Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01003624.1 Corchorus capsularis cultivar CVL-1 contig03632, whole genome shotgun sequence
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, 643
Length: 1073
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.31
Found at i:302 original size:37 final size:38
Alignment explanation
Indices: 243--328 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 38
233 CTCAAATAGG
* *
243 ACGTTGGAGACAAATACAAAAAGA-AAAATTAAATACA
1 ACGTTGGAAACAAAGACAAAAAGACAAAATTAAATACA
**
280 ACGATTGGAAACAAAGAC-AAAAGACAAAATTAAATAGG
1 ACG-TTGGAAACAAAGACAAAAAGACAAAATTAAATACA
318 ACGTTGGAAAC
1 ACGTTGGAAAC
329 GAAAAGCCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
37 17 0.40
38 26 0.60
ACGTcount: A:0.56, C:0.12, G:0.17, T:0.15
Consensus pattern (38 bp):
ACGTTGGAAACAAAGACAAAAAGACAAAATTAAATACA
Found at i:513 original size:31 final size:32
Alignment explanation
Indices: 463--525 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
453 AATTTAGAAT
*
463 TATGTTTTTATAAAAAAGGGTACAATTGGAAA
1 TATGTTTTTATAAAAAAGGGTACAATCGGAAA
495 TATG-TTTTA-AAAATAAGGGTACAATCGGAAA
1 TATGTTTTTATAAAA-AAGGGTACAATCGGAAA
526 ACATAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 4 0.14
31 21 0.72
32 4 0.14
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (32 bp):
TATGTTTTTATAAAAAAGGGTACAATCGGAAA
Done.