Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_26144
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: 1737
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.28
Found at i:1498 original size:615 final size:615
Alignment explanation
Indices: 306--1536 Score: 2086
Period size: 615 Copynumber: 2.0 Consensus size: 615
296 CTGGGGCTGA
306 GGTGGTGATGGATGCTGTCAACAAACCAAGAAATATCACATATAAAGGACTAACTGACTTGGTAA
1 GGTGGTGATGGATGCTGTCAACAAACCAAGAAATATCACATATAAAGGACTAACTGACTTGGTAA
* * * * * *
371 CCGACACAGATAAAATGAGTGAGGTTGCTATTCTTGATGTAGTAAAAAATAATTTTGGAGATCAT
66 CCGACACAGATAAAATGAGTGAGGTCGCTATTCTGGAGGTAATAAAAAAGAATTTTGCAGATCAT
* * * *
436 CTGATCCTTGGGGAGGAGGGAGGAATTATAGGGGATACCTCATCAGGCTATCTATGGTGTATTGA
131 CTGATCCTCGGGGAGGAAGGAGGAATTACAGGGGATACCTCATCAGACTATCTATGGTGTATTGA
*
501 TCCTTTAGATGGAACAACAAATTTTGCACATTGTTATCCTAGCTTTGCAGTTTCAGTGGGTGTAC
196 TCCTTTAGATGGAACAACAAATTTTGCACACTGTTATCCTAGCTTTGCAGTTTCAGTGGGTGTAC
*
566 TGTTTCAAGGAAATCCTGCCGCTGCTGCTGTGGTGGAATTTGTTGGAGGACCTATGTGTTGGAAT
261 TGTTTCAAGGAAATCCTGCCGCTGCTACTGTGGTGGAATTTGTTGGAGGACCTATGTGTTGGAAT
* *
631 ACCCGTACATTTACTGCTACTGCTGGTGGGGGAGCATTTTGTAATGGACAGAAAATCCATCCCAG
326 ACCCGTACATATACTGCTACTGCTGGTGGGGGAGCATTTTGTAACGGACAGAAAATCCATCCCAG
* * *
696 TAAAACGGATAAGGTGGAGCAGTCTCTTCTTGTGACTGGGTTTGGATATGACCACGATGATGCAT
391 TAAAACAGATAAGGTGGAGCAATCTCTTCTTGTGACTGGGTTTGGATATGAACACGATGATGCAT
* *
761 GGATTACCAACATTGAATTATTCAAGGAATTTACTGACATCAGTAGAGGTGTAAGAAGGCTTGGT
456 GGAATACCAACATTGAATTATTCAAGGAATTTACCGACATCAGTAGAGGTGTAAGAAGGCTTGGT
* ** *
826 GCTGCAGCTGTGGACATGTGCCATGTAGCTCTGGGAGTTGCAGAAGCGTATTGGGAATATCGTCT
521 GCTGCAGCTGTGGACATGTGCCATGTAGCTCTAGGAGTAACAGAAGCGTACTGGGAATATCGTCT
* * *
891 AAAACCATGGGATATGGCTGCTGGTGTATT
586 AAAACCATGGGACATAGCTGCTGCTGTATT
* *
921 GGTGGTGATGGATGCTGTCAACAAACCAAGAAATGTCACATATAAAGGACTAGCTGACTTGGTAA
1 GGTGGTGATGGATGCTGTCAACAAACCAAGAAATATCACATATAAAGGACTAACTGACTTGGTAA
986 CCGACACAGATAAAATGAGTGAGGTCGCTATTCTGGAGGTAATAAAAAAGAATTTTGCAGATCAT
66 CCGACACAGATAAAATGAGTGAGGTCGCTATTCTGGAGGTAATAAAAAAGAATTTTGCAGATCAT
* * *
1051 TTGATCCTCGGGGAGGAAGGAGGAATTACAGGGGATACCTCATCAGACTATCTCTGGTGTGTTGA
131 CTGATCCTCGGGGAGGAAGGAGGAATTACAGGGGATACCTCATCAGACTATCTATGGTGTATTGA
1116 TCCTTTAGATGGAACAACAAATTTTGCACACTGTTATCCTAGCTTTGCAGTTTCAGTGGGTGTAC
196 TCCTTTAGATGGAACAACAAATTTTGCACACTGTTATCCTAGCTTTGCAGTTTCAGTGGGTGTAC
* *
1181 TGTTTCAAGGAAATCCTGCTGCTGCTACTGTGGTGGAATTTGTTGGGGGACCTATGTGTTGGAAT
261 TGTTTCAAGGAAATCCTGCCGCTGCTACTGTGGTGGAATTTGTTGGAGGACCTATGTGTTGGAAT
1246 ACCCGTACATATACTGCTACTGCTGGTGGGGGAGCATTTTGTAACGGACAGAAAATCCATCCCAG
326 ACCCGTACATATACTGCTACTGCTGGTGGGGGAGCATTTTGTAACGGACAGAAAATCCATCCCAG
* *
1311 TAAAACAGATAAGGTGGAGCAATCTCTTCTTGTGACTGGGTTTGGATGTGAACATGATGATGCAT
391 TAAAACAGATAAGGTGGAGCAATCTCTTCTTGTGACTGGGTTTGGATATGAACACGATGATGCAT
* *
1376 GGAATACCAAC-TTCGAATTATTCAAGGAATTTACCGGCATTAGTAGAGGTGTAAGAAGGCTTGG
456 GGAATACCAACATT-GAATTATTCAAGGAATTTACCGACATCAGTAGAGGTGTAAGAAGGCTTGG
* * *
1440 TGGTGCAGCTGTGGACATGTGCCATGTAGCTCTAGGAGTAACGGAAGGGTACTGGGAATATCGTC
520 TGCTGCAGCTGTGGACATGTGCCATGTAGCTCTAGGAGTAACAGAAGCGTACTGGGAATATCGTC
1505 TAAAACCATGGGACATAGCTGCTGCTGTATT
585 TAAAACCATGGGACATAGCTGCTGCTGTATT
1536 G
1 G
1537 ATAATTGAAG
Statistics
Matches: 575, Mismatches: 40, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
614 2 0.00
615 573 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (615 bp):
GGTGGTGATGGATGCTGTCAACAAACCAAGAAATATCACATATAAAGGACTAACTGACTTGGTAA
CCGACACAGATAAAATGAGTGAGGTCGCTATTCTGGAGGTAATAAAAAAGAATTTTGCAGATCAT
CTGATCCTCGGGGAGGAAGGAGGAATTACAGGGGATACCTCATCAGACTATCTATGGTGTATTGA
TCCTTTAGATGGAACAACAAATTTTGCACACTGTTATCCTAGCTTTGCAGTTTCAGTGGGTGTAC
TGTTTCAAGGAAATCCTGCCGCTGCTACTGTGGTGGAATTTGTTGGAGGACCTATGTGTTGGAAT
ACCCGTACATATACTGCTACTGCTGGTGGGGGAGCATTTTGTAACGGACAGAAAATCCATCCCAG
TAAAACAGATAAGGTGGAGCAATCTCTTCTTGTGACTGGGTTTGGATATGAACACGATGATGCAT
GGAATACCAACATTGAATTATTCAAGGAATTTACCGACATCAGTAGAGGTGTAAGAAGGCTTGGT
GCTGCAGCTGTGGACATGTGCCATGTAGCTCTAGGAGTAACAGAAGCGTACTGGGAATATCGTCT
AAAACCATGGGACATAGCTGCTGCTGTATT
Done.