Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_25544
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, 367
Length: 612
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Found at i:108 original size:6 final size:6
Alignment explanation
Indices: 97--138 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
87 TTTTTTCAGC
* * *
97 CCCAAA CCCAAA TCCAAA TCCAAA CCCAAA TCCAAA CCCAAA
1 CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA CCCAAA
139 TCTAATTCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (6 bp):
CCCAAA
Found at i:119 original size:12 final size:12
Alignment explanation
Indices: 97--140 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
87 TTTTTTCAGC
*
97 CCCAAACCCAAA
1 CCCAAATCCAAA
*
109 TCCAAATCCAAA
1 CCCAAATCCAAA
121 CCCAAATCCAAA
1 CCCAAATCCAAA
133 CCCAAATC
1 CCCAAATC
141 TAATTCCCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.48, C:0.43, G:0.00, T:0.09
Consensus pattern (12 bp):
CCCAAATCCAAA
Found at i:121 original size:18 final size:18
Alignment explanation
Indices: 97--138 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
87 TTTTTTCAGC
97 CCCAAACCCAAATCCAAA
1 CCCAAACCCAAATCCAAA
*
115 TCCAAACCCAAATCCAAA
1 CCCAAACCCAAATCCAAA
133 CCCAAA
1 CCCAAA
139 TCTAATTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.43, G:0.00, T:0.07
Consensus pattern (18 bp):
CCCAAACCCAAATCCAAA
Done.