Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1597
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: 43746
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Found at i:5521 original size:39 final size:39
Alignment explanation
Indices: 5317--5539 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
5307 TTGAATGCTG
* * * * * *
5317 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTACTAAA
** * *
5357 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAGT
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGTTACTAA-A
* * *
5397 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGTTACTAAA
*
5437 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
5477 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
* * *
5516 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
5540 TGAACGAGGA
Statistics
Matches: 154, Mismatches: 22, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
39 38 0.25
40 106 0.69
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:5559 original size:79 final size:80
Alignment explanation
Indices: 5397--5573 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
5387 AGATACAAGT
* * * *
5397 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
5462 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
5477 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
5541 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
5556 TCC-GGTTAAAT-CCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
5574 TACGTGATTT
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
77 7 0.09
78 8 0.10
79 48 0.59
80 19 0.23
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:10131 original size:25 final size:24
Alignment explanation
Indices: 10055--10131 Score: 93
Period size: 24 Copynumber: 3.2 Consensus size: 24
10045 CAGCTTGTAT
* *
10055 GAGCTTACTAATTTTAGCTCATGA
1 GAGCTTACCAATTTTAGCTCGTGA
*
10079 GAGCTTACCAAATTTAGCTCGT-A
1 GAGCTTACCAATTTTAGCTCGTGA
*
10102 TGAGCTTACCGATTTATAGCTCGTGA
1 -GAGCTTACCAATTT-TAGCTCGTGA
10128 GAGC
1 GAGC
10132 ATATCGATTC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.02
24 31 0.69
25 12 0.27
26 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.32
Consensus pattern (24 bp):
GAGCTTACCAATTTTAGCTCGTGA
Found at i:10139 original size:25 final size:24
Alignment explanation
Indices: 10093--10160 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
10083 TTACCAAATT
* *
10093 TAGCTCGTATGAGCTTACCGATTTA
1 TAGCTCGTA-GAGCATACCGATTCA
*
10118 TAGCTCGTGAGAGCATATCGATTCA
1 TAGCTCGT-AGAGCATACCGATTCA
*
10143 TAGCTTGTAAGAGCATAC
1 TAGCTCGT-AGAGCATAC
10161 ATGTACAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
25 35 0.97
26 1 0.03
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (24 bp):
TAGCTCGTAGAGCATACCGATTCA
Found at i:19189 original size:8 final size:8
Alignment explanation
Indices: 19178--19202 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19168 TATAACATTA
19178 TATTATAT
1 TATTATAT
19186 TATTATAT
1 TATTATAT
19194 TATTATAT
1 TATTATAT
19202 T
1 T
19203 TTAACTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATTATAT
Found at i:26276 original size:43 final size:43
Alignment explanation
Indices: 26221--26334 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 43
26211 AGCTCGTACA
* * *
26221 ATGCCAA-GTCCCAGACGTGATCTTACATGTAATCACATA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-ACTCG
**
26263 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAACTTT
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAACTCG
26306 ATGCCAACGTCCCAGACGTGGTCTTACAC
1 ATGCCAACGTCCCAGACGTGGTCTTACAC
26335 AAAAAACACA
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
41 1 0.02
42 7 0.11
43 50 0.82
44 3 0.05
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAACTCG
Found at i:36224 original size:40 final size:39
Alignment explanation
Indices: 36150--36347 Score: 166
Period size: 40 Copynumber: 5.0 Consensus size: 39
36140 CTTCGCATAG
* * *
36150 CCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAA
1 CCCGGATTTAGTAACTCGCACAACGCCTTCGGGACTTAA
*
36189 CCCGGATTTAATAACTCGCACGAACGCCTTCGGGACTTAA
1 CCCGGATTTAGTAACTCGCAC-AACGCCTTCGGGACTTAA
* * *
36229 CCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAA
1 CCCGGATTTAGTAACTCGCAC-AACGCCTTCGGGACTTAA
* * * * *
36269 CCCAGAACTT-GTATCTCGCACAAATGCCTTC-GGATCTTAG
1 CCC-GGATTTAGTAACTCGCAC-AACGCCTTCGGGA-CTTAA
* * * * * *
36309 TCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTA
1 CCCGGATTTAGTAAC-TCGCACAACGCCTTCGGGACTTA
36348 GCCGGCAGCT
Statistics
Matches: 130, Mismatches: 23, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
39 23 0.18
40 95 0.73
41 12 0.09
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (39 bp):
CCCGGATTTAGTAACTCGCACAACGCCTTCGGGACTTAA
Found at i:36287 original size:80 final size:79
Alignment explanation
Indices: 36150--36347 Score: 184
Period size: 80 Copynumber: 2.5 Consensus size: 79
36140 CTTCGCATAG
* * * * *
36150 CCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACGAACG
1 CCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGAACTTAATAACTCGCACAAACG
36215 CCTTCGGGACTTAA
66 CCTTCGGGACTTAA
* * * * *
36229 CCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCAGAACTT-GTATCTCGCACAAA
1 CCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACTTAACCC-GAACTTAATAACTCGCACAAA
* *
36293 TGCCTTC-GGATCTTAG
64 CGCCTTCGGGA-CTTAA
* * * * * *
36309 TCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTA
1 CCCGGATTTAGTAACTCA-CACAAGGCCTTCGGGACTTA
36348 GCCGGCAGCT
Statistics
Matches: 94, Mismatches: 21, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
79 21 0.22
80 66 0.70
81 7 0.07
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (79 bp):
CCCGGATTTAGTAACTCACACAAGGCCTTCGGGACTTAACCCGAACTTAATAACTCGCACAAACG
CCTTCGGGACTTAA
Done.