Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold736
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: 41287
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Found at i:4342 original size:27 final size:27
Alignment explanation
Indices: 4311--4451 Score: 173
Period size: 27 Copynumber: 5.2 Consensus size: 27
4301 GTGATGAAGT
4311 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATATTGTGGCAGAGC
* *
4338 TACCAGA-ATAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
4365 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
*
4392 CACCAG-GACAGATATATGTGGCAGAGC
1 CACCAGATACAGATAT-TGTGGCAGAGC
*
4419 CACCAGAT-CAGATAATTGTGGCATAGC
1 CACCAGATACAGAT-ATTGTGGCAGAGC
4446 CACCAG
1 CACCAG
4452 GACGCTTCCT
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
26 9 0.09
27 85 0.87
28 4 0.04
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CACCAGATACAGATATTGTGGCAGAGC
Found at i:4452 original size:54 final size:54
Alignment explanation
Indices: 4311--4454 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
4301 GTGATGAAGT
* * * *
4311 CACCAGATACAGAT-ATTGTGGCAGAGCTACCAGAATAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
4365 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
4419 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
4455 GCTTCCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 5 0.06
54 80 0.94
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:6074 original size:26 final size:26
Alignment explanation
Indices: 6044--6151 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
6034 TAAAATTCCC
6044 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
6070 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6096 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
6122 ATCATGGAACATTTACCTAACTCATT
1 ATCATGGAACATTTACCTAACCCATT
6148 ATCA
1 ATCA
6152 ATTTGTATCA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 79 1.00
ACGTcount: A:0.36, C:0.26, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:7212 original size:24 final size:25
Alignment explanation
Indices: 7185--7236 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
7175 GCCTAGCCTC
7185 TTTTAATAAT-TAGGGCAAAGCCCT
1 TTTTAATAATATAGGGCAAAGCCCT
** *
7209 TTTTCGTAATATGGGGCAAAGCCCT
1 TTTTAATAATATAGGGCAAAGCCCT
7234 TTT
1 TTT
7237 CGCACTTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (25 bp):
TTTTAATAATATAGGGCAAAGCCCT
Found at i:7907 original size:27 final size:27
Alignment explanation
Indices: 7495--7894 Score: 471
Period size: 27 Copynumber: 14.8 Consensus size: 27
7485 GGGTATTTTA
* * *
7495 GTAATTTTGTAAATCAAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7522 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7549 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
7576 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
**
7603 GTAATTCTGTAAATCGAGGGTAATTTG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * * ** *
7630 GTAATTTTGTAAACCAAGGGT-ATTTCA
1 GTAATTCTGTAAATCGAGGGTAAAAT-G
* * * *
7657 GTAATTTTGTAAATTGAGGGGAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7684 GTAATTCTGTAAATC-AGGGGTAAAACG
1 GTAATTCTGTAAATCGA-GGGTAAAATG
* * *
7711 ATAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
7738 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7765 GTAATTCTGTAAATCGAGGGTGAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7792 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7819 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * **
7846 GTAATTCTATAAATCAAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
7873 GTAATTTTGTAAATCGAGGGTA
1 GTAATTCTGTAAATCGAGGGTA
7895 CTTTGGTAAT
Statistics
Matches: 326, Mismatches: 43, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
26 5 0.02
27 319 0.98
28 2 0.01
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:7918 original size:27 final size:27
Alignment explanation
Indices: 7872--7933 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
7862 AGGGTAAAAC
** *
7872 AGTAATTTTGTAAATCGAGGGTACTTT
1 AGTAATTTTACAAATCGAGGGCACTTT
* * *
7899 GGTAATTTTACAAATTGAGGGCATTTT
1 AGTAATTTTACAAATCGAGGGCACTTT
7926 AGTAATTT
1 AGTAATTT
7934 GGTAAACTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.06, G:0.21, T:0.42
Consensus pattern (27 bp):
AGTAATTTTACAAATCGAGGGCACTTT
Found at i:14980 original size:21 final size:21
Alignment explanation
Indices: 14954--14995 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
14944 ATACATGAGT
* * *
14954 ATTTTGATTTTTTTATGATAG
1 ATTTTGAATGTTTGATGATAG
14975 ATTTTGAATGTTTGATGATAG
1 ATTTTGAATGTTTGATGATAG
14996 TTACACAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.19, T:0.55
Consensus pattern (21 bp):
ATTTTGAATGTTTGATGATAG
Found at i:22337 original size:15 final size:15
Alignment explanation
Indices: 22319--22388 Score: 95
Period size: 15 Copynumber: 4.7 Consensus size: 15
22309 GATATTGTAC
*
22319 CTTGGATTTCTGTAT
1 CTTGGATTTCTTTAT
22334 CTTGGATTTCTTTAT
1 CTTGGATTTCTTTAT
*
22349 CTTGGATTTCTTTTT
1 CTTGGATTTCTTTAT
* *
22364 CCTGGACTTCTTTAT
1 CTTGGATTTCTTTAT
*
22379 CTTGGTTTTC
1 CTTGGATTTC
22389 ATGTCATCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (15 bp):
CTTGGATTTCTTTAT
Found at i:22355 original size:30 final size:30
Alignment explanation
Indices: 22319--22397 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
22309 GATATTGTAC
*
22319 CTTGGATTTCTGTATCTTGGATTTCTTTAT
1 CTTGGATTTCTGTATCTTGGACTTCTTTAT
* * *
22349 CTTGGATTTCTTTTTCCTGGACTTCTTTAT
1 CTTGGATTTCTGTATCTTGGACTTCTTTAT
*
22379 CTTGGTTTTCATGTCATCT
1 CTTGGATTTC-TGT-ATCT
22398 CTATTCCGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 35 0.90
31 2 0.05
32 2 0.05
ACGTcount: A:0.11, C:0.18, G:0.15, T:0.56
Consensus pattern (30 bp):
CTTGGATTTCTGTATCTTGGACTTCTTTAT
Found at i:29434 original size:79 final size:81
Alignment explanation
Indices: 29332--29516 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
29322 GCTCCTCGTT
* *
29332 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
29395 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
29412 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
29476 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
29492 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29517 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:29516 original size:40 final size:40
Alignment explanation
Indices: 29332--29516 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
29322 GCTCCTCGTT
* *
29332 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
29372 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
29412 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
29451 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
29492 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29517 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:37349 original size:39 final size:39
Alignment explanation
Indices: 37299--37478 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 39
37289 AGCTCTCGTT
*
37299 CAAATGCCTTCGGGACATAGCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCGGTTATAGTAACTCGCA
*
37338 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-AGCCGG-TTATAGTAACTCGCA
* *
37378 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCG-A
1 CAAATGCCTTCGGGACTTAG-CCGGTTA-TAGTAACTCGCA
* * * *
37416 CAAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 C-AAATGCCTTCGGGA-CTTAG-CCGGTTATAGTAAC-TCGCA
37458 CAAA-GCCTTC-GGACTTTAGCC
1 CAAATGCCTTCGGGAC-TTAGCC
37479 CGGACATCAT
Statistics
Matches: 118, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
38 5 0.04
39 46 0.39
40 57 0.48
41 8 0.07
42 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCGGTTATAGTAACTCGCA
Found at i:37381 original size:40 final size:40
Alignment explanation
Indices: 37299--37429 Score: 171
Period size: 39 Copynumber: 3.3 Consensus size: 40
37289 AGCTCTCGTT
* *
37299 CAAATGCCTTCGGGACAT-AGCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
37338 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
37378 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCG-A
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
37416 CAAAATGCCTTCGG
1 C-AAATGCCTTCGG
37430 ATCTTAGTCC
Statistics
Matches: 84, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
38 2 0.02
39 49 0.58
40 31 0.37
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:37442 original size:79 final size:81
Alignment explanation
Indices: 37299--37482 Score: 193
Period size: 79 Copynumber: 2.3 Consensus size: 81
37289 AGCTCTCGTT
* *
37299 CAAATGCCTTCGGGACATAG-CCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* *
37362 GATTTAGTAAC-TCGCA
65 GATATAGTAACTTAGCA
* **
37378 CAAATGCCTTCGGGCTTAGCCCGGAAT-TAGTATCTCG-ACAAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCAC-AAATGCCTTCGGGA-CTTAACCC
* *
37440 GGATATGGTCACTTAGCA
64 GGATATAGTAACTTAGCA
*
37458 CAAA-GCCTTCGGACTTTAGCCCGGA
1 CAAATGCCTTCGGGC-TTAGCCCGGA
37483 CATCATTTCA
Statistics
Matches: 89, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
78 9 0.10
79 61 0.69
80 19 0.21
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Done.