Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010945.1 Corchorus olitorius cultivar O-4 contig10977, 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, 612
Length: 1020
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Found at i:279 original size:154 final size:152
Alignment explanation
Indices: 1--1020 Score: 1375
Period size: 154 Copynumber: 6.6 Consensus size: 152
*
1 AGACGATTCAAAACGGAACTAATGCG-CCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
1 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC-AATGAGCT
* * *
65 -AAAACTTCACAGTGTAATAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
65 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
129 AAGCATTTAGGTTTGCCAAATCGA
130 AAGCATTGAGGTTT-CCAAATCGA
* *
153 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACACGTGTTCCAACTGACCT
1 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAA-TGAGCT
* * *
218 AAAAAGTTCACAGTGGACTAAACTCACCAAACTGATTATAGTTAGGCCATAAACAATGGAAAGAA
65 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
283 AACCATTGAGGTTTGCCAAATCGA
130 AAGCATTGAGGTTT-CCAAATCGA
* ** * * *
307 AGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTTCAAATGAACT
1 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT-GTTCCAATGAGCT
* *
372 AAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAA
65 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
437 AAGCATTGAGGTTTTCCAAATCGA
130 AAGCATTGAGG-TTTCCAAATCGA
* ** * *
461 GGACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
1 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC-AATGAGCT
* *
526 AAAAACTTCACAGTTGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAA
65 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* *
591 AAGCATTGAGGTTTCTAAATAGA
130 AAGCATTGAGGTTTCCAAATCGA
* * ** * **
614 TGACGATTCAAAATGTCACTAATGGGTCTTGATAGGCCCAAAATAATC-AGTGTTCCAAATGAGC
1 AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA-CAAGTGTTCC-AATGAGC
**
678 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGCCAAGA
64 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
743 AAAGCATTGAGGTTTCCGAAATCGA
129 AAAGCATTGAGGTTTCC-AAATCGA
* * * *
768 ATACGGTTCAAAAC-GACACTTATGGGCCCCGATAGGCCCAAAATTACAAGTGTTCCGAATGAGC
1 AGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC-AATGAGC
** * * *
832 TAAAAACTTCACAGTGTTCTAATCTCACCGAAATGATTACAGTTAGGCCATAAACAATGCAAAGA
64 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
*
897 AAAGCATTGAGGTTTACGAAATCGA
129 AAAGCATTGAGGTTT-CCAAATCGA
* * * *
922 AGACGGTTCTAAAC-GACACTAATGGGCCCCCATAGGCCCAAAATTACAAGTGTTCCGAATGAGC
1 AGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCC-AATGAGC
*** *
986 TAAAAACTTCACAGTATTCTAATCTCACCGAAATG
64 TAAAAACTTCACAGTGGACTAATCTCACCAAAATG
Statistics
Matches: 786, Mismatches: 71, Indels: 20
0.90 0.08 0.02
Matches are distributed among these distances:
152 27 0.03
153 181 0.23
154 569 0.72
155 9 0.01
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (152 bp):
AGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAATGAGCTA
AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCATTGAGGTTTCCAAATCGA
Found at i:767 original size:307 final size:307
Alignment explanation
Indices: 1--1020 Score: 1431
Period size: 307 Copynumber: 3.3 Consensus size: 307
** * *
1 AGACGATTCAAAACGGAACTAATGCG-CCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
1 AGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* * *
65 -AAAACTTCACAGTGTAATAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
66 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
*
129 AAGCATTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCA
131 AAGCATTGAGGTTT-CCAAATCGAAGACGATTCAAAAC-GACACTAATGGGCCCCGATAGGCCCA
* * * * * * *
193 AAATAACACGTGTTCCAACTGACCTAAAAAGTTCACAGTGGACTAAACTCACCAAACTGATTATA
194 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATA
* *
258 GTTAGGCCATAAACAATGGAAAGAAAACCATTGAGGTTTGCCAAATCGA
259 GTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGA
* * * *
307 AGACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTTCAAATGAACT
1 AGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
* *
372 AAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAA
66 AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * *
437 AAGCATTGAGGTTTTCCAAATCGAGGACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAA
131 AAGCATTGAGG-TTTCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAA
*
502 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATTATTATAG
195 AATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAG
* *
567 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTT-CTAAATAGA
260 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGA
* * * **
614 TGACGATTCAAAATGTCACTAATGGGTCTTGATAGGCCCAAAATAATC-AGTGTTCCAAATGAGC
1 AGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAA-CAAGTGTTCCAAATGAGC
