Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016238.1 Corchorus capsularis cultivar CVL-1 contig16259, 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: 8078
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:2411 original size:78 final size:78
Alignment explanation
Indices: 2280--2434 Score: 292
Period size: 78 Copynumber: 2.0 Consensus size: 78
2270 TTGCCCGGCC
*
2280 ACAACCGGCCACGCGATCCTTTGTCTATGCCGTTGGGTCCAATCACAATGGCTCGGGCTAAAAGG
1 ACAACCGGCCACGCGATCCTTTGTCTATGCCGTTGGGTCCAATCACAAGGGCTCGGGCTAAAAGG
2345 TTTAAGGAAGCTA
66 TTTAAGGAAGCTA
*
2358 ACAACCGGCCACGCGATCCTTTGTCTATGTCGTTGGGTCCAATCACAAGGGCTCGGGCTAAAAGG
1 ACAACCGGCCACGCGATCCTTTGTCTATGCCGTTGGGTCCAATCACAAGGGCTCGGGCTAAAAGG
2423 TTTAAGGAAGCT
66 TTTAAGGAAGCT
2435 TTGGTGGGCT
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.23
Consensus pattern (78 bp):
ACAACCGGCCACGCGATCCTTTGTCTATGCCGTTGGGTCCAATCACAAGGGCTCGGGCTAAAAGG
TTTAAGGAAGCTA
Found at i:6921 original size:27 final size:27
Alignment explanation
Indices: 6899--6950 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
6889 GGCATTTTTG
6899 CATTCAAGGGCATTTTGGTCATTTTCA
1 CATTCAAGGGCATTTTGGTCATTTTCA
* *
6926 CATTTAGGGGCATTTTGGTCATTTT
1 CATTCAAGGGCATTTTGGTCATTTT
6951 AAGGTCACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (27 bp):
CATTCAAGGGCATTTTGGTCATTTTCA
Done.