Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_3112
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: 20150
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Found at i:6241 original size:40 final size:40
Alignment explanation
Indices: 6143--6445 Score: 387
Period size: 40 Copynumber: 7.6 Consensus size: 40
6133 TCCTCGTTCA
* * * * * *
6143 AATGCCTTCGGGACATAGCTCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
6182 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
6222 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
6262 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
6302 AATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
6342 AATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
6382 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
6422 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
6446 CAGCATTCAA
Statistics
Matches: 238, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
39 36 0.15
40 194 0.82
41 8 0.03
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:6454 original size:41 final size:41
Alignment explanation
Indices: 6377--6454 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
6367 TTAATATCTC
* * *
6377 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
6418 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
6455 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:14233 original size:40 final size:40
Alignment explanation
Indices: 14136--14436 Score: 378
Period size: 40 Copynumber: 7.6 Consensus size: 40
14126 TCCTCGTTCA
* * * * *
14136 AATGCCTTCGGGACAT-AGCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
14174 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
14214 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
14254 AATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
14293 AATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
14333 AATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
14373 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
14413 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
14437 CAGCATTCAA
Statistics
Matches: 236, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
38 16 0.07
39 59 0.25
40 153 0.65
41 8 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:14276 original size:79 final size:80
Alignment explanation
Indices: 14136--14436 Score: 378
Period size: 79 Copynumber: 3.8 Consensus size: 80
14126 TCCTCGTTCA
* * * * * *
14136 AATGCCTTCGGGACAT-AGCCGGTTTTAGTAACTCACAC-AATGCCTTCGGGACATAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
*
14199 TTAACAACTCGCACG
66 TTAATAACTCGCACG
14214 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTC-GGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
14278 TTAATAACTCGCACG
66 TTAATAACTCGCACG
*
14293 AATGCCTTCGGGACTTAACCCAGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
* *
14358 TTAATATCTCGCACA
66 TTAATAACTCGCACG
* ** * * * * * *
14373 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGG
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACGAATGCCTTCGGGACTTAACCCGG
14436 A
64 A
14437 CAGCATTCAA
Statistics
Matches: 198, Mismatches: 20, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
78 15 0.08
79 97 0.49
80 81 0.41
81 5 0.03
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.25
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGAT
TTAATAACTCGCACG
Found at i:14319 original size:119 final size:118
Alignment explanation
Indices: 14134--14429 Score: 387
Period size: 119 Copynumber: 2.5 Consensus size: 118
14124 GCTCCTCGTT
* * * * * * *
14134 CAAATGCCTTCGGGACAT-AGCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTC-GGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCAGA
14198 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
65 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
*
14252 CGAATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCAGA
1 CAAATGCCTTCGGACTTAACCCGGATTTAATAACTCGCAC-AATGCCTTCGGGACTTAACCCAGA
* *
14317 TTTAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATATCTCGCA
65 TTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
* ** * * * * *
14371 CAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTA
1 CAAATGCCTTCGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCGGGACTTA
14430 GCCCGGACAG
Statistics
Matches: 155, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
117 5 0.03
118 28 0.18
119 86 0.55
120 31 0.20
121 5 0.03
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (118 bp):
CAAATGCCTTCGGACTTAACCCGGATTTAATAACTCGCACAATGCCTTCGGGACTTAACCCAGAT
TTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
Found at i:14445 original size:41 final size:41
Alignment explanation
Indices: 14368--14445 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
14358 TTAATATCTC
* * *
14368 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
14409 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
14446 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Done.