Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005009.1 Corchorus capsularis cultivar CVL-1 contig05027, 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: 3366
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Found at i:1271 original size:664 final size:662
Alignment explanation
Indices: 1--2022 Score: 3221
Period size: 664 Copynumber: 3.0 Consensus size: 662
*
1 AGTATTGTGGCAAAAAATTGAGGAAAAACCTTTCAGGTCAGTTTTT-CTAAAATTTTAGCCGAAA
1 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGC-AAAATTTTAGCCGAAA
* * *
65 TCGTGTACTAATCATCACGGTTTTTAGCTAAAAACGTGTTTTGGGGCGTCGACTCAGTTTTGCAT
65 TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAGTTTTGCAT
* *
130 GATTTTTTGTAGAATGACTCTTTGAAATATCCATATTCATCTAACCAAATCTCAACCACAATGGA
130 GATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGA
* * *
195 CTAAAGG-TTTTTTTGTTATGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAA
195 TTAAAGGATTTGTTT-TTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGG-A
* *
259 AAATAAAAAAGGAAAAACGATATTAGAAACGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTA
258 AAA-AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTA
* * *
324 TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAATCTGATCGGGTCAGTTTTTGCAATA
322 TATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAATCT-TTCGGGTCAGTTTTTGCAAAA
* * *
389 TTTTTGCCGAAATCGTGTAATAACTATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGAC
386 TTTTTGCCGAAATCGTGT-ACAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGAC
*
454 TCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTCAAATATATATATTCATCTAATCAAATCTC
450 TCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCTAATCAAATCTC
*
519 AGCCACATTGAATTTAAGGATTTGATTTTACGT-GCATCTGAATTTTCTTTCGATTTAATAAGAA
515 AGCCACATTGAATTTAAGGATTTGTTTTTAC-TAGCATCTGAATTTTCTTTCGATTTAATAAGAA
583 ATAAATTCGGTAAAAATGGAAAAACGATATTAGAAGCGAAAAAACCCTTCAATTTTTTTGGTGTT
579 ATAAATTCGGTAAAAATGGAAAAACGATATTAGAAGCGAAAAAACCCTTCAATTTTTTTGGTGTT
*
648 GAATTATATATTTCTTATG
644 GAATTATATATTTTTTATG
* *
667 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTTAGGTCAGTTTTTGCAAAATTTTAGCTGAAAT
1 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
732 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAGTTTTGCATG
66 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAGTTTTGCATG
* *
797 ATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTTACCAAATCTCAGCCACAATGGAT
131 ATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGAT
862 TAAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
196 TAAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
927 AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATATA
261 AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATATA
* *
992 TTTTTTATGAGTATTGTGGCCAAAAATTGAGAAAAATCGTTTCGGGTCTGTTTTTGCAAAATTTT
326 TTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAATC-TTTCGGGTCAGTTTTTGCAAAATTTT
* * * * * *
1057 TGTCGAAATCGTGTACCACCCATCACGGTTTTTGGCTAAAAACTTATTTCGCGGCCTCAACTCAG
390 TGCCGAAATCGTGTA-CAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGACTCAG
* *
1122 TTTTGCATGATTTTTGGCAAAAAGACTCCTAGAAATATATATATTCATCTAATCAAATCTCAGCC
454 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCAGCC
* * *
1187 ACATTGAATTTGAGGATTTGTTTTTACTAGTATCTGAATTTTCTTTGGATTTAATAAGAAATAAA
519 ACATTGAATTTAAGGATTTGTTTTTACTAGCATCTGAATTTTCTTTCGATTTAATAAGAAATAAA
* *
1252 TTCGGTAAAAATGGAAAAACGATATTAAGAAGCGAAAAAACCCTTCAATTTTTTCGGCGTTGAAT
584 TTCGGTAAAAATGGAAAAACGATATT-AGAAGCGAAAAAACCCTTCAATTTTTTTGGTGTTGAAT
1317 TATATATTTTTTATG
648 TATATATTTTTTATG
* * * * *
1332 AGCATAGTGGGAAAAAATCGAGGAAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
1 AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
*
1397 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAATTTTGCATG
66 CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAGTTTTGCATG
1462 ATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGAT
131 ATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGAT
1527 TAAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGGAAA
196 TAAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTC-GGAAA
1592 AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATAT
260 AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATAT
1657 ATTTTTTATGAGTATTGTGGCAAAAAATTGAGGAAAAAAT-TTTCGGGTCAGTTTTTGCAAAATT
325 ATTTTTTATGAGTATTGTGGCAAAAAATTGA-G-AAAAATCTTTCGGGTCAGTTTTTGCAAAATT
* * * *
1721 TTAGCCGAAATCGTGTAC-TCCATCACGGTTTTTGGCTAAAAACGTGTTCCGGGGCCTCGACTTA
388 TTTGCCGAAATCGTGTACAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGACTCA
* * * * *
1785 GTTTTGAATGATTTTT-GCAGAAAGACTCCTTGAAATATCTATATTTATCTAAGCAAATCTCAAC
453 GTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCAGC
* * * * * * *
1849 CACAATGGATTTAATGATTTCTTTTTACAAGCATCTGAATCTTT-TTTCAATTTAATTAGAAATA
518 CACATTGAATTTAAGGATTTGTTTTTACTAGCATCTGAAT-TTTCTTTCGATTTAATAAGAAATA
* * * * * * * *
1913 TATTCGGGAAAAATGGGAAAATGGTATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGGTGTAGA
582 AATTCGGTAAAAATGGAAAAACGATATTAGAAGCG-AAAAAACCCTTCAATTTTTTTGGTGTTGA
*
1978 ATTATATATTTTTTCTG
646 ATTATATATTTTTTATG
*
1995 AATATTGTGGCAAAAAATTGAGGAAAAA
1 AGTATTGTGGCAAAAAATTGAGGAAAAA
2023 ATTGTGTCTT
Statistics
Matches: 1252, Mismatches: 93, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
662 7 0.01
663 180 0.14
664 379 0.30
665 300 0.24
666 372 0.30
667 8 0.01
668 6 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (662 bp):
AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
CGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTGGGGCGTCGACTCAGTTTTGCATG
ATTTTTGGTAGAATGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCAACCACAATGGAT
TAAAGGATTTGTTTTTATGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
AAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCATTGAATTATATA
TTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAATCTTTCGGGTCAGTTTTTGCAAAATTTTT
GCCGAAATCGTGTACAACCATCACGGTTTTTGGCTAAAAACGTGTTTCGGGGCCTCGACTCAGTT
TTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATATATATTCATCTAATCAAATCTCAGCCAC
ATTGAATTTAAGGATTTGTTTTTACTAGCATCTGAATTTTCTTTCGATTTAATAAGAAATAAATT
CGGTAAAAATGGAAAAACGATATTAGAAGCGAAAAAACCCTTCAATTTTTTTGGTGTTGAATTAT
ATATTTTTTATG
Done.