Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2567
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: 41162
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:152 original size:40 final size:40
Alignment explanation
Indices: 106--286 Score: 274
Period size: 40 Copynumber: 4.5 Consensus size: 40
96 TTTTGAATAC
106 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
146 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
186 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
226 ATCCGGGCTAAGA-CCGAAGGCATTCGTCGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGT-GCAAGTTGATAT
* *
266 AACCCGGGTTAAGACCCGAAG
1 -ATCCGGGCTAAGACCCGAAG
287 CAATTGAGCT
Statistics
Matches: 129, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 12 0.09
40 100 0.78
41 11 0.09
42 6 0.05
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:307 original size:80 final size:80
Alignment explanation
Indices: 108--315 Score: 269
Period size: 80 Copynumber: 2.6 Consensus size: 80
98 TTGAATACAT
* * * *
108 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCGGGCTAAGACCCGAAGGCATTCG
*
173 TGCGAGTTGATATAT
66 TGCGAGTTGATATAC
* *
188 CCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATCCGGGCTAAGA-CCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCGGGCTAAGACCCGAAGGCATTCG
*
252 TCGCGAGTTGCTATAAC
66 T-GCGAGTTGATAT-AC
* ** *
269 CCGGGTTAAGACCCGAA-GCAATTGAGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCGGGCTAA
316 ATTCCAAAGA
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
79 19 0.16
80 80 0.69
81 17 0.15
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGAGCAAGTGGATATATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTTGATATAC
Found at i:8508 original size:40 final size:40
Alignment explanation
Indices: 8453--8632 Score: 297
Period size: 40 Copynumber: 4.5 Consensus size: 40
8443 ATTTGAATAC
8453 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
8493 ATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
*
8533 ATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
8573 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* *
8613 ACCCGGGTTAAGACCCGAAG
1 ATCCGGGCTAAGACCCGAAG
8633 CAATTGAGCT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 131 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:22546 original size:14 final size:14
Alignment explanation
Indices: 22527--22579 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
22517 TTCAATTTGA
22527 TTTATTTTTTTATT
1 TTTATTTTTTTATT
**
22541 TTTATTTAATTATT
1 TTTATTTTTTTATT
*
22555 TTT-TATTTTCTATT
1 TTTAT-TTTTTTATT
22569 CTTTATTTTTT
1 -TTTATTTTTT
22580 GTGATTTCTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 1 0.03
14 21 0.70
15 7 0.23
16 1 0.03
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTATTTTTTTATT
Found at i:22578 original size:22 final size:20
Alignment explanation
Indices: 22527--22579 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 20
22517 TTCAATTTGA
22527 TTTATTTTTTTATTTTTATT
1 TTTATTTTTTTATTTTTATT
22547 TAATTA-TTTTTTATTTTCTATT
1 T--TTATTTTTTTATTTT-TATT
22569 CTTTATTTTTT
1 -TTTATTTTTT
22580 GTGATTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.04
21 14 0.50
22 12 0.43
23 1 0.04
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTATTTTTTTATTTTTATT
Found at i:23338 original size:14 final size:14
Alignment explanation
Indices: 23319--23347 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23309 TAATAATTAT
23319 AAAAAATTATAATA
1 AAAAAATTATAATA
23333 AAAAAATTATAATA
1 AAAAAATTATAATA
23347 A
1 A
23348 GAGATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAAATTATAATA
Found at i:31576 original size:39 final size:40
Alignment explanation
Indices: 31459--31642 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
31449 GCTACTCGTT
* *
31459 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
31499 CAAATGCCTTTGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
31539 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
31578 CAAATGCCTT-TGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
31619 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
31643 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 42 0.34
40 68 0.56
41 10 0.08
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:31580 original size:79 final size:81
Alignment explanation
Indices: 31459--31642 Score: 216
Period size: 79 Copynumber: 2.3 Consensus size: 81
31449 GCTACTCGTT
* * *
31459 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTTGCACAAATGCCTTTGGGA-CTTAACCC
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTT-GGATCTTAACCC
* *
31522 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
31539 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTTGGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTTGGATCTTAACCCGG
* *
31603 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
*
31619 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTCGGGCTTAGCCCGGA
31643 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
78 3 0.03
79 64 0.71
80 23 0.26
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTTGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:39495 original size:78 final size:82
Alignment explanation
Indices: 39373--39556 Score: 229
Period size: 78 Copynumber: 2.3 Consensus size: 82
39363 GCTACTCGTT
* *
39373 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
39436 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
39453 CAAATGCCTTC-GG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
39515 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
39532 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
39557 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
77 3 0.03
78 52 0.58
79 13 0.14
80 22 0.24
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:39556 original size:40 final size:40
Alignment explanation
Indices: 39354--39556 Score: 229
Period size: 40 Copynumber: 5.1 Consensus size: 40
39344 CGGAATTTAA
** *
39354 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39394 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
39434 CCGGATTTAGTAACTCGCACAAATGCCTTC-GG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
39472 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
39512 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
39552 CCGGA
1 CCGGA
39557 CATCATTCAA
Statistics
Matches: 140, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 34 0.24
39 3 0.02
40 91 0.65
41 12 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.