Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2174
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: 11373
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Found at i:1463 original size:76 final size:77
Alignment explanation
Indices: 1301--1560 Score: 323
Period size: 76 Copynumber: 3.3 Consensus size: 77
1291 GCTCCTCGTT
* *
1301 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGGAT-TAGT-ACTCGCACAAATGCCTTCGGGACTTAACCCGG
*
1366 ATTTAGTAACTCGCA
63 AATTAGTAACTCGCA
*
1381 CAAATGCCTTCGGGCTTAACCCGGATTAGTACTCGCACAAATGCCTTCGGGACTT-ACCCGGAAT
1 CAAATGCCTTCGGGCTTAGCCCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
*
1445 TAGTATCTCGCA
66 TAGTAACTCGCA
**
1457 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 CAAATGCCTTCGGGCTTAGCCCGG-ATTAGTA-CTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
1521 ATATT-GTCACTTAGCA
63 A-ATTAGTAAC-TCGCA
1537 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
1561 CATCATTCAA
Statistics
Matches: 162, Mismatches: 11, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
76 42 0.26
77 35 0.22
78 34 0.21
79 29 0.18
80 22 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (77 bp):
CAAATGCCTTCGGGCTTAGCCCGGATTAGTACTCGCACAAATGCCTTCGGGACTTAACCCGGAAT
TAGTAACTCGCA
Found at i:1466 original size:39 final size:39
Alignment explanation
Indices: 1301--1560 Score: 295
Period size: 39 Copynumber: 6.6 Consensus size: 39
1291 GCTCCTCGTT
* *
1301 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTA-CCCGGAAT-TAGTAACTCGCA
*
1341 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTT-ACCCGGAATTAGTAACTCGCA
1381 CAAATGCCTTCGGG-CTTAACCCGG-ATTAGT-ACTCGCA
1 CAAATGCCTTCGGGACTT-ACCCGGAATTAGTAACTCGCA
*
1418 CAAATGCCTTCGGGACTTACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTACCCGGAATTAGTAACTCGCA
*
1457 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTA-CCCGGAATTAGTAACTCGCA
* * *
1496 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTA-CCCGGA-ATTAGTAAC-TCGCA
1537 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTA-CCCGGA
1561 CATCATTCAA
Statistics
Matches: 201, Mismatches: 8, Indels: 23
0.87 0.03 0.10
Matches are distributed among these distances:
37 27 0.13
38 20 0.10
39 77 0.38
40 66 0.33
41 11 0.05
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTACCCGGAATTAGTAACTCGCA
Found at i:9278 original size:39 final size:39
Alignment explanation
Indices: 9235--9404 Score: 229
Period size: 39 Copynumber: 4.3 Consensus size: 39
9225 GCTCCTCGTT
* *
9235 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTA-ATCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATATCGCA
* *
9274 CAAATGCCTTCGGGACTTAACCCGGATTTAGTA-ACTCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATA-TCGCA
*
9314 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATATCGCA
*
9353 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATATCGCA
9392 CAAATGCCTTCGG
1 CAAATGCCTTCGG
9405 ATCTTAGTCC
Statistics
Matches: 123, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
39 102 0.83
40 21 0.17
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATATCGCA
Found at i:9336 original size:78 final size:78
Alignment explanation
Indices: 9235--9455 Score: 256
Period size: 78 Copynumber: 2.8 Consensus size: 78
9225 GCTCCTCGTT
* *
9235 CAAATGCCTTCGGGACATAGCCCGGTTATAGTA-ATCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGG-CTTAGCCCGG-TATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGG
*
9299 ATTTAGTAACTCGCA
64 AATTAGTAACTCGCA
*
9314 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATC-TCGCACAAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGCTTAGCCCGGTA-TAGTA-CATCGCACAAATGCCTTCGGGACTTAGCCCGG
*
9377 AATTAGTATCTCGCA
64 AATTAGTAACTCGCA
* * * *
9392 CAAATGCCTTCGGATCTTAGTCCGG-ATATGTCACTTAGCAC-AA-GCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGG-GCTTAGCCCGGTATA-GT-ACATCGCACAAATGCCTTCGGGACTTAGCCCG
9454 GA
63 GA
9456 CATCATTCAA
Statistics
Matches: 126, Mismatches: 8, Indels: 17
0.83 0.05 0.11
Matches are distributed among these distances:
77 12 0.10
78 66 0.52
79 48 0.38
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGCTTAGCCCGGTATAGTACATCGCACAAATGCCTTCGGGACTTAGCCCGGAA
TTAGTAACTCGCA
Done.