Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01001349.1 Corchorus capsularis cultivar CVL-1 contig01349, 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: 4748
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:736 original size:114 final size:114
Alignment explanation
Indices: 605--836 Score: 428
Period size: 114 Copynumber: 2.0 Consensus size: 114
595 TTCATCTTAC
605 ATATGAATTACAAATTATAATATTTACATTATTTTAATATTTCTTATATATTTTATAAATTATTA
1 ATATGAATTACAAATTATAATATTTACATTATTTTAATATTTCTTATATATTTTATAAATTATTA
670 AAATACGTACAACGCACGTGTCATTACTAGTATGTATATATATATATAT
66 AAATACGTACAACGCACGTGTCATTACTAGTATGTATATATATATATAT
719 ATATGAATTACAAATTATAATATTTACATTATTTTAATATTTCTTATATATTTTATAAATTATTA
1 ATATGAATTACAAATTATAATATTTACATTATTTTAATATTTCTTATATATTTTATAAATTATTA
* * * *
784 ACATACGTGCAGCGCACGTGTCATTACTAGTGTGTATATATATATATAT
66 AAATACGTACAACGCACGTGTCATTACTAGTATGTATATATATATATAT
833 ATAT
1 ATAT
837 ATGCCTAGTT
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (114 bp):
ATATGAATTACAAATTATAATATTTACATTATTTTAATATTTCTTATATATTTTATAAATTATTA
AAATACGTACAACGCACGTGTCATTACTAGTATGTATATATATATATAT
Found at i:1059 original size:1 final size:1
Alignment explanation
Indices: 1012--1051 Score: 80
Period size: 1 Copynumber: 40.0 Consensus size: 1
1002 CACTCTGAGG
1012 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1052 GGTAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Done.