Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013537.1 Corchorus olitorius cultivar O-4 contig13570, 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: 6244
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:767 original size:57 final size:57
Alignment explanation
Indices: 703--819 Score: 234
Period size: 57 Copynumber: 2.1 Consensus size: 57
693 CACACCTAAT
703 TTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAA
1 TTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAA
760 TTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAA
1 TTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAA
817 TTT
1 TTT
820 GACTTACAGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 60 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (57 bp):
TTTATACTTCCTTATGTTGCATTAAGTTTAGTTATAAGTTATAACCTTATATGGAAA
Found at i:911 original size:36 final size:36
Alignment explanation
Indices: 864--933 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
854 GAGATTTTGG
** *
864 AGAAATATGATAATTAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
900 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
934 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.60, C:0.07, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Found at i:2257 original size:57 final size:58
Alignment explanation
Indices: 2185--2298 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
2175 ATAGCATCAT
*
2185 GCCTCGGTCCTAAAACGTC-TTTTTTAGGCATCTAAAAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAAAAAAAAACATGTCACTCGATAA
* * * * *
2242 GCCTCGGTCCGAAAACGTCTTTTTTTATGCATCTAATAAAGAACATGTTACTTGATA
1 GCCTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAAAAAAAAACATGTCACTCGATA
2299 TTTGATTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 18 0.36
58 32 0.64
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (58 bp):
GCCTCGGTCCGAAAACGTCTTTTTTTAGGCATCTAAAAAAAAACATGTCACTCGATAA
Found at i:5476 original size:558 final size:559
Alignment explanation
Indices: 4457--5571 Score: 2187
Period size: 558 Copynumber: 2.0 Consensus size: 559
4447 AAAAATATTT
4457 AATTTTTATTCCACGTCATCTGCCACGTCATCAAATTTCACACCGTTAGTACCACGTCAGCACGC
1 AATTTTTATTCCACGTCATCTGCCACGTCATCAAATTTCACACCGTTAGTACCACGTCAGCACGC
4522 TTGACGGGTCTGTTACGACTCACTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAGTAGAGGG
66 TTGACGGGTCTGTTACGACTCACTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAGTAGAGGG
4587 ACGAATTTGTTGAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCC
131 ACGAATTTGTTGAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCC
*
4652 CGGGTACTTTTACCTCCCTCCCCATTATGGATTAATTAGGATTAAGTGAATTTACTGGGATTTTT
196 CGGGTACTTTTACCTCCCTCCCCATTATGGATTAATTAGGATTAAGTGAATTTAATGGGATTTTT
4717 TTTGTACAAGTTAGAATATAGTAATAGCATTCAAAACTTATTTGATAGCGAACATTATAGTTATT
261 TTTGTACAAGTTAGAATATAGTAATAGCATTCAAAACTTATTTGATAGCGAACATTATAGTTATT
4782 TTGATATAATCTTAAATAGTTTTAAGTAAGAAAATTCATAACCTTTTTTTTATATAAAAAGTTAC
326 TTGATATAATCTTAAATAGTTTTAAGTAAGAAAATTCATAACCTTTTTTTTATATAAAAAGTTAC
4847 TAAAATCATCCAAGAGCACAATTAGATTTGTAGAGAGCATTATAGCAATTTTAATACCTTTTATA
391 TAAAATCATCCAAGAGCACAATTAGATTTGTAGAGAGCATTATAGCAATTTTAATACCTTTTATA
4912 ATTTTTTTAGTAATTTTAGATTACAAGATTAATAACATTCATAATTGACGAAAATTATTAATTAA
456 ATTTTTTTAGTAATTTTAGATTACAAGATTAATAACATTCATAATTGACGAAAATTATTAATTAA
4977 AAGTAATAAAAACATAAGGTTACTGAATTTGTTGATACA
521 AAGTAATAAAAACATAAGGTTACTGAATTTGTTGATACA
5016 AATTTTTATTCCACGTCATCTGCCACGTCATCAAATTTCACACCGTTAGTACCACGTCAGCACGC
1 AATTTTTATTCCACGTCATCTGCCACGTCATCAAATTTCACACCGTTAGTACCACGTCAGCACGC
5081 TTGACGGGTCTGTTACGACTCACTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAGTAGAGGG
66 TTGACGGGTCTGTTACGACTCACTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAGTAGAGGG
5146 ACGAATTTGTTGAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCC
131 ACGAATTTGTTGAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCC
5211 CGGGTACTTTTACCTCCCTCCCCATTATGGATTAATTAGGATTAAGTGAATTTAATGGGA-TTTT
196 CGGGTACTTTTACCTCCCTCCCCATTATGGATTAATTAGGATTAAGTGAATTTAATGGGATTTTT
*
5275 TTTGTACAAGTTAGAATATAGTAGTAGCATTCAAAACTTATTTGATAGCGAACATTATAGTTATT
261 TTTGTACAAGTTAGAATATAGTAATAGCATTCAAAACTTATTTGATAGCGAACATTATAGTTATT
5340 TTGATATAATCTTAAATAGTTTTAAGTAAGAAAATTCATAACCTTTTTTTTATATAAAAAGTTAC
326 TTGATATAATCTTAAATAGTTTTAAGTAAGAAAATTCATAACCTTTTTTTTATATAAAAAGTTAC
* *
5405 TAAAATCATCCAAGAGCACAATTAGGTTTGTAGAGAGCATTATAGCTATTTTAATACCTTTTATA
391 TAAAATCATCCAAGAGCACAATTAGATTTGTAGAGAGCATTATAGCAATTTTAATACCTTTTATA
5470 ATTTTTTTAGTAATTTTAGATTACAAGATTAATAACATTCATAATTGACGAAAATTATTAATTAA
456 ATTTTTTTAGTAATTTTAGATTACAAGATTAATAACATTCATAATTGACGAAAATTATTAATTAA
5535 AAGTAATAAAAACATAAGGTTACTGAATTTGTTGATA
521 AAGTAATAAAAACATAAGGTTACTGAATTTGTTGATA
5572 GGACTATAGC
Statistics
Matches: 552, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
558 298 0.54
559 254 0.46
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (559 bp):
AATTTTTATTCCACGTCATCTGCCACGTCATCAAATTTCACACCGTTAGTACCACGTCAGCACGC
TTGACGGGTCTGTTACGACTCACTAACGTGAGGGACCTCGGGTGATAGGCTCTGATAGTAGAGGG
ACGAATTTGTTGAAAAAAAAAGTACAGGGACCAAAATCAACATTTCGTATAGTACAGGGACCTCC
CGGGTACTTTTACCTCCCTCCCCATTATGGATTAATTAGGATTAAGTGAATTTAATGGGATTTTT
TTTGTACAAGTTAGAATATAGTAATAGCATTCAAAACTTATTTGATAGCGAACATTATAGTTATT
TTGATATAATCTTAAATAGTTTTAAGTAAGAAAATTCATAACCTTTTTTTTATATAAAAAGTTAC
TAAAATCATCCAAGAGCACAATTAGATTTGTAGAGAGCATTATAGCAATTTTAATACCTTTTATA
ATTTTTTTAGTAATTTTAGATTACAAGATTAATAACATTCATAATTGACGAAAATTATTAATTAA
AAGTAATAAAAACATAAGGTTACTGAATTTGTTGATACA
Done.