Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2639
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: 32870
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Found at i:5864 original size:20 final size:20
Alignment explanation
Indices: 5839--5901 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
5829 ATTTTGATAA
5839 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
5859 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
*
5879 ACATGATTTGTATGATATGC
1 ACATGATATGTATGATATGC
5899 ACA
1 ACA
5902 CGAGATGTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:6271 original size:9 final size:9
Alignment explanation
Indices: 6259--6315 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
6249 TTTGATAAAC
6259 ATGATATGT
1 ATGATATGT
*
6268 ATGATATGCAC
1 ATGATATG--T
*
6279 ATGACATGT
1 ATGATATGT
*
6288 ATGATATGCAC
1 ATGATATG--T
6299 ATGATATGT
1 ATGATATGT
6308 ATGATATG
1 ATGATATG
6316 CACACGATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:6275 original size:418 final size:416
Alignment explanation
Indices: 5498--6333 Score: 1523
Period size: 418 Copynumber: 2.0 Consensus size: 416
5488 TTTCAGGCCC
*
5498 ATTTGGGGTAAATTTGGTCAGGAATTGGAAATCTGTTAAATTGCATGTTAAAACTGTTAATACTG
1 ATTTGGGGTAAATTTGGTCAGGAATTCGAAATCTGTTAAATTGCATGTTAAAACTGTTAATACTG
*
5563 TTTGGATATAGGCTAAATGGACCAGATGACAGAATTGGCTAAGTAGGGCCCATTAGGGGTTTTTG
66 TTTGGATATAGGCTAAATGGACCAGATGACAGAATCGGCTAAGTAGGGCCCATTAGGGGTTTTTG
5628 GCCCAATAACTTATTTTCGCTAAAAATGGGCCAGAATCACTGTTTGCACCCATGAATTGTTTGTA
131 GCCCAATAACTTATTTTCGCTAAAAATGGGCCAGAATCACTGTTTGCACCCATGAATTGTTTGTA
*
5693 ACCGTTAATGGACATGGAAACCCTAATTTTTGGTAAAATTACAAGATTACCCTTATAATATGAAA
196 ACCGTTAATGAACATGGAAACCCTAATTTTTGGTAAAATTACAAGATTACCCTTATAATATGAAA
*
5758 ATGACCGTTTTGCCCCAAGGTAAAAATGACCATTATACCCCTAGGGTTTATATATGAACTTAATG
261 ATGACCATTTTGCCCCAAGGTAAAAATGACCATTATACCCCTAGGGTTTATATATGAACTTAATG
*
5823 CATGGGATTTTGATAAACATGATATGTATGATATGCACATGACATGTATGATATGCACATGATTT
326 CATGGGATTTTGATAAACATGATATGTATGATATGCACATGACATGTATGATATGCACATGATAT
5888 GTATGATATGCACACGAGATGTTCATAA
391 GTATGATATGCACAC--GATGTTCATAA
5916 ATTTGGGGTAAATTTGGT-AGGAATTCGAAATCTGTTAAATTGCATGTTAAAACTGTTAATACTG
1 ATTTGGGGTAAATTTGGTCAGGAATTCGAAATCTGTTAAATTGCATGTTAAAACTGTTAATACTG
5980 TTATGGATATAGGCTAAATGGACCTAGATGACAGAATCGGCTAAGTAGGGCCCATTAGGGGTTTT
66 TT-TGGATATAGGCTAAATGGACC-AGATGACAGAATCGGCTAAGTAGGGCCCATTAGGGGTTTT
*
6045 TGGCCCAATAACTTGTTTTCGCTAAAAATGGGCCAGAATCACTGTTTGCA-CCATGAATTGTTTG
129 TGGCCCAATAACTTATTTTCGCTAAAAATGGGCCAGAATCACTGTTTGCACCCATGAATTGTTTG
6109 TAACCGTTAATGAACATGGAAACCCTAATTTTTGGTAAAATTACAAGATTACCCTTATAATATGA
194 TAACCGTTAATGAACATGGAAACCCTAATTTTTGGTAAAATTACAAGATTACCCTTATAATATGA
* * ** *
6174 AAATGACCATTTTGCCCCTAGGTGAAAATGATGATTATACCCTTAGGGTTTATATATGAACTTAA
259 AAATGACCATTTTGCCCCAAGGTAAAAATGACCATTATACCCCTAGGGTTTATATATGAACTTAA
6239 TGCATGGGATTTTGATAAACATGATATGTATGATATGCACATGACATGTATGATATGCACATGAT
324 TGCATGGGATTTTGATAAACATGATATGTATGATATGCACATGACATGTATGATATGCACATGAT
6304 ATGTATGATATGCACACGATGTTCATAA
389 ATGTATGATATGCACACGATGTTCATAA
6332 AT
1 AT
6334 GCATTGGGTT
Statistics
Matches: 405, Mismatches: 11, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
416 13 0.03
417 47 0.12
418 257 0.63
419 88 0.22
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Consensus pattern (416 bp):
ATTTGGGGTAAATTTGGTCAGGAATTCGAAATCTGTTAAATTGCATGTTAAAACTGTTAATACTG
TTTGGATATAGGCTAAATGGACCAGATGACAGAATCGGCTAAGTAGGGCCCATTAGGGGTTTTTG
GCCCAATAACTTATTTTCGCTAAAAATGGGCCAGAATCACTGTTTGCACCCATGAATTGTTTGTA
ACCGTTAATGAACATGGAAACCCTAATTTTTGGTAAAATTACAAGATTACCCTTATAATATGAAA
ATGACCATTTTGCCCCAAGGTAAAAATGACCATTATACCCCTAGGGTTTATATATGAACTTAATG
CATGGGATTTTGATAAACATGATATGTATGATATGCACATGACATGTATGATATGCACATGATAT
GTATGATATGCACACGATGTTCATAA
Found at i:6282 original size:20 final size:20
Alignment explanation
Indices: 6257--6319 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
6247 ATTTTGATAA
6257 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
6277 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
