Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011714.1 Corchorus olitorius cultivar O-4 contig11747, 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, 789
Length: 1315
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:283 original size:154 final size:154
Alignment explanation
Indices: 3--1315 Score: 1899
Period size: 154 Copynumber: 8.6 Consensus size: 154
1 GT
** * *
3 GATTCAAAACGGAACTAATGGGCTACGATATGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * *
68 ACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATATATAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* *
133 TTTAAGGTTTGCCACATCGAAGAC
131 TTTGAGGTTTGCCAAATCGAAGAC
* *
157 GATTCAAAACGGAACTAATGGGCCCCGATATGCCTAAAATAACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * * *
222 ACATCACAGTGGACTAATCTCACCAAAATTATTACAGTTAGTCCATAAATAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
287 ATTGAGGTTTGCCAAATCGAAGAC
131 TTTGAGGTTTGCCAAATCGAAGAC
** *
311 GATTCAAAACGTCACTAATGGGTACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
1 GATTCAAAACGGAACTAATGGG-CCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * *
376 AACTTCACAGGGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATAAATAATGGAAAGAAAAG
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
*
441 CTTTTAGGTTTGCCAAATCGAAGAC
130 CTTTGAGGTTTGCCAAATCGAAGAC
* *
466 GATTCAAAACGGAACTAATGGGCCCCAATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * *
531 ACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
596 TTTGAGGTTTGCCAAATCGAAGAC
131 TTTGAGGTTTGCCAAATCGAAGAC
* * * *
620 AATTCAAAACGGAACTAATGGG-CCCAATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * *
684 ACATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAACAACT-TAAA-AAAA-
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAAG
**
746 CTTTGAGGTTTGCCAAATCGAAGGT
130 CTTTGAGGTTTGCCAAATCGAAGAC
* *
771 GATTGAAAACGGAACTAATAGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
835 ACTTCACAGTGGACTAATCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
900 CTTGAGGTTTGCCAAATCGAAGAC
131 TTTGAGGTTTGCCAAATCGAAGAC
* ** * *
924 GATTCAAAATGTTAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTAT-CAAATGAGCTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGT-TCCAAATGAGCTAAA
* * * *
988 AACATCATAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA-AAAA
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAGAAAA
* **
1051 ACTTTGAGGTTTGCCAAATCGAAGGT
129 GCTTTGAGGTTTGCCAAATCGAAGAC
* *
1077 GATTCAAAACGGAACTAATAGG-CCCGATAGGCCCAAAATAACAAGTAGTTCCGAATGAGC-AAC
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGT-GTTCCAAATGAGCTAA-
1140 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
64 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
* *
1205 GCATTGAGGTTTGCTAAATCGAAGAC
129 GCTTTGAGGTTTGCCAAATCGAAGAC
* ** * *
1231 GATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTCTTCCAAATGAGATAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
1296 AGTTCACAGTGGACTAATCT
66 ACTTCACAGTGGACTAATCT
Statistics
Matches: 1043, Mismatches: 101, Indels: 30
0.89 0.09 0.03
Matches are distributed among these distances:
150 1 0.00
151 132 0.13
152 36 0.03
153 232 0.22
154 472 0.45
155 170 0.16
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
TTTGAGGTTTGCCAAATCGAAGAC
Found at i:593 original size:309 final size:306
Alignment explanation
Indices: 3--1315 Score: 1893
Period size: 309 Copynumber: 4.3 Consensus size: 306
1 GT
* * * *
3 GATTCAAAACGGAACTAATGGG-CTACGATATGCCCAAAATTACAAGTGTTCCAAATGAGCTAAA
1 GATTCAAAACGTAACTAATGGGAC-CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * *
67 AACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATATATAA-TGGAAAGAAAA
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-GAAA-AAAA
* * * * *
131 GCTTTAAGGTTTGCCACATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCTAAAA
128 GCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGG-CCCGATAGGCCCAAAA
* * *
196 TAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATTATTACAGTT
192 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
261 AGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
257 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
*
311 GATTCAAAACGTCACTAATGGGTACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
1 GATTCAAAACGTAACTAATGGG-ACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAA
* * * *
376 AACTTCACAGGGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATAAATAA-TGGAAAGAAAA
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-GAAA-AAAA
* * * *
440 GCTTTTAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAATATGCCCAAAA
128 GCