Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_01296
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: 2289
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Found at i:1489 original size:87 final size:87
Alignment explanation
Indices: 1343--1690 Score: 651
Period size: 87 Copynumber: 4.0 Consensus size: 87
1333 CATACACGGA
1343 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
** * *
1408 GAAACCAAAATACTAGACGAGG
66 GAAACCACGACACTAGACAAGG
1430 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
*
1495 GAAAACACGACACTAGACAAGG
66 GAAACCACGACACTAGACAAGG
1517 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1582 GAAACCACGACACTAGACAAGG
66 GAAACCACGACACTAGACAAGG
1604 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1 AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
1669 GAAACCACGACACTAGACAAGG
66 GAAACCACGACACTAGACAAGG
1691 TTAATGTGAC
Statistics
Matches: 255, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 255 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (87 bp):
AGCATTTTCCCTTGCAAGCTTTTAGTGCAGAAGAAAGTGACATGACAGTTAAGGCTACTACACAA
GAAACCACGACACTAGACAAGG
Done.