Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015240.1 Corchorus olitorius cultivar O-4 contig15273, 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: 11154
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.31
Found at i:6445 original size:709 final size:700
Alignment explanation
Indices: 5084--6492 Score: 2037
Period size: 700 Copynumber: 2.0 Consensus size: 700
5074 GTCATCCTAG
* * *
5084 AGTAGAATCCAAGTTAAAGTAGGATCCTGAAATTTTGCTGAATTCGTGCAGTGACTTTGACGGCA
1 AGTAGAATCCAAGTTAAAATAGGATCCTGAAATTTTGCTGAATTCGTGCAGGGACTTCGACGGCA
*
5149 TTTTTGGGCTTGAAAACGGCAGAATTGGGTCTTGGACTTCAAAGGAAAGTTGTAGATCTCGGAGT
66 TTTTTGGGCTTGAAAACGGCAGAACTGGGTCTTGGACTTCAAAGGAAAGTTGTAGATCTCGGAGT
* * * * ** *
5214 TAGCTTTCCAACGAGTACTCATGGGCTTCAAACGGAGGTCTGAGCAGAAAGTTATTAATTTTCTA
131 TAGCTTTCCAACGACTACTCACGGGCCTAAAACGGACATCTGAGCAGAAAGTTATGAATTTTCTA
* *
5279 CCAAAACTGCTCCTGAATCCTAATCCTGTTAGGACTAGAATCGGAATCTACAGGATTTTGGTATT
196 CCAAAACTGCTCCTGAATCCTAATCCTGTTAGGACTAGAATCGGAATCTACAGGATTTAGATATT
* *
5344 TCCTTGGATTTAGGAGTCATTAATTGGGATTTTAATTCCAATTAATATTTTATATGGGCTGAGTA
261 TCCTTGAATATAGGAGTCATTAATTGGGATTTTAATTCCAATTAATATTTTATATGGGCTGAGTA
* *
5409 TTTTCCCACATAAATTATCCATAAATACCAAAGCTCGAGAATTTATCCATGACTTGTCTTCAATT
326 TTATCCCACATAAATTATCCATAAATACCAAAGCTCGAGAATTTATCCATGACTTATCTTCAATT
*
5474 AAAGCTCCAATCTTCAATCCTTGCTTCTTGAAATAATTCTTCAAAGTCTTCAAATCTGCAATTTA
391 AAAGCTCCAATCTTCAATCCTTGCTTCTTGAAATAATTCTTCAAAGTCTTCAAATCTGCAAATTA
** * *
5539 TCTTCAAATGGTCTTCAAACACGAACTTCGAATCTCCAAATCTATGCTCAAAATTGCTTTGCTCA
456 TCTTCAAATAATCTTCAAACACGAACTTCGAATCTCCAAATCTATACTCAAAATTACTTTGCTCA
*
5604 AATCTGTGTAAAAAGTCATAAAAATAGCTCCAAAAGTAGTGAAAATTATCAAATTATCAATTTCA
521 AATATGTGTAAAAAGTCATAAAAATAGCTCCAAAAGTAGTGAAAATTATCAAATTATCAATTTCA
* * * *
5669 CATCTCATAAAGACTCAAATCACAAATATTAACAAAATAACATATATTTAAGCATGAATTGATCC
586 CATCTCATAAAGACTCAAAACACAAATATTAACAAAATAACATATAATTAAGCATAAATAGATCC
*
5734 AAAAACATAATAAAATAGCCATAAAACTAGGGTTGTTTTTGGCTCGATCA
651 AAAAACATAATAAAATAGCCATAAAAATAGGGTTGTTTTTGGCTCGATCA
* *
5784 AGTAGAATCCAAGTTAAAATAGGATCCTGAAATTTTGCTGAATTCGTGCAGGGACTTCGATGTCA
1 AGTAGAATCCAAGTTAAAATAGGATCCTGAAATTTTGCTGAATTCGTGCAGGGACTTCGACGGCA
* * * *
5849 TTTTTGGGCTTGAAGATGGCAGAACTGTGTCTTGGACTTCGAAGGAAAGTTGTCA-ATCTCGGAG
66 TTTTTGGGCTTGAAAACGGCAGAACTGGGTCTTGGACTTCAAAGGAAAGTTGT-AGATCTCGGAG
*
5913 TTAGCTTTCCAAC-ACCTACTCACGGGCCTAAAACGGACATCTGAGCAGAAAGTTATGATTTTTC
