Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010399.1 Corchorus capsularis cultivar CVL-1 contig10420, 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: 9460
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Found at i:4308 original size:6 final size:6
Alignment explanation
Indices: 4294--4370 Score: 91
Period size: 6 Copynumber: 12.8 Consensus size: 6
4284 TTTGTCCTTT
* * * * *
4294 CCGCCG CCGCTG CCGCCG CTGCCG CCGCTG CCGCCG CTGCCG CCGCTG
1 CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG CCGCCG
* *
4342 CCGCTG CCGCCG CCGCTG CCGCCG CCGCC
1 CCGCCG CCGCCG CCGCCG CCGCCG CCGCC
4371 CGATCTTTCT
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.00, C:0.58, G:0.32, T:0.09
Consensus pattern (6 bp):
CCGCCG
Found at i:4310 original size:9 final size:9
Alignment explanation
Indices: 4296--4366 Score: 124
Period size: 9 Copynumber: 7.9 Consensus size: 9
4286 TGTCCTTTCC
4296 GCCGCCGCT
1 GCCGCCGCT
4305 GCCGCCGCT
1 GCCGCCGCT
4314 GCCGCCGCT
1 GCCGCCGCT
4323 GCCGCCGCT
1 GCCGCCGCT
4332 GCCGCCGCT
1 GCCGCCGCT
* *
4341 GCCGCTGCC
1 GCCGCCGCT
4350 GCCGCCGCT
1 GCCGCCGCT
4359 GCCGCCGC
1 GCCGCCGC
4367 CGCCCGATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 58 1.00
ACGTcount: A:0.00, C:0.56, G:0.34, T:0.10
Consensus pattern (9 bp):
GCCGCCGCT
Done.