Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004293.1 Corchorus capsularis cultivar CVL-1 contig04301, 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: 12410
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:8923 original size:65 final size:65
Alignment explanation
Indices: 8850--8979 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
8840 CCCTTTAAAG
8850 TTTCTTTCTTTTATATGGGTTGCAATTCTCAGTTTTCCATATTGCAGTTGCTTTTTCCCGGAAAA
1 TTTCTTTCTTTTATATGGGTTGCAATTCTCAGTTTTCCATATTGCAGTTGCTTTTTCCCGGAAAA
*
8915 TTTCTTTCTTTTATATGGGTTGCAATTCTCAGTTTTCCATATTGCTGTTGCTTTTTCCCGGAAAA
1 TTTCTTTCTTTTATATGGGTTGCAATTCTCAGTTTTCCATATTGCAGTTGCTTTTTCCCGGAAAA
8980 GAAACTATTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.48
Consensus pattern (65 bp):
TTTCTTTCTTTTATATGGGTTGCAATTCTCAGTTTTCCATATTGCAGTTGCTTTTTCCCGGAAAA
Found at i:11234 original size:26 final size:26
Alignment explanation
Indices: 11198--11251 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
11188 ACGACCTAAA
11198 TTTGCCAAAGTACAAGTAGTGATTAG
1 TTTGCCAAAGTACAAGTAGTGATTAG
11224 TTTGCCAAAGTACAAGTAGTGATTAG
1 TTTGCCAAAGTACAAGTAGTGATTAG
11250 TT
1 TT
11252 CATTGGAGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (26 bp):
TTTGCCAAAGTACAAGTAGTGATTAG
Done.