130 TTAGCTTTCCAACGA-CTACTCACGGGCCTAAAACGGACATCTGAGCAGAAAGTTATGAATTTTC
* * * *
5977 ATA-CGAGACTGC-GCTGAATCCTAATCCTGTTAGGACTAGAATCGGGAATCTACGGGATTTAGA
194 -TACCAAAACTGCTCCTGAATCCTAATCCTGTTAGGACTAGAATC-GGAATCTACAGGATTTAGA
* *
6040 TATTTCCTTGAATATAGGAGTCCTTAATTGGGATTTTAATTTCAATTAATGA-TTTATATGGGCT
257 TATTTCCTTGAATATAGGAGTCATTAATTGGGATTTTAATTCCAATTAAT-ATTTTATATGGGCT
* * * ** * * *
6104 GAGTATTATCCCATATGAAA-TATCCA-AAATTCCAAAGCTTCCGGGCTTCTTCATGGCTTGTCT
321 GAGTATTATCCCACAT-AAATTATCCATAAATACCAAAGC-T-CGAGAAT-TT-AT-CCATGACT
* * * * *
6167 TCAATCCTTCGCAATTAAAGTTCCATTCTTCAATTCTTGCTTC-TGAAATTATTCTTCAATGGTC
380 T--AT-CTT--CAATTAAAGCTCCAATCTTCAATCCTTGCTTCTTGAAATAATTCTTCAA-AGTC
*
6231 TTCAAATCCT-CAAATTGTCTTC-AATAAATCTTCAAACACGAACTTCGAATCTCCAAATCTATA
439 TTCAAAT-CTGCAAATTATCTTCAAAT-AATCTTCAAACACGAACTTCGAATCTCCAAATCTATA
* * *
6294 CTCAAAATTACTTTGCTCATATATGTGTAAAAAGTCATCAAAATAGCTCCAAATGTAGTGAAAAT
502 CTCAAAATTACTTTGCTCAAATATGTGTAAAAAGTCATAAAAATAGCTCCAAAAGTAGTGAAAAT
*
6359 TATCAAATTATCAATTTCACATCTTATAAAGACTCAAAACACAAATATTAACAAAATAACATATA
567 TATCAAATTATCAATTTCACATCTCATAAAGACTCAAAACACAAATATTAACAAAATAACATATA
*
6424 ATTAAGCATAAATAGATCCAAAAACATAGTAAAATAGCCATAAAAATAGGGTTGTTTTTGGCTCG
632 ATTAAGCATAAATAGATCCAAAAACATAATAAAATAGCCATAAAAATAGGGTTGTTTTTGGCTCG
6489 ATCA
697 ATCA
6493 GGTGGTTTGA
Statistics
Matches: 630, Mismatches: 60, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
699 42 0.07
700 273 0.43
701 11 0.02
702 2 0.00
703 2 0.00
704 6 0.01
706 1 0.00
707 3 0.00
708 18 0.03
709 270 0.43
710 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (700 bp):
AGTAGAATCCAAGTTAAAATAGGATCCTGAAATTTTGCTGAATTCGTGCAGGGACTTCGACGGCA
TTTTTGGGCTTGAAAACGGCAGAACTGGGTCTTGGACTTCAAAGGAAAGTTGTAGATCTCGGAGT
TAGCTTTCCAACGACTACTCACGGGCCTAAAACGGACATCTGAGCAGAAAGTTATGAATTTTCTA
CCAAAACTGCTCCTGAATCCTAATCCTGTTAGGACTAGAATCGGAATCTACAGGATTTAGATATT
TCCTTGAATATAGGAGTCATTAATTGGGATTTTAATTCCAATTAATATTTTATATGGGCTGAGTA
TTATCCCACATAAATTATCCATAAATACCAAAGCTCGAGAATTTATCCATGACTTATCTTCAATT
AAAGCTCCAATCTTCAATCCTTGCTTCTTGAAATAATTCTTCAAAGTCTTCAAATCTGCAAATTA
TCTTCAAATAATCTTCAAACACGAACTTCGAATCTCCAAATCTATACTCAAAATTACTTTGCTCA
AATATGTGTAAAAAGTCATAAAAATAGCTCCAAAAGTAGTGAAAATTATCAAATTATCAATTTCA
CATCTCATAAAGACTCAAAACACAAATATTAACAAAATAACATATAATTAAGCATAAATAGATCC
AAAAACATAATAAAATAGCCATAAAAATAGGGTTGTTTTTGGCTCGATCA
Done.