Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold574
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: 24306
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:2277 original size:11 final size:11
Alignment explanation
Indices: 2261--2301 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
2251 CCATTTCTAT
2261 TTTTTTCTTTC
1 TTTTTTCTTTC
2272 TTTTTTCTTCATC
1 TTTTTTCTT--TC
*
2285 TTCTTTCTTTC
1 TTTTTTCTTTC
2296 TTTTTT
1 TTTTTT
2302 ACCTAAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
11 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:2315 original size:24 final size:22
Alignment explanation
Indices: 2261--2315 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
2251 CCATTTCTAT
**
2261 TTTTTTCTTTCTTTTTTCTTCA
1 TTTTTTCTTTCTTTTTTCTAAA
2283 TCTTCTTTCTTTCTTTTTTACCTAAA
1 T-TT-TTTCTTTCTTTTTT--CTAAA
2309 TTTTTTC
1 TTTTTTC
2316 AACCCATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 2 0.07
24 18 0.67
25 2 0.07
26 4 0.15
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTCTTTCTTTTTTCTAAA
Found at i:8575 original size:97 final size:95
Alignment explanation
Indices: 8399--8635 Score: 357
Period size: 96 Copynumber: 2.5 Consensus size: 95
8389 TGAAAAATGG
* *
8399 GGTTGGAGTATCCCCTCGGAAGAATGGGGTTGGAGTGTCCCGATGATGACAATTTAAGTGAGAAT
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCGATGATGACAATTTAAGTAAGAAT
8464 AAGATTTAAACTTTGATGTGTTTAAAAGCAA
66 AAGATTTAAACTTTGATGTG-TTAAAAGCAA
8495 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCTCGATGATGACAATTTAAGTAAGAA
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCC-CGATGATGACAATTTAAGTAAGAA
***
8560 TAAGATTTAAACTTTGATGTGTTAAAAGTGG
65 TAAGATTTAAACTTTGATGTGTTAAAAGCAA
* * * * *
8591 GGTTAGAGTATCCTCTCGAAGGAATAGGGTTGGAGTATCACCGAT
1 GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTC-CCGAT
8636 AAATAAAATT
Statistics
Matches: 129, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
96 84 0.65
97 45 0.35
ACGTcount: A:0.30, C:0.12, G:0.30, T:0.29
Consensus pattern (95 bp):
GGTTGGAGTATCCCCTCGGAGGAATGGGGTTGGAGTGTCCCGATGATGACAATTTAAGTAAGAAT
AAGATTTAAACTTTGATGTGTTAAAAGCAA
Found at i:10718 original size:34 final size:34
Alignment explanation
Indices: 10638--10747 Score: 105
Period size: 34 Copynumber: 3.2 Consensus size: 34
10628 TTTTCCTGTT
* * * ***
10638 TCTTTACAGCTCCATGCTGCTGTTTGATGCTTAT
1 TCTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
* *
10672 TGCTTTGTAGCTCCAAGCTGCTGTTCGATGCTGCC
1 T-CTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
* *
10707 TCTTTGCAGCTCCATA-CTGCTATTAGGTGCTGCC
1 TCTTTGCAGCTCCA-AGCTGCTGTTAGATGCTGCC
10741 TCTTTGC
1 TCTTTGC
10748 TGGAGCTATT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 35 0.56
35 28 0.44
ACGTcount: A:0.13, C:0.27, G:0.21, T:0.39
Consensus pattern (34 bp):
TCTTTGCAGCTCCAAGCTGCTGTTAGATGCTGCC
Found at i:15039 original size:20 final size:20
Alignment explanation
Indices: 15002--15040 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
14992 ACAATTTGTA
*
15002 TTGATACAATAGGTAATGTT
1 TTGATACAATAAGTAATGTT
15022 TTGATAC-ATAAGTGAATGT
1 TTGATACAATAAGT-AATGT
15041 ATCGATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (20 bp):
TTGATACAATAAGTAATGTT
Found at i:17601 original size:50 final size:50
Alignment explanation
Indices: 17526--17672 Score: 149
Period size: 49 Copynumber: 3.0 Consensus size: 50
17516 AAAATAAATT
* * * *
17526 TTTATCAAGGGGGCGAAAATCTTTTTAACCATA-GAAAATCTTTTTAACCG
1 TTTATCAAGGGGGAG-AAATTTTTTTTACCAAAGGAAAATCTTTTTAACCG
* * * *
17576 TTTATCAAGGGGGAGAATTTTTTTTTATCAAAGGGAAATTTTTTTTAACCG
1 TTTATCAAGGGGGAGAAATTTTTTTTACCAAA-GGAAAATCTTTTTAACCG