**
678 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGCCAAGA
65 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* * *
743 AAAGCATTGAGGTTTCCGAAATCGAATACGGTTCAAAACGACACTTATGGGCCCCGATAGGCCCA
130 AAAGCATTGAGGTTTCC-AAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCA
* * * * *
808 AAATTACAAGTGTTCCGAATGAGCTAAAAACTTCACAG-TGTTCTAATCTCACCGAAATGATTAC
194 AAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTG-ACTAATCTCACCAAAATGATTAT
* *
872 AGTTAGGCCATAAACAATGCAAAGAAAAGCATTGAGGTTTACGAAATCGA
258 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGA
* * * * * *
922 AGACGGTTCTAAACGACACTAATGGGCCCCCATAGGCCCAAAATTACAAGTGTTCCGAATGAGCT
1 AGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
*** *
987 AAAAACTTCACAGTATTCTAATCTCACCGAAATG
66 AAAAACTTCACAGTGGACTAATCTCACCAAAATG
Statistics
Matches: 632, Mismatches: 73, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
306 29 0.05
307 303 0.48
308 297 0.47
309 3 0.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (307 bp):
AGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
AAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
AAGCATTGAGGTTTCCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATAGGCCCAAA
ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGT
TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTACCAAATCGA
Found at i:898 original size:461 final size:461
Alignment explanation
Indices: 1--1020 Score: 1469
Period size: 461 Copynumber: 2.2 Consensus size: 461
* *
1 AGACGATTCAAAACGGA-ACTAATGCGCCCGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
1 AGACGATTCAAAAC-GACACTAATGGGCCCAATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
* *
65 -AAAACTTCACAG-TGTAATAATCTCAGCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
65 AAAAACTTCACAGTTG-ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
128 AAAGCATTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
129 AAAGCATTGAGGTTTGCCAAATAGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCA
* * *
193 AAATAACACGTGTTCCAACTGACCTAAAAAGTTCACAGTGGACTAAACTCACCAAACTGATTATA
194 AAATAACACGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATA
* * *
258 GTTAGGCCATAAACAATGGAAAGAAAACCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGT
259 GTTAGGCCATAAACAATGCAAAGAAAACCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGA
*
323 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTTCAAATGAACTAAAAACTTCACAGTGG
324 CACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAACTAAAAACTTCACAGTGG
* * * *
388 ACTAATTTCACCAAAATGATTATAGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGTTTTC
389 ACTAATCTCACCAAAATGATTACAGTTAGACCATAAACAATGCAAAGAAAAGCATTGAGGTTTAC
453 CAAATCGA
454 CAAATCGA
* * *
461 GGACGATTCAAAACGTCACTAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
1 AGACGATTCAAAACGACACTAATGGGCC-CAATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
*
526 AAAAACTTCACAGTTGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGAAAGAA
65 AAAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAA
* * * ** * **
591 AAGCATTGAGGTTT-CTAAATAGATGACGATTCAAAATGTCACTAATGGGTCTTGATAGGCCCAA
130 AAGCATTGAGGTTTGCCAAATAGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAA
* *
655 AATAATCA-GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATA
195 AATAA-CACGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATA
* * * *
719 GTTAGGCCATAAACAATGCCAAGAAAAGCATTGAGGTTT-CCGAAATCGAATACGGTTCAAAACG
259 GTTAGGCCATAAACAATGCAAAGAAAACCATTGAGGTTTGCC-AAATCGAAGACGATTCAAAACG
* * * * *
783 ACACTTATGGGCCCCGATAGGCCCAAAATTACAAGTGTTCCGAATGAGCTAAAAACTTCACAGTG
323 ACACTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAACTAAAAACTTCACAGTG
** * *
848 TTCTAATCTCACCGAAATGATTACAGTTAGGCCATAAACAATGCAAAGAAAAGCATTGAGGTTTA
388 GACTAATCTCACCAAAATGATTACAGTTAGACCATAAACAATGCAAAGAAAAGCATTGAGGTTTA
*
913 CGAAATCGA
453 CCAAATCGA
* * * *
922 AGACGGTTCTAAACGACACTAATGGGCCCCCATAGGCCCAAAATTACAAGTGTTCCGAATGAGCT
1 AGACGATTCAAAACGACACTAATGGG-CCCAATAGGCCCAAAATAACAAGTGTTCCGAATGAGCT
* *
987 AAAAACTTCACAGTAT-TCTAATCTCACCGAAATG
65 AAAAACTTCACAGT-TGACTAATCTCACCAAAATG
Statistics
Matches: 497, Mismatches: 55, Indels: 15
0.88 0.10 0.03
Matches are distributed among these distances:
459 1 0.00
460 25 0.05
461 393 0.79
462 76 0.15
463 2 0.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (461 bp):
AGACGATTCAAAACGACACTAATGGGCCCAATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTA
AAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCATTGAGGTTTGCCAAATAGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
ATAACACGTGTTCCAAATGACCTAAAAACTTCACAGTGGACTAAACTCACCAAAATGATTATAGT
TAGGCCATAAACAATGCAAAGAAAACCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGACA
CTAATGGGCCCCGATAGGCCCAAAATAACAAGTATTCCAAATGAACTAAAAACTTCACAGTGGAC
TAATCTCACCAAAATGATTACAGTTAGACCATAAACAATGCAAAGAAAAGCATTGAGGTTTACCA
AATCGA
Done.