Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Cotton_A_36439
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, 579
Length: 966
ACGTcount: A:0.25, C:0.36, G:0.17, T:0.21
Found at i:183 original size:12 final size:12
Alignment explanation
Indices: 175--206 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
165 CCACCATCAC
175 CATCCCCATCCG
1 CATCCCCATCCG
*
187 CATCCGCATCCG
1 CATCCCCATCCG
199 CATCCCCA
1 CATCCCCA
207 CCAGCCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.56, G:0.09, T:0.16
Consensus pattern (12 bp):
CATCCCCATCCG
Found at i:338 original size:39 final size:39
Alignment explanation
Indices: 292--462 Score: 252
Period size: 39 Copynumber: 4.4 Consensus size: 39
282 AGTTTATCCA
292 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
* *
331 CCTCCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
370 CCACCCAAGTCACCCAGCAAGCCGCCAACTTACGCTCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
* * * * * *
409 CCGCCCAAGCCACCGACCAAGCCACCAACTTACGCCCCT
1 CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
*
448 CCACCCAAGCCACCA
1 CCACCCAAGTCACCA
463 GTTTATCCTC
Statistics
Matches: 121, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 121 1.00
ACGTcount: A:0.26, C:0.50, G:0.12, T:0.11
Consensus pattern (39 bp):
CCACCCAAGTCACCAAGCAAGCCGCCAACTTACGCTCCT
Done.