Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007487.1 Corchorus capsularis cultivar CVL-1 contig07508, 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, 1000
Length: 5741
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Found at i:4688 original size:31 final size:30
Alignment explanation
Indices: 4640--4730 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 30
4630 TATATTAAAC
4640 AAATAAGGAT-AATAGGAATATTAAAAGTT
1 AAATAAGGATAAATAGGAATATTAAAAGTT
4669 AAATAAGGATAAAATAGGAATATTAAAAGTT
1 AAATAAGGAT-AAATAGGAATATTAAAAGTT
*
4700 AAATAAGGATATAATAGGCAAT-TCAAAAGTT
1 AAATAAGGATA-AATAGG-AATATTAAAAGTT
4731 TCTCAAAACT
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
29 10 0.18
30 1 0.02
31 43 0.75
32 3 0.05
ACGTcount: A:0.55, C:0.02, G:0.16, T:0.26
Consensus pattern (30 bp):
AAATAAGGATAAATAGGAATATTAAAAGTT
Found at i:5620 original size:25 final size:25
Alignment explanation
Indices: 5571--5621 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
5561 TTAGTAGAAT
*
5571 AATTGTAAAAGTTTATTTCTAAAAA
1 AATTGTAAAAGTATATTTCTAAAAA
5596 AATTGTAAAAGAATATATTT-TAAAAA
1 AATTGTAAAAG--TATATTTCTAAAAA
5622 TTCTAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 6 0.26
27 6 0.26
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
AATTGTAAAAGTATATTTCTAAAAA
Done.