Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020725.1 Corchorus olitorius cultivar O-4 contig20758, 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: 4690
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:4584 original size:566 final size:567
Alignment explanation
Indices: 3624--4682 Score: 1596
Period size: 566 Copynumber: 1.9 Consensus size: 567
3614 AAAGACTCCT
* * ** **
3624 TGAAATATCTATATTTATCAAACCAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTACGAG
1 TGAAATATCTATATTCATCAAACAAAATCCCAGCCACATTCAATATAAGGATTTGTTTTTACGAG
* * * * * *
3689 CATCTGAATCTTGTTTCGATTTAATTAGATATTAATTCGGAAAAAAATGGAAAAATGATATTAAA
66 CATCTGAATCATGTTTCAATTTAACTAAAAATTAATTCAGAAAAAAATGGAAAAATGATATTAAA
*
3754 AGCGTGAAAAGACCATCAATATTTTTGGTGTTGAATTATATATTTTTCTGAGTATTGTGGCAAAA
131 AGCGTGAAAAGACCATCAATATTTTTGGCGTTGAATTATATATTTTTCTGAGTATTGTGGCAAAA
*
3819 AATTCATAAAAATCAAAAAATCGGGTCAGATTTTAGTCGAAAATATCGTCTACTAACCATATTGG
196 AATTCA-AAAAA-CAAAAAATCGGGTCAGATTTTAGCCGAAAATATCGTCTACTAACCATATTGG
* *
3884 TTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGCTTGATTTTTGGCAGAAAGAC
259 TTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGCCTGATTTTTGGCAGAAAAAC
*
3949 TCCTTGAAATATCTATATTCATCTAACCAACTTCAGGCTCTCAGCCACATTAGATTTAAGGAATT
324 TCCTTGAAATATCTATATTCATCTAACCAACTTCAGACTCTCAGCCACATTAGATTTAAGGAATT
4014 GTTTTTACGAGCATCTGAATAATT-TTTCGATTTAATTAGAAATAAATTCAGGCAAAA-AATAGA
389 GTTTTTACGAGCATCTGAAT-ATTGTTTCGATTTAATTAGAAATAAATTC-GG-AAAAGAATAGA
* *
4077 AAAATAATATTTAAAGCGAGAAAAATATTTCAAATTTTTTTTTAGCGTTGAATTGTGTATTTTTT
451 AAAATAATATTTAAAGCAAGAAAAATATCTC-AATTTTTTTTTAGCGTTGAATTGTGTATTTTTT
4142 GCCGAAAATATATATATTTTTTTTTTGCATGATTTTTGACGTTAATATTTTAC
515 GCCGAAAATATATATATTTTTTTTTTGCATGATTTTTGACGTTAATATTTTAC
* * * *
4195 TGAAATATCTATATTCATCGAACAAAATCCCAGCCACGTTCAATTTAAGTATTTGTTTTTACGAG
1 TGAAATATCTATATTCATCAAACAAAATCCCAGCCACATTCAATATAAGGATTTGTTTTTACGAG
* *
4260 CATCTGAATCATGTTTCAATTTAACTAAAAATTAATTCAGAAAAAAATGGAAAAATGTTATTAGA
66 CATCTGAATCATGTTTCAATTTAACTAAAAATTAATTCAGAAAAAAATGGAAAAATGATATTAAA
* * * *
4325 AGCGTGAAAAGCCCGTCAGTCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAA
131 AGCGTGAAAAGACCATCAATATTTTTGGCGTTGAATTATATA-TTTTTCTGAGTATTGTGGCAAA
* ** * *
4390 AAATTC-AGAAA-AAAATTTCGGGT-ATGTTTTTAGCCG-AAA-ATCGTGTACTAACCATCA-TG
195 AAATTCAAAAAACAAAAAATCGGGTCA-GATTTTAGCCGAAAATATCGTCTACTAACCAT-ATTG
* *
4449 GTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGGCTTAGTTTTGCCTGATTTTTGGCAGAAAAA
258 GTTTTTGGGCTAAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGCCTGATTTTTGGCAGAAAAA
* *
4514 CTCCTTGAAATATTTATATTCATCTAACCAA-TCTCAGACTCTCAGCCACATTAGATTTAAGGAT
323 CTCCTTGAAATATCTATATTCATCTAACCAACT-TCAGACTCTCAGCCACATTAGATTTAAGGAA
*
4578 TTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAGATTCGGAAAAGAATAGAA
387 TTGTTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAATAGAA
* *
4643 AATTGATATTTAAAGCAAGAAAAATATCTCAATTTTTTTT
452 AAATAATATTTAAAGCAAGAAAAATATCTCAATTTTTTTT
4683 GAGTTGAA
Statistics
Matches: 441, Mismatches: 41, Indels: 19
0.88 0.08 0.04
Matches are distributed among these distances:
564 14 0.03
565 39 0.09
566 183 0.41
567 5 0.01
568 19 0.04
570 4 0.01
571 149 0.34
572 28 0.06
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (567 bp):
TGAAATATCTATATTCATCAAACAAAATCCCAGCCACATTCAATATAAGGATTTGTTTTTACGAG
CATCTGAATCATGTTTCAATTTAACTAAAAATTAATTCAGAAAAAAATGGAAAAATGATATTAAA
AGCGTGAAAAGACCATCAATATTTTTGGCGTTGAATTATATATTTTTCTGAGTATTGTGGCAAAA
AATTCAAAAAACAAAAAATCGGGTCAGATTTTAGCCGAAAATATCGTCTACTAACCATATTGGTT
TTTGGGCTAAAAACGCGTTTCGGGGGCCCCGACTCAGTTTTGCCTGATTTTTGGCAGAAAAACTC
CTTGAAATATCTATATTCATCTAACCAACTTCAGACTCTCAGCCACATTAGATTTAAGGAATTGT
TTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAATAGAAAAAT
AATATTTAAAGCAAGAAAAATATCTCAATTTTTTTTTAGCGTTGAATTGTGTATTTTTTGCCGAA
AATATATATATTTTTTTTTTGCATGATTTTTGACGTTAATATTTTAC
Done.