTCTATTTTGTTTCATTTTAAAACCGAAACGAATCCATCCTTACTCAATTCACGATTGG
1 CATTATCTCTATTTTGTTTCATTTTAAAACCGAAACGAATCAATCCTTACTCAATTCACGATTGG
107097 GCAACACATACGACTCAAAACATCACGAGACGAGTTCGTAT
66 GCAACACATACGACTCAAAACATCACGAGACGAGTTCGTAT
*
107138 CATTATCTCTATTTTGTTTCATTTTAAAACCGAAACGAATCAATCCTTATTCAATTCACGATTGG
1 CATTATCTCTATTTTGTTTCATTTTAAAACCGAAACGAATCAATCCTTACTCAATTCACGATTGG
107203 GCAACACATACGACTCAAAACATCACGAGACGAGTTCGTAT
66 GCAACACATACGACTCAAAACATCACGAGACGAGTTCGTAT
107244 CA
1 CA
107246 AATTGGTATC
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
106 106 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (106 bp):
CATTATCTCTATTTTGTTTCATTTTAAAACCGAAACGAATCAATCCTTACTCAATTCACGATTGG
GCAACACATACGACTCAAAACATCACGAGACGAGTTCGTAT
Found at i:109769 original size:23 final size:22
Alignment explanation
Indices: 109717--109769 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
109707 TCCACGTCTT
*
109717 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
109739 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
109762 TTTCTTTT
1 TTTCTTTT
109770 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:113060 original size:14 final size:15
Alignment explanation
Indices: 113043--113071 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
113033 AAGAGCAGCA
113043 AGAAAAAAA-GAAAT
1 AGAAAAAAACGAAAT
113057 AGAAAAAAACGAAAT
1 AGAAAAAAACGAAAT
113072 CAAACGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.03, G:0.14, T:0.07
Consensus pattern (15 bp):
AGAAAAAAACGAAAT
Done.