Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_40334
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: 2334
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Found at i:660 original size:252 final size:252
Alignment explanation
Indices: 210--716 Score: 960
Period size: 252 Copynumber: 2.0 Consensus size: 252
200 ATGGTACAAA
*
210 TGACTTGTCTGAAATTATGAACTATCTACCTGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCCGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
*
275 TTGCAACCACTATTTCAAGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAAGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
* *
340 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGAGAAATGGCAGGTATTTTGCGTGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGACAAATGGCAGGTATTTTGCATGA
405 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
196 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
462 TGACTTGTCTGAAATTATGAACTATCTACCCGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
1 TGACTTGTCTGAAATTATGAACTATCTACCCGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
*
527 GTGCAACCACTATTTCAGGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
66 GTGCAACCACTATTTCAAGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
592 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGACAAATGGCAGGTATTTTGCATGA
131 ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGACAAATGGCAGGTATTTTGCATGA
*
657 TACTTTAGCACCAACTGAATCTTTGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
196 TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
714 TGA
1 TGA
717 TTCAATTGAA
Statistics
Matches: 249, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
252 249 1.00
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.24
Consensus pattern (252 bp):
TGACTTGTCTGAAATTATGAACTATCTACCCGGGAACAGAACTGCTACTTCTGTTCAAAGGCCAA
GTGCAACCACTATTTCAAGAAAAAAGCATGCATCGTCCAAAAGTTCTTCAAGAATTGAGGACTTG
ATGAAAGTTATTAATAGAGAAAAGAACGATCCAACAGCAGGACAAATGGCAGGTATTTTGCATGA
TACTTTAGCACCAACTGAATCTTCGAAAGGGAACAAAATAGAGAAGGAAAAAAATAG
Done.