Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2630
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: 34770
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Found at i:1283 original size:27 final size:27
Alignment explanation
Indices: 1253--1457 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
1243 ATATTGAGTC
* * * *
1253 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
1280 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1307 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
1335 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
1362 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
1389 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1416 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1443 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1458 GTACAATTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:9362 original size:27 final size:27
Alignment explanation
Indices: 9332--9536 Score: 259
Period size: 27 Copynumber: 7.6 Consensus size: 27
9322 ATATTGAGTC
* * * *
9332 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
9359 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
9386 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
9414 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
9441 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
9468 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
9495 CGCACACTTAGTGCTACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
9522 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
9537 GTACAATTTA
Statistics
Matches: 157, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
27 133 0.85
28 24 0.15
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:13557 original size:16 final size:16
Alignment explanation
Indices: 13532--13563 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13522 CAATCTTTAT
*
13532 AAAATTTTTGTTTTTG
1 AAAATCTTTGTTTTTG
13548 AAAATCTTTGTTTTTG
1 AAAATCTTTGTTTTTG
13564 TAAACCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
AAAATCTTTGTTTTTG
Found at i:14573 original size:27 final size:27
Alignment explanation
Indices: 14543--14683 Score: 182
Period size: 27 Copynumber: 5.2 Consensus size: 27
14533 CTGACGAGGT
14543 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
14570 CACCAGA-ACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
14597 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
* *
14624 CACCAG-GACATATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
14651 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
14678 CACCAG
1 CACCAG
14684 GACGCTTCCT
Statistics
Matches: 100, Mismatches: 7, Indels: 14
0.83 0.06 0.12
Matches are distributed among these distances:
26 10 0.10
27 86 0.86
28 4 0.04
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:14684 original size:54 final size:54
Alignment explanation
Indices: 14543--14686 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
14533 CTGACGAGGT
* *
14543 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
14597 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACATATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
14651 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
14687 GCTTCCTCCA
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 81 0.94
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:15593 original size:26 final size:26
Alignment explanation
Indices: 15557--15742 Score: 345
Period size: 26 Copynumber: 7.2 Consensus size: 26
15547 TGAAATTCTC
*
15557 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15583 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15609 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
15635 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15661 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
15687 ATCATGGAACATTTACCTAACCCATA
1 ATCATGGAACATTTACCTAACCCATT
15713 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
15739 ATCA
1 ATCA
15743 ATTTGTATCA
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 155 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:24510 original size:40 final size:40
Alignment explanation
Indices: 24443--24619 Score: 214
Period size: 40 Copynumber: 4.5 Consensus size: 40
24433 ACCCAAGTAT
** * *
24443 CTTCGGGAATTAG-CCGGATATAACAACTCGTACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
24482 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
24522 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * * *
24562 CTTCAGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
24602 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
24620 TTATCATCCG
Statistics
Matches: 116, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
39 13 0.11
40 101 0.87
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:32529 original size:40 final size:40
Alignment explanation
Indices: 32462--32637 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
32452 ACCCAAGTAT
*
32462 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
32501 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * *
32541 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
32581 CTTC-GGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
32620 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
32638 TTATCATCCG
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
38 3 0.03
39 41 0.35
40 72 0.61
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:32598 original size:79 final size:79
Alignment explanation
Indices: 32462--32637 Score: 241
Period size: 79 Copynumber: 2.2 Consensus size: 79
32452 ACCCAAGTAT
* * *
32462 CTTCGGGAT-TTAGCCGGATATAACAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGC
1 CTTCGGG-TCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGC
32526 AACTCGCACAAATGC
65 AACTCGCACAAATGC
*
32541 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATGCCTTC-GGACATAGCCCGGATATAG
1 CTTCGGGTCTTAG-CCGGATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAG
*
32604 CAACTCGCACGAATGC
64 CAACTCGCACAAATGC
*
32620 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAG-CCGG
32638 TTATCATCCG
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
78 1 0.01
79 59 0.68
80 26 0.30
81 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCGGATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCA
ACTCGCACAAATGC
Found at i:34731 original size:26 final size:25
Alignment explanation
Indices: 34675--34735 Score: 95
Period size: 26 Copynumber: 2.4 Consensus size: 25
34665 ATAAATTTTC
34675 TCAAAATTTTATCGGGGTAAAATCG
1 TCAAAATTTTATCGGGGTAAAATCG
* *
34700 TAAAAATTTTATCGGCGGTGAAATCG
1 TCAAAATTTTATCGG-GGTAAAATCG
34726 TCAAAATTTT
1 TCAAAATTTT
34736 CATGGAGGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 14 0.44
26 18 0.56
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (25 bp):
TCAAAATTTTATCGGGGTAAAATCG
Done.