Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010623.1 Corchorus capsularis cultivar CVL-1 contig10644, 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: 10794
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1932 original size:6 final size:6
Alignment explanation
Indices: 1921--1947 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1911 TATATTCTGC
1921 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1948 GCTTTGCTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:8979 original size:2 final size:2
Alignment explanation
Indices: 8972--8997 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8962 GGGAAGGCTT
8972 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
8998 AAAAATGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:9068 original size:21 final size:23
Alignment explanation
Indices: 9018--9069 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
9008 ATCTTTAAAA
*
9018 GATTTGGGGATCATGCATATAAT
1 GATTTGGGGATCATGCAGATAAT
* *
9041 TATTTGGGGATGATG-AGA-AAT
1 GATTTGGGGATCATGCAGATAAT
9062 GATTTGGG
1 GATTTGGG
9070 TATAAAGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 10 0.40
22 2 0.08
23 13 0.52
ACGTcount: A:0.29, C:0.04, G:0.33, T:0.35
Consensus pattern (23 bp):
GATTTGGGGATCATGCAGATAAT
Done.