Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_03555
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: 2586
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Found at i:638 original size:216 final size:212
Alignment explanation
Indices: 240--670 Score: 542
Period size: 216 Copynumber: 2.0 Consensus size: 212
230 AAGATGCACA
* * *
240 AGTATCCATTAGATCTTCTGTTGATAAGGATTCATTGCGATCGGAGTCTAACAAGCAACTGCCTA
1 AGTATCCATTAGATCTTCTGTTGATAAGGATACATTGCAATCCGAGTCTAACAA-CAACTGCCTA
* * * * *
305 CTACAAAAGATTCAGTTGATTTAAGAAGAAATGAGATACCGGAGGAACCTGTAAAGCTTCCAGAA
65 CTACAAAAGATTCACTTGATTCAAGAAAAAATGAGATACCGGAGAAACCTGGAAAGCTTCCAGAA
* * * *
370 TCTTCGTTTGGAGCAACCGAAAAGAAGGTGGACACTTCAAGTTCTGCATCTAGCAATGCATCTGA
130 TCTTCGTCTAGACCAACAGAAAAGAAGGTGGACACTTCAAGTTCTGCATCTAGCAATGCATCTGA
*
435 GAGCAATTCAGTTGAGTC
195 GAACAATTCAGTTGAGTC
* * *
453 AGTATCCATTATATCTTTTGTTGATAAGGATACATTGCAATCCGAGTCTAATGAA-AAGCTGCCT
1 AGTATCCATTAGATCTTCTGTTGATAAGGATACATTGCAATCCGAGTCTAA-CAACAA-CTGCCT
* * * * * * * * *
517 ACTTCTCAAAAAGGTTCTCTTGATTCAAGAAAAAATGGGGTGCTGGAGAAACCTGGACAGCTTTC
64 AC-T-AC-AAAAGATTCACTTGATTCAAGAAAAAATGAGATACCGGAGAAACCTGGAAAGCTTCC
*
582 AGAATCATT-GTCTAGACCAACAGAAAAGAAGGTGGACACTTCCAGTTCTGCATCTAGCAATGCA
126 AGAATC-TTCGTCTAGACCAACAGAAAAGAAGGTGGACACTTCAAGTTCTGCATCTAGCAATGCA
*
646 TCTGAGAACAATTCAGTTGATTC
190 TCTGAGAACAATTCAGTTGAGTC
669 AG
1 AG
671 GCTGTGATCT
Statistics
Matches: 185, Mismatches: 27, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
212 2 0.01
213 54 0.29
214 3 0.02
215 1 0.01
216 123 0.66
217 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (212 bp):
AGTATCCATTAGATCTTCTGTTGATAAGGATACATTGCAATCCGAGTCTAACAACAACTGCCTAC
TACAAAAGATTCACTTGATTCAAGAAAAAATGAGATACCGGAGAAACCTGGAAAGCTTCCAGAAT
CTTCGTCTAGACCAACAGAAAAGAAGGTGGACACTTCAAGTTCTGCATCTAGCAATGCATCTGAG
AACAATTCAGTTGAGTC
Done.