Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009363.1 Corchorus olitorius cultivar O-4 contig09393, 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, 649
Length: 1082
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Found at i:281 original size:154 final size:154
Alignment explanation
Indices: 1--601 Score: 988
Period size: 154 Copynumber: 3.9 Consensus size: 154
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * *
66 ACTATTCAAAACGAAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAA
66 ACGATTCAAAACGTAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
131 AAACTTCACAGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* * *
155 CCAAAATTATTATAATTAGGCCATAAACAATAGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * * *
220 ATGATTCGAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
66 ACGATTCAAAACGTAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
*
285 AAACTTCACAGTTGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
* * *
309 CCAAAATGATTATAGTTTGGCAATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
* * * *
374 ACGATTCAAAACGTCACAAATGGACCACGATAGGCCCAAAATAACAAGTATTCCAAATGAGCTAA
66 ACGATTCAAAACGTAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
* *
439 ATACTTCACGGTGGACTAATCTCA
131 AAACTTCACAGTGGACTAATCTCA
*
463 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAG
1 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
*
528 ACGATTCAAAACAG-AACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTA
66 ACGATTCAAAAC-GTAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
592 AAAACTTCAC
130 AAAACTTCAC
602 TGTTATTTTG
Statistics
Matches: 410, Mismatches: 36, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
154 409 1.00
155 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (154 bp):
CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAG
ACGATTCAAAACGTAACTAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AAACTTCACAGTGGACTAATCTCA
Found at i:696 original size:110 final size:109
Alignment explanation
Indices: 504--710 Score: 333
Period size: 110 Copynumber: 1.9 Consensus size: 109
494 GGAAAGAAAA
* * * *
504 GCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACAGAACTAATGGACCCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATACAAAACAGAACTAAAGGACCCCGATAGGCCAAAAA
*
569 TAACAAGTGTTCTAAATGAGCTAAAAACTTCACTGTTATTTTGG
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTTATTTTGG
*
613 GCATTGAGGTTTGCCAAATCGAAGACGACTACAAAACGGAACTAAAGGACCCCGATAGGCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGA-TACAAAACAGAACTAAAGGACCCCGATAGGCCAAAA
**
678 ATAACTTGTGTTCCAAATGAGCTAAAAACTTCA
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCA
711 AAGTGGACTA
Statistics
Matches: 89, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 27 0.30
110 62 0.70
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (109 bp):
GCATTGAGGTTTGCCAAATCGAAGACGATACAAAACAGAACTAAAGGACCCCGATAGGCCAAAAA
TAACAAGTGTTCCAAATGAGCTAAAAACTTCACTGTTATTTTGG
Found at i:852 original size:264 final size:263
Alignment explanation
Indices: 350--865 Score: 820
Period size: 264 Copynumber: 2.0 Consensus size: 263
340 GGAAAGAAAA
* ** *
350 GCATTGAGATTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCACGATAGGCCCAAAA
1 GCATTGAGATTTGCCAAATCGAAGACGATACAAAACGGAACAAATGGACCACGATAGGCCAAAAA
* **
415 TAACAAGTATTCCAAATGAGCTAAATACTTCACGGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTATTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTT
**
480 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATTGAAGACGATTCAAAACAGAAC
131 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTCAAAACAGAAC
* * *
545 TAATGGACCCCGATAGGCCCAAAATAACAAGTGTTCTAAATGAGCTAAAAACTTCACTGTTATTT
196 AAATGGACCCCGATAGGCCAAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACTGTTATTT
610 TGG
261 TGG
* *
613 GCATTGAGGTTTGCCAAATCGAAGACGACTACAAAACGGAACTAAA-GGACCCCGATAGGCCAAA
1 GCATTGAGATTTGCCAAATCGAAGACGA-TACAAAACGGAAC-AAATGGACCACGATAGGCCAAA
** *
677 AATAACTTGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
64 AATAACAAGTATTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
*
742 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTTAAAAC-GT
129 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTCAAAACAG-
*
806 CACAAATGGACCCCGATAGGCCAAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAC
193 AACAAATGGACCCCGATAGGCCAAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCAC
866 AGTGGACTAA
Statistics
Matches: 231, Mismatches: 19, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
263 28 0.12
264 200 0.87
265 3 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (263 bp):
GCATTGAGATTTGCCAAATCGAAGACGATACAAAACGGAACAAATGGACCACGATAGGCCAAAAA
TAACAAGTATTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTCAAAACAGAAC
AAATGGACCCCGATAGGCCAAAAATAACAAGTGTTCAAAATGAGCTAAAAACTTCACTGTTATTT
TGG
Found at i:894 original size:154 final size:154
Alignment explanation
Indices: 613--1079 Score: 749
Period size: 154 Copynumber: 3.0 Consensus size: 154
603 GTTATTTTGG
* **
613 GCATTGAGGTTTGCCAAATCGAAGACGACTACAAAACGGAACTAAA-GGACCCCGATAGGCCAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGA-TTCAAAACGTCAC-AAATGGACCCCGATAGGCCAAA
** * *
677 AATAACTTGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAG
64 AATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
742 TTAGGCCATAAACAATGGAAAGAAAA
129 TTAGGCCATAAACAATGGAAAGAAAA
* *
768 GCATTGAGGTTTGCCAAATCAAAGACGATTTAAAACGTCACAAATGGACCCCGATAGGCCAAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCAAAAA
833 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
898 AGGCCATAAACACTGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * * *
922 GTATTGAGGTTTGCCAAATCGAAGATGATTCGAAACGTCACTAATGGACCCCGATAGGACC-AAT
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGG-CCAAAA
*
986 ATAACAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
65 ATAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
1051 TAGGCCATAAACAATGGAAAGAAAA
130 TAGGCCATAAACAATGGAAAGAAAA
1076 GCAT
1 GCAT
1080 GGA
Statistics
Matches: 290, Mismatches: 20, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
153 3 0.01
154 258 0.89
155 29 0.10
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.21
Consensus pattern (154 bp):
GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACAAATGGACCCCGATAGGCCAAAAA
TAACAAGTGTTCAAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAA
Done.