Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1001
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: 23680
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Found at i:1405 original size:40 final size:40
Alignment explanation
Indices: 1368--1550 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
1358 GCTACTCGTT
*
1368 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
1408 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
1448 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGAAACT--CA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * *
1485 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
1526 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1551 CATCATTCGA
Statistics
Matches: 123, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
36 2 0.02
37 12 0.10
38 15 0.12
39 19 0.15
40 64 0.52
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:1534 original size:77 final size:78
Alignment explanation
Indices: 1368--1550 Score: 203
Period size: 77 Copynumber: 2.3 Consensus size: 78
1358 GCTACTCGTT
* * *
1368 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAAT-TAGAAACT--CACAAATGCCTTCGGGACTTAACCCG
* *
1432 GATTTAGTAACTCGCAC
62 GATATAGTAACTAGCAC
* **
1449 CAATGCCTTCGGG-CTTAGCCCGGAATTAGAAACTCACAAATGCCTTC-GGATCTTAGTCCGGAT
1 CAAAGCCTTCGGGACTTAGCCCGGAATTAGAAACTCACAAATGCCTTCGGGA-CTTAACCCGGAT
*
1512 ATAGTCACTTAGCA-
65 ATAGTAAC-TAGCAC
1526 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
1551 CATCATTCGA
Statistics
Matches: 88, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
76 3 0.03
77 41 0.47
78 15 0.17
79 16 0.18
80 10 0.11
81 3 0.03
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (78 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATTAGAAACTCACAAATGCCTTCGGGACTTAACCCGGATA
TAGTAACTAGCAC
Found at i:9483 original size:79 final size:81
Alignment explanation
Indices: 9374--9556 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 81
9364 TACTCGTTCA
* *
9374 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
9437 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
9454 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
*
9517 TATAGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
9533 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9557 CATCATTCGA
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
78 3 0.03
79 60 0.66
80 28 0.31
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:9556 original size:40 final size:40
Alignment explanation
Indices: 9353--9556 Score: 247
Period size: 40 Copynumber: 5.1 Consensus size: 40
9343 CGGAATTTAA
** *
9353 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9393 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9433 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
9472 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
9512 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9552 CCGGA
1 CCGGA
9557 CATCATTCGA
Statistics
Matches: 142, Mismatches: 15, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 95 0.67
41 12 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:13587 original size:38 final size:38
Alignment explanation
Indices: 13509--13689 Score: 220
Period size: 38 Copynumber: 4.6 Consensus size: 38
13499 GCTACTCGTT
*
13509 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGACTTAGCCCGGTT-TAGTAACTCGCA
*
13549 CAAATGCCTTCGGACTTAACCCGGTTTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGTTTAGTAACTCGCA
* *
13587 CAAATGCCTTCGGGCTTAGCCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGACTTAGCCCGGTTTAGTAACTCGCA
* * * * *
13625 CAAATGCCTTCGGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGA-CTTAGCCCGG-TTTAGTAAC-TCGCA
13666 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTC-GGACTTAGCCCGG
13690 ACATCATTCA
Statistics
Matches: 124, Mismatches: 13, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
38 60 0.48
39 22 0.18
40 31 0.25
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (38 bp):
CAAATGCCTTCGGACTTAGCCCGGTTTAGTAACTCGCA
Found at i:21790 original size:79 final size:82
Alignment explanation
Indices: 21679--21863 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
21669 GCTACTCGTT
* *
21679 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
21742 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
21759 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
21822 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
21839 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
21864 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 (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:21863 original size:40 final size:40
Alignment explanation
Indices: 21660--21863 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
21650 CGGAATTTAA
** *
21660 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
21700 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
21740 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
21779 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
21819 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
21859 CCGGA
1 CCGGA
21864 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.