Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_20857
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: 1758
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Found at i:1655 original size:186 final size:186
Alignment explanation
Indices: 1333--1708 Score: 545
Period size: 186 Copynumber: 2.0 Consensus size: 186
1323 CTATTATGCA
*
1333 TATGCCGATCTTAAGCCCCCTACATCACCATCTCCTAGAGCACCAACAAATGCACCAGCAGACAG
1 TATGCCGATCTTAAGCCCCCTACAACACCATCTCCTAGAGCACCAACAAATGCACCAGCAGACAG
* * *
1398 TGGGTCCAAAGGTGATACATTGTCAGGAAACAGCACAGCTCAATCTCCAATAGCTGAGAAACCAG
66 TGGGTCCAAAGGTGATACATTATCAGGAAACAGCACAGCTCAATCTCCAATAGCAGAGAAACCAA
* * *
1463 GTGATGAACAGCCTGATACCAAACCAACACCAAGACCACTTTCTCCTTTTGCTATG
131 GTGATGAACAGCATAATACCAAACCAACACCAAGACCACTTTCTCCTTTTGCAATG
* * * *** ** *
1519 TATGCCGATCTTAAGCCTCCTTCAACGCCATCTCCTAGAGCACCAACTTCTGCACCAGTGGATAG
1 TATGCCGATCTTAAGCCCCCTACAACACCATCTCCTAGAGCACCAACAAATGCACCAGCAGACAG
** * * * * *
1584 TGGGTCTGAAGGTGCTACATTATCAGGAAATAGCACAGCTCAATCTTCTATAGCAGATAAACCAA
66 TGGGTCCAAAGGTGATACATTATCAGGAAACAGCACAGCTCAATCTCCAATAGCAGAGAAACCAA
1649 GTGATGAACAGCATAATACCAAACCAACACCAAGACCACTTTCTCCTTTTGCAATG
131 GTGATGAACAGCATAATACCAAACCAACACCAAGACCACTTTCTCCTTTTGCAATG
1705 TATG
1 TATG
1709 AGGACTTGAA
Statistics
Matches: 167, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
186 167 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.22
Consensus pattern (186 bp):
TATGCCGATCTTAAGCCCCCTACAACACCATCTCCTAGAGCACCAACAAATGCACCAGCAGACAG
TGGGTCCAAAGGTGATACATTATCAGGAAACAGCACAGCTCAATCTCCAATAGCAGAGAAACCAA
GTGATGAACAGCATAATACCAAACCAACACCAAGACCACTTTCTCCTTTTGCAATG
Done.