Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005038.1 Corchorus capsularis cultivar CVL-1 contig05056, 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: 3194
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Found at i:612 original size:80 final size:80
Alignment explanation
Indices: 519--670 Score: 277
Period size: 80 Copynumber: 1.9 Consensus size: 80
509 TTAAGCATTC
*
519 TAAATTATCATTTATTCAATGAAATTTATATTATTGTTATAATTTTACCTATTATGATTAAATTT
1 TAAATTATAATTTATTCAATGAAATTTATATTATTGTTATAATTTTACCTATTATGATTAAATTT
*
584 TTTAAACAACAATTT
66 GTTAAACAACAATTT
*
599 TAAATTATAATTTATTCAATGAAATTTATATTATTGTTATAATTTTACCTATTGTGATTAAATTT
1 TAAATTATAATTTATTCAATGAAATTTATATTATTGTTATAATTTTACCTATTATGATTAAATTT
664 GTTAAAC
66 GTTAAAC
671 TTCATTATAG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 69 1.00
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (80 bp):
TAAATTATAATTTATTCAATGAAATTTATATTATTGTTATAATTTTACCTATTATGATTAAATTT
GTTAAACAACAATTT
Found at i:1333 original size:12 final size:12
Alignment explanation
Indices: 1316--1341 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1306 AACCTTTGGC
1316 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1328 AAAAAAGAAAAA
1 AAAAAAGAAAAA
1340 AA
1 AA
1342 CCTTCTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAGAAAAA
Done.