Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012274.1 Corchorus capsularis cultivar CVL-1 contig12295, 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: 4251
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Found at i:3686 original size:49 final size:48
Alignment explanation
Indices: 3507--3790 Score: 313
Period size: 49 Copynumber: 5.9 Consensus size: 48
3497 CAACTTTTAG
* * * * *
3507 TTTTACTCGCTTCTCCCCAAAATGCCCTTCCCGGACGGAAGACACTGA
1 TTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* *
3555 TTATTACCTG-TTTTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTAA
1 TT-TTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
*
3603 TCTTTACTTG-TTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTA
1 T-TTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
* * * * *
3651 TTTTACTTGCTATTTTCCAAAAATGCCCTTCCCGGACGGGAGACGCTTAT
1 TTTTACTTGCT-TTTTCCCAAAATGCCCTTCCCGGACGGAAGGCAC-TAA
* * * *
3701 TTTTACCTACTTTTTCCCAAAGTGCCCTTCCCGGAC-GAAGGGCGCTAA
1 TTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAA-GGCACTAA
* * *
3749 TTTTTACTTGCTTTTTCCTAAAACGCCCTTCCCGGATGGAAG
1 -TTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAG
3791 ACGTTGGTTT
Statistics
Matches: 199, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
47 8 0.04
48 84 0.42
49 94 0.47
50 13 0.07
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (48 bp):
TTTTACTTGCTTTTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTAA
Done.