* *
17627 TTTCTCAAGGGGGAGAAA--TTTTTTATCAAAGGGAAAAT-TTTTTAAC
1 TTTATCAAGGGGGAGAAATTTTTTTTACCAAA-GGAAAATCTTTTTAAC
17673 GAGAGTCTTA
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
48 8 0.10
49 31 0.37
50 14 0.17
51 31 0.37
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.38
Consensus pattern (50 bp):
TTTATCAAGGGGGAGAAATTTTTTTTACCAAAGGAAAATCTTTTTAACCG
Found at i:17617 original size:21 final size:23
Alignment explanation
Indices: 17576--17621 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
17566 TTTTTAACCG
*
17576 TTTATCAAGGGGGAGAATTTTTT
1 TTTATCAAGAGGGAGAATTTTTT
17599 TTTATCAA-AGGGA-AATTTTTT
1 TTTATCAAGAGGGAGAATTTTTT
17620 TT
1 TT
17622 AACCGTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 4 0.18
23 8 0.36
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (23 bp):
TTTATCAAGAGGGAGAATTTTTT
Found at i:17653 original size:49 final size:50
Alignment explanation
Indices: 17559--17669 Score: 170
Period size: 51 Copynumber: 2.2 Consensus size: 50
17549 TTTAACCATA
* *
17559 GAAAATCTTTTTAACCGTTTATCAAGGGGGAGAATTTTTTTTTATCAAAGG
1 GAAAATTTTTTTAACCGTTTATCAAGGGGGAGAA-TATTTTTTATCAAAGG
* *
17610 GAAATTTTTTTTAACCGTTTCTCAAGGGGGAGAA-ATTTTTTATCAAAGG
1 GAAAATTTTTTTAACCGTTTATCAAGGGGGAGAATATTTTTTATCAAAGG
17659 GAAAATTTTTT
1 GAAAATTTTTT
17670 AACGAGAGTC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
49 24 0.44
51 31 0.56
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.41
Consensus pattern (50 bp):
GAAAATTTTTTTAACCGTTTATCAAGGGGGAGAATATTTTTTATCAAAGG
Found at i:18107 original size:22 final size:22
Alignment explanation
Indices: 18082--18136 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
18072 GAGTTATAAA
*
18082 CAAATGTTTTTGAACCTTAATT
1 CAAATGTTTTTGAACCTCAATT
18104 CAAATGTTTTTGAACCTCAATT
1 CAAATGTTTTTGAACCTCAATT
18126 CAAATGTTTTT
1 CAAATGTTTTT
18137 AAGTAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (22 bp):
CAAATGTTTTTGAACCTCAATT
Found at i:18282 original size:13 final size:13
Alignment explanation
Indices: 18264--18288 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18254 ACATTATGCT
18264 TTGTATCGATACG
1 TTGTATCGATACG
18277 TTGTATCGATAC
1 TTGTATCGATAC
18289 ATGAAACTGG
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:0.24, C:0.16, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACG
Found at i:22442 original size:113 final size:113
Alignment explanation
Indices: 22127--22442 Score: 339
Period size: 113 Copynumber: 2.8 Consensus size: 113
22117 AAAAAGTTCA
* * * ** * *
22127 AAATAAATTAATTAAATATGCATATAGGCCCTATTTTATCTAACGTAGATTTTT-TAAGGCTTAG
1 AAATAAATTAATTAAATAAGCATGTAGGACCTATTTTATCTAATATATATTTTTATAAGACTTA-
* ** ** * * *
22191 CCTTAAATTAAATAATTTATAATATGACATAATTAGGTAAAATAAGCCC
65 CTTTAAATTAAATAATTTACGACCTAACATAATTAGATAAAATAAACCC
* * * * * * * *
22240 GAGTAAATTAATTAAATAAGCACGTGGGACTTATTTTATCTAATATATTTTTTTATAAGATTTAA
1 AAATAAATTAATTAAATAAGCATGTAGGACCTATTTTATCTAATATATATTTTTATAAGACTTAC
* * *
22305 TCTTAGATTAAATAATTTAGGACCTAATATAATTAGAT-AAATAAACCC
66 T-TTAAATTAAATAATTTACGACCTAACATAATTAGATAAAATAAACCC
* *
22353 AAATAAATTAATTAAATAAGCATGTAAGACCTATTTTATCTAATATATATTTTTATAAAACTTGA
1 AAATAAATTAATTAAATAAGCATGTAGGACCTATTTTATCTAATATATATTTTTATAAGACTT-A
22418 CTTTAAATTAAATAATTTACGACCT
65 CTTTAAATTAAATAATTTACGACCT
22443 TACTTAGCTA
Statistics
Matches: 163, Mismatches: 37, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
113 126 0.77
114 37 0.23
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.38
Consensus pattern (113 bp):
AAATAAATTAATTAAATAAGCATGTAGGACCTATTTTATCTAATATATATTTTTATAAGACTTAC
TTTAAATTAAATAATTTACGACCTAACATAATTAGATAAAATAAACCC
Done.