Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_24469
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: 3152
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.23
Found at i:1759 original size:21 final size:22
Alignment explanation
Indices: 1735--1776 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1725 TTAGTCAAGG
1735 AGCTTG-TGTCTCT-ACAAGAAA
1 AGCTTGAT-TCTCTAACAAGAAA
1756 AGCTTGATTCTCTAACAAGAA
1 AGCTTGATTCTCTAACAAGAA
1777 GGTGGACTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (22 bp):
AGCTTGATTCTCTAACAAGAAA
Found at i:2602 original size:90 final size:90
Alignment explanation
Indices: 2447--2667 Score: 397
Period size: 90 Copynumber: 2.5 Consensus size: 90
2437 CCATTTCCAA
* * *
2447 AATTGATGAGCATTTACTTGAAGCAGAACCAAACTACAGTGTAGAGGATGAGAAAGAGATTGACT
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
2512 TGTTCAAAGAGTTGCCAGCTGGAGT
66 TGTTCAAAGAGTTGCCAGCTGGAGT
2537 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
2602 TGTTCAAAGAGTTGCCAGCTGGAGT
66 TGTTCAAAGAGTTGCCAGCTGGAGT
* *
2627 AATTGATGAGCATTTACTTGAAGCAAAATCAAACAACGGTG
1 AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTG
2668 AAAAAAATAA
Statistics
Matches: 126, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 126 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.24
Consensus pattern (90 bp):
AATTGATGAGCATTTACTTGAAGCAGAACCAAACAACGGTGTAGAGGATGAGAAAGAGATCGACT
TGTTCAAAGAGTTGCCAGCTGGAGT
Done.