Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009533.1 Corchorus capsularis cultivar CVL-1 contig09554, 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: 50268
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:10181 original size:2 final size:2
Alignment explanation
Indices: 10174--10199 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10164 AAATAAATTC
10174 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
10200 TGTTAAACTG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11947 original size:22 final size:22
Alignment explanation
Indices: 11919--11964 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
11909 TGCGTACATG
11919 GTATAATTGGTTTAATTGGTTT
1 GTATAATTGGTTTAATTGGTTT
* *
11941 GTATAATTTGTTTAATTTGTTT
1 GTATAATTGGTTTAATTGGTTT
11963 GT
1 GT
11965 GTGTCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.20, T:0.59
Consensus pattern (22 bp):
GTATAATTGGTTTAATTGGTTT
Found at i:18376 original size:29 final size:28
Alignment explanation
Indices: 18336--18427 Score: 112
Period size: 29 Copynumber: 3.2 Consensus size: 28
18326 ACTTATAGCG
* *
18336 TTTGGACGTTTTGCCACCTAAACTTTAAT
1 TTTGGACATTTTGCC-CCTAAACTTCAAT
*
18365 TTTGGATATTTTGCCCCCTAAACTTCAAT
1 TTTGGACATTTTG-CCCCTAAACTTCAAT
* *
18394 TTTGGACATTTTACCCCATGAACTTCAAT
1 TTTGGACATTTTGCCCC-TAAACTTCAAT
18423 TTTGG
1 TTTGG
18428 GATGTCAGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
28 4 0.07
29 49 0.89
30 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (28 bp):
TTTGGACATTTTGCCCCTAAACTTCAAT
Found at i:25482 original size:2 final size:2
Alignment explanation
Indices: 25475--25528 Score: 85
Period size: 2 Copynumber: 27.5 Consensus size: 2
25465 ATATAATACC
25475 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25516 TA GTA TA -A TA TA T
1 TA -TA TA TA TA TA T
25529 GGGTCGCTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.04
2 45 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39328 original size:46 final size:46
Alignment explanation
Indices: 39276--39373 Score: 196
Period size: 46 Copynumber: 2.1 Consensus size: 46
39266 TCGTCTCATA
39276 AGAAAACTTTCTATTTCTATTCATCCCTATAACAATTTAGGTCCAT
1 AGAAAACTTTCTATTTCTATTCATCCCTATAACAATTTAGGTCCAT
39322 AGAAAACTTTCTATTTCTATTCATCCCTATAACAATTTAGGTCCAT
1 AGAAAACTTTCTATTTCTATTCATCCCTATAACAATTTAGGTCCAT
39368 AGAAAA
1 AGAAAA
39374 AACAAGCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 52 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.37
Consensus pattern (46 bp):
AGAAAACTTTCTATTTCTATTCATCCCTATAACAATTTAGGTCCAT
Found at i:50166 original size:2 final size:2
Alignment explanation
Indices: 50159--50184 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50149 TTATTAATAC
50159 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50185 CTACTCCTTC
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.