6297 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
6317 ACA
1 ACA
6320 CGATGTTCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:6412 original size:22 final size:23
Alignment explanation
Indices: 6372--6504 Score: 165
Period size: 22 Copynumber: 6.0 Consensus size: 23
6362 AGGAAGTGCA
6372 AAAGGGCTTATG-CCCAGTTA-T
1 AAAGGGCTTATGCCCCAGTTATT
6393 AAAGGGCTTATGCCCCAG---TT
1 AAAGGGCTTATGCCCCAGTTATT
6413 AAAGGGCTTATG-CCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
6435 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
6458 AAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAGGGCTTATGCCCCAGTTATT
*
6482 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
6505 ATGATAAAGC
Statistics
Matches: 100, Mismatches: 1, Indels: 19
0.83 0.01 0.16
Matches are distributed among these distances:
19 5 0.05
20 13 0.13
21 12 0.12
22 24 0.24
23 16 0.16
24 21 0.21
25 9 0.09
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:6417 original size:41 final size:42
Alignment explanation
Indices: 6372--6503 Score: 162
Period size: 47 Copynumber: 3.0 Consensus size: 42
6362 AGGAAGTGCA
6372 AAAGGGCTTATGCCCAGTTA-TAAAGGGCTTATGCCCCAGTT
1 AAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTT
6413 AAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAG---TT
*
6458 AAAAAGGGCTT-TGCCCCAGTTATTAAAGAGGC-TAGGCCTCCAGTT
1 --AAAGGGCTTATG-CCCAGTTATTAAAG-GGCTTATGCC-CCAGTT
6503 A
1 A
6504 TATGATAAAG
Statistics
Matches: 81, Mismatches: 1, Indels: 16
0.83 0.01 0.16
Matches are distributed among these distances:
41 20 0.25
42 19 0.23
43 1 0.01
45 4 0.05
46 2 0.02
47 28 0.35
48 7 0.09
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.27
Consensus pattern (42 bp):
AAAGGGCTTATGCCCAGTTATTAAAGGGCTTATGCCCCAGTT
Found at i:6500 original size:24 final size:23
Alignment explanation
Indices: 6372--6504 Score: 115
Period size: 24 Copynumber: 6.0 Consensus size: 23
6362 AGGAAGTGCA
6372 AAAG-GGCTTATG-CCCAGTTA-T
1 AAAGAGGC-TATGCCCCAGTTATT
6393 AAAG-GGCTTATGCCCCAG---TT
1 AAAGAGGC-TATGCCCCAGTTATT
6413 AAAG-GGCTTATG-CCCAGTTATT
1 AAAGAGGC-TATGCCCCAGTTATT
6435 AAAG-GGCTTATGCCCCAGTTATT
1 AAAGAGGC-TATGCCCCAGTTATT
* *
6458 AAAAAGGGCTTTGCCCCAGTTATT
1 AAAGA-GGCTATGCCCCAGTTATT
*
6482 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAGAGGCTATGCC-CCAGTTAT
6505 ATGATAAAGC
Statistics
Matches: 98, Mismatches: 5, Indels: 15
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.05
20 13 0.13
21 12 0.12
22 19 0.19
23 20 0.20
24 26 0.27
25 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (23 bp):
AAAGAGGCTATGCCCCAGTTATT
Found at i:6732 original size:31 final size:31
Alignment explanation
Indices: 6697--6760 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
6687 CGTTTACAGT
*
6697 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
**
6728 AAAGGCTTCGGCCCAGTGTTATGAAAAATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
6759 AA
1 AA
6761 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAAAATGA
Found at i:14298 original size:25 final size:25
Alignment explanation
Indices: 14252--14299 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
14242 TTATAATATG
* * *
14252 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
*
14277 AAAATGACCATTATACCTCTAGG
1 AAAATGACCATTATACCCCTAGG
14300 GTTTATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:14361 original size:20 final size:20
Alignment explanation
Indices: 14336--14398 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
14326 ATTTTGATAA
14336 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
* *
14356 ACATGACATGTATGATGTGC
1 ACATGATATGTATGATATGC
14376 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
14396 ACA
1 ACA
14399 CGAGATGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:14591 original size:25 final size:24
Alignment explanation
Indices: 14452--14595 Score: 195
Period size: 24 Copynumber: 6.0 Consensus size: 24
14442 GAGGAAGTGC
14452 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
14476 AAAAGGGCTTATGCCCCAGTTTTT
1 AAAAGGGCTTATGCCCCAGTTATT
*
14500 ACAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
14524 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
14547 AAAAAAGGGCTT-TTCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
14572 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
14596 ATGATAAAGC
Statistics
Matches: 107, Mismatches: 7, Indels: 11
0.86 0.06 0.09
Matches are distributed among these distances:
23 28 0.26
24 50 0.47
25 20 0.19
26 9 0.08
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:14824 original size:31 final size:31
Alignment explanation
Indices: 14789--14852 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
14779 CGTTTACAGT
*
14789 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
**
14820 AAAGGCTTCGGCCCAGTGTTATGAAAAATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
14851 AA
1 AA
14853 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAAAATGA
Found at i:20442 original size:40 final size:42
Alignment explanation
Indices: 20390--20485 Score: 128
Period size: 40 Copynumber: 2.4 Consensus size: 42
20380 TATCTCGGTA
*
20390 TCGCACACTTAGTGCCT-TATATAGCCGAAGCTA-TTCCAAC
1 TCGCACACTTAGTGCCTATATATAGCCGAAGCTATTTCAAAC
* *
20430 TCGCACACTTAGTG-CTATTTGTAGCCGAAGCTATTTCAAAC
1 TCGCACACTTAGTGCCTATATATAGCCGAAGCTATTTCAAAC
*
20471 -CGTACACTTAGTGCC
1 TCGCACACTTAGTGCC
20486 GAACATAGTC
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.04
40 40 0.82
41 7 0.14
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (42 bp):
TCGCACACTTAGTGCCTATATATAGCCGAAGCTATTTCAAAC
Found at i:25071 original size:40 final size:40
Alignment explanation
Indices: 24993--25336 Score: 486
Period size: 40 Copynumber: 8.7 Consensus size: 40
24983 GCTACTTGCT
24993 CAAATGCCTTCGGGACTTAGCCC-GTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
25032 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
25072 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
25112 CAAATGCCTTTGGGACTTAGCCCGGTTATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
25152 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACT-GCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
25191 CAAATGCCTTCGGG-CTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * *
25230 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* ** * *
25269 GAAATGCCTTCGGG-CTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* *
25308 CAAATGCCTTCGAGACTTAGCCCGATTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
25337 CATCCGAATA
Statistics
Matches: 281, Mismatches: 18, Indels: 11
0.91 0.06 0.04
Matches are distributed among these distances:
38 22 0.08
39 124 0.44
40 134 0.48
41 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:25243 original size:78 final size:80
Alignment explanation
Indices: 24970--25336 Score: 491
Period size: 78 Copynumber: 4.7 Consensus size: 80
24960 CGTTCGGAAT
* *
24970 TTAG-CCGGATATAGCT-ACTTGCTCAAATGCCTTCGGGACTTAGCCC-GTTATAGTAACTCGCA
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
25032 CAAATGCCTTCGGGAC
65 CAAATGCCTTCGGGAC
* * *
25048 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGTAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
*
25113 AAATGCCTTTGGGAC
66 AAATGCCTTCGGGAC
* *
25128 TTAGCCCGGTTATAGTAACTCACACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACT-GCAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
25192 AAATGCCTTCGGG-C
66 AAATGCCTTCGGGAC
* * *
25206 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCA
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
25269 GAAATGCCTTCGGG-C
65 CAAATGCCTTCGGGAC
* * * * *
25284 TTAGCCC-GAAATTAGTCACTAGCACAAATGCCTTCGAGACTTAGCCCGATTAT
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
25337 CATCCGAATA
Statistics
Matches: 260, Mismatches: 21, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
76 1 0.00
77 20 0.08
78 89 0.34
79 62 0.24
80 88 0.34
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (80 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCAC
AAATGCCTTCGGGAC
Done.