Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2366
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: 19439
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Found at i:1340 original size:40 final size:39
Alignment explanation
Indices: 1296--1479 Score: 230
Period size: 40 Copynumber: 4.7 Consensus size: 39
1286 ATAGCTCGTT
* *
1296 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
1336 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
* *
1376 CCAATGCCTTCGGG-CTTAGCCCGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
* * *
1414 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TAGTAAC-TCGCA
1455 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
1480 CATCATTCGA
Statistics
Matches: 126, Mismatches: 12, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
37 2 0.02
38 23 0.18
39 19 0.15
40 70 0.56
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:1414 original size:78 final size:80
Alignment explanation
Indices: 1298--1477 Score: 233
Period size: 78 Copynumber: 2.3 Consensus size: 80
1288 AGCTCGTTCA
* **
1298 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGA
* *
1362 TTTAGTAAC-TCGCACC
65 TATAGTAACTTAGCA-C
**
1378 AATGCCTTCGGG-CTTAGCCCGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
*
1441 ATAGTCACTTAGCAC
66 ATAGTAACTTAGCAC
*
1456 AAAGCCTTCGGGACTTAGCCCG
1 AATGCCTTCGGGACTTAGCCCG
1478 GACATCATTC
Statistics
Matches: 88, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 51 0.58
79 22 0.25
80 12 0.14
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGACTTAGCCCGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:9453 original size:79 final size:81
Alignment explanation
Indices: 9344--9526 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
9334 TACTCGTTCA
* *
9344 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
9407 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
9424 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
9487 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
9503 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
9527 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:9526 original size:40 final size:40
Alignment explanation
Indices: 9323--9526 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
9313 CGGAATTTAA
** *
9323 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9363 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
9403 CCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
9442 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
9482 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
9522 CCGGA
1 CCGGA
9527 CATCATTCGA
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:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:12563 original size:93 final size:94
Alignment explanation
Indices: 12390--12572 Score: 305
Period size: 93 Copynumber: 2.0 Consensus size: 94
12380 ACAAACTTGG
* * *
12390 ACCTAAACTTAGAAATTGTAAGTCAATTTGATATTTTTTTTTAGATACCTGACTAACTATCGTTA
1 ACCTAAACTTAGAAATTGTAAGCCAATTTGATATTTTTCTTTAAATACCTGACTAACTATCGTTA
*
12455 AATTATTATTTTCATCCAATCATATCAAT
66 AATTATTAATTTCATCCAATCATATCAAT
* *
12484 ACCTAAATTTAGAAATTGTAAGCCAATTTGATA-TTTTCTTTAAATACCTGACTAACTGTCGTTA
1 ACCTAAACTTAGAAATTGTAAGCCAATTTGATATTTTTCTTTAAATACCTGACTAACTATCGTTA
12548 AATTATTAATTTCATCCAATCATAT
66 AATTATTAATTTCATCCAATCATAT
12573 TGACACCACA
Statistics
Matches: 83, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
93 52 0.63
94 31 0.37
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (94 bp):
ACCTAAACTTAGAAATTGTAAGCCAATTTGATATTTTTCTTTAAATACCTGACTAACTATCGTTA
AATTATTAATTTCATCCAATCATATCAAT
Found at i:13384 original size:30 final size:30
Alignment explanation
Indices: 13350--13408 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
13340 TATTTTATTA
13350 TTAATTTTGTTATTATTTTAAAGATATTTG
1 TTAATTTTGTTATTATTTTAAAGATATTTG
* *
13380 TTAATTTTGTTATTATTTTAGAGGTATTT
1 TTAATTTTGTTATTATTTTAAAGATATTT
13409 ACTTATTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGATATTTG
Done.