Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014618.1 Corchorus olitorius cultivar O-4 contig14651, 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: 1999
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:627 original size:333 final size:332
Alignment explanation
Indices: 1--1999 Score: 2641
Period size: 333 Copynumber: 6.0 Consensus size: 332
* *
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCAAACAAAACTT
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
* * * * **
66 AGTCGGGGCCCCGGAACGCGTTTTCAG-CGCAAACTGTGATGGTTATCACACGATGACGGTCAAG
66 AG-CGGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
* * * * *
130 ATTTTGCAAAATTTAACCCGAATGATTTTTCCTAAATTTTTTGCCAAAATACTAATAAAAGATAT
130 ATTTTGCAAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATAT
* * * * * * *
195 TTAAATAATCGCCAAAAAGATTGAAGGGTTTTTCATGCTTCGAAGATCGTTTTTGC-TATGTTTT
195 ATAAATCATCACCAAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTT-CTTATGCTTT
* * *
259 TCCGAATTAATTTCCAATTAAATAAAAAGTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATA
259 TCCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAATA
324 TTATGTGGC
324 TTATGTGGC
* * * *
333 TGTGATTTGGGTAGATGAATTTACATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTA
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
*
398 AGTCGGGGCCCTAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
66 AG-CGGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
* * * *
463 ATTTTGCAAAAAATGACCCAAATTATTTTTCCTAAATTTTTTGCTAAAATACTCATAAAATATAT
130 ATTTTGCAAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATAT
* * *
528 AGAAATCATCACCAAAAAGTTTGGAGGGTTTTTCACGCTTCGAATATCATTTTTCTTATGCTTTT
195 ATAAATCATCACCAAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTTATGCTTTT
* * * * *
593 ACGAATTAATTTCCAGTTAAATCGAAACTGGATTCCGATGCTAGTAAAAACAAATCTTTAAATCT
260 CCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAATAT
658 TATGTGGC
325 TATGTGGC
*
666 TGAGATTTGGGTAGATTAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCA-ACAAAACTG
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
* * *
730 AGCAGGGCCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCAGACTATTTCGGTCAAG
66 AGC-GGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
* * * * * ** *
795 AATTTGCAAAAAATTGATCCGAATGATTTTTACTCAATTTTTACCCAAAATACTCTTAAAAAATA
130 ATTTTGC-AAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATA
** * * * * * * *
860 TATAAATCATTGCCAAAAAGATTGAAGGATTTTTTGACACTTCGAAAATCGTTTTTCCTATGTTT
194 TATAAATCATCACCAAAAAGTTTGAAGG-GTTTTTCACGCTTCGAATATCGTTTTTCTTATGCTT
* *
925 TTCCGAATTAATTTCCAATTAAATAGAAACTGGATTCTGATGCTCGT-TAAACAAATCTTTAAAT
258 TTCCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAAT
*
989 ATTATGTGGT
323 ATTATGTGGC
* * * **
999 TGAGATTTGGATAGATGAAAATAGATATTCGAAGGAGTCTTGGCGTAAAAAATCATACAAAACTG
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
** * *
1064 AGCCGGGGCCCTGGAACGCGTTTTTAGTCGAAAACTGTGATGTTTAAGCACACGATTTCGGTCAA
66 AG-CGGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTT-AGCACACGATTTCGGTCAA
* * * *
1129 GATTTTGCAAAAATTGACCCAAAAGATTTTCCCTCAATTTTTTGCTAAAATACTCATAAAAAATA
129 GATTTTGCAAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATA
*
1194 TATAAATCATCACCAAAAAGTTTGGAGGGTTTTTCACGCTTCGAATATCG-TTTTCTTATGCTTT
194 TATAAATCATCACCAAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTTATGCTTT
* * * * *
1258 TCCGACTTAATTTCCATTTAGATAGAAACTGGATTCCGATGCTAGTAAAAACAAATCTTTAAATC
259 TCCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAATA
1323 TTATGTGGC
324 TTATGTGGC
* *
1332 TGAGATTTGGGTAGATGAATATAGTTATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTT
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
* * * *
1397 AGCCGGGGCCCTAGAACGCGTTTTTAACCAAAAACTGTGATGGTTAGCACACGATTTCGGTCAAC
66 AG-CGGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
* * **
1462 ATTTTGCAAAAATTGACCCAAACGATTTTTCCTCAATTTTTTGTTAAAATACTCATAAAAAATAT
130 ATTTTGCAAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATAT
* * * * * *
1527 ATACATCATCACCAAAAACTTTGGAGGGCTTTTCACGCTTCGAATATCATTTTTCTTATGATTTT
195 ATAAATCATCACCAAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTTATGCTTTT
* * * * * *
1592 CCGAATTAATTTCCAATTAAATCGAAACTGGATTCCGATACTTGTAAAAACAAATTTTTAAGTCT
260 CCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAATAT
*
1657 TACGTGGC
325 TATGTGGC
*
1665 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCG-CAAAAATCTTAC-AAACTG
1 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
* * *
1728 AGCGGAGGCCCCGGAACGC-CTTTTAGACGAAAACGTGTGATGGTTAGCACACGATTTCGGTCAA
66 AGCGG-GGCCCCAGAACGCGTTTTTAGCCGAAAAC-TGTGATGGTTAGCACACGATTTCGGTCAA
* * * *
1792 TAATTTGCAAAAATTGATCCGAAA-GATTTTTCCTAAATTTTTAGCCAAAATACTCATAAAAAAA
129 GATTTTGCAAAAATTGA-CCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCAT-AAAAAA
* * * * * * * *
1856 TATATGAATCATCGCCAAAAAAGTTAGAAGGGTTTTTAAAGCTTCGAATATTGTTTTTCCTATAC
192 TATATAAATCATCACC-AAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTTATGC
* ** * *
1921 TTTTCCGAATTAATTTCCAATTAAATCGAAACTGGATTATGATGCTCGTAAAAAAAAAATCTTCA
256 TTTTCCGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGT-AAAAACAAATCTTTA
1986 AATCA-TATGTGGC
320 AAT-ATTATGTGGC
1999 T
1 T
Statistics
Matches: 1460, Mismatches: 190, Indels: 32
0.87 0.11 0.02
Matches are distributed among these distances:
330 14 0.01
331 92 0.06
332 372 0.25
333 745 0.51
334 212 0.15
335 25 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (332 bp):
TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATACAAAACTG
AGCGGGGCCCCAGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAGA
TTTTGCAAAAATTGACCCAAATGATTTTTCCTAAATTTTTTGCCAAAATACTCATAAAAAATATA
TAAATCATCACCAAAAAGTTTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTTATGCTTTTC
CGAATTAATTTCCAATTAAATAGAAACTGGATTCCGATGCTCGTAAAAACAAATCTTTAAATATT
ATGTGGC
Done.