Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007120.1 Corchorus capsularis cultivar CVL-1 contig07141, 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: 10790
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.29
Found at i:7685 original size:73 final size:73
Alignment explanation
Indices: 7587--7736 Score: 291
Period size: 73 Copynumber: 2.1 Consensus size: 73
7577 TCAAAAGTTC
*
7587 AATTAATGGTCAAAGTGTTTTTTTTTCCAGGTTGTGGATGGAGAAAATGAGACCATTACAAATCA
1 AATTAATGGTCAAAGTGTTTTTTTTTCCAGGTTGTAGATGGAGAAAATGAGACCATTACAAATCA
7652 ATAAAGAA
66 ATAAAGAA
7660 AATTAATGGTCAAAGTGTTTTTTTTTCCAGGTTGTAGATGGAGAAAATGAGACCATTACAAATCA
1 AATTAATGGTCAAAGTGTTTTTTTTTCCAGGTTGTAGATGGAGAAAATGAGACCATTACAAATCA
7725 ATAAAGAA
66 ATAAAGAA
7733 AATT
1 AATT
7737 GCATAGCTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 76 1.00
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (73 bp):
AATTAATGGTCAAAGTGTTTTTTTTTCCAGGTTGTAGATGGAGAAAATGAGACCATTACAAATCA
ATAAAGAA
Found at i:9141 original size:245 final size:245
Alignment explanation
Indices: 8829--9320 Score: 939
Period size: 245 Copynumber: 2.0 Consensus size: 245
8819 TAGTTTAAGT
8829 AATGATATTTAAGAAATATATTCGAAAAAGAAAGGTATAATCGTCGATTCAAAAATTTTACAACA
1 AATGATATTTAAGAAATATATTCGAAAAAGAAAGGTATAATCGTCGATTCAAAAATTTTACAACA
*
8894 TTCATAATTTTATATATTGTGTAGAATAGATATAGATATAAACATAAATATAGATTATATGAACC
66 TTCATAATTTTATATATTGTATAGAATAGATATAGATATAAACATAAATATAGATTATATGAACC
8959 TTACTATTTAAAACTAAATTTCTATTCATGAAATGAAGGGTACAATATTCAAATATTATTACAAT
131 TTACTATTTAAAACTAAATTTCTATTCATGAAATGAAGGGTACAATATTCAAATATTATTACAAT
9024 CAAATAATTCTTACATGCCCAAACATCCAATGAGAATCTTTATATGCCCA
196 CAAATAATTCTTACATGCCCAAACATCCAATGAGAATCTTTATATGCCCA
*
9074 AATGATATTTAAGAAATATATTCGAAAAAGAAAGGTATAATCGTTGATTCAAAAATTTTACAACA
1 AATGATATTTAAGAAATATATTCGAAAAAGAAAGGTATAATCGTCGATTCAAAAATTTTACAACA
*
9139 TTCATAATTTTATATATTGTATAGAATAGATATAGATATAAACATAAATATAGATTATATGGACC
66 TTCATAATTTTATATATTGTATAGAATAGATATAGATATAAACATAAATATAGATTATATGAACC
* *
9204 TTAGTATTTAAAACTAAATTTCTATTCATGAAATGAAGGGTATAATATTCAAATATTATTACAAT
131 TTACTATTTAAAACTAAATTTCTATTCATGAAATGAAGGGTACAATATTCAAATATTATTACAAT
9269 CAAATAATTCTTACATGCCCAAACATCCAATGAGAATCTTTATATGCCCA
196 CAAATAATTCTTACATGCCCAAACATCCAATGAGAATCTTTATATGCCCA
9319 AA
1 AA
9321 CCAAATATAG
Statistics
Matches: 242, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
245 242 1.00
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (245 bp):
AATGATATTTAAGAAATATATTCGAAAAAGAAAGGTATAATCGTCGATTCAAAAATTTTACAACA
TTCATAATTTTATATATTGTATAGAATAGATATAGATATAAACATAAATATAGATTATATGAACC
TTACTATTTAAAACTAAATTTCTATTCATGAAATGAAGGGTACAATATTCAAATATTATTACAAT
CAAATAATTCTTACATGCCCAAACATCCAATGAGAATCTTTATATGCCCA
Found at i:10232 original size:2 final size:2
Alignment explanation
Indices: 10225--10263 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
10215 TCTTTTAGCG
10225 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10264 CACTAAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10755 original size:24 final size:25
Alignment explanation
Indices: 10695--10753 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
10685 TTCAAGCCCT
* *
10695 AAACTTCATTTCTAACAACTTTTTC
1 AAACTTCATTTCTAACAACATCTTC
10720 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
10744 AAA-TTCATTT
1 AAACTTCATTT
10754 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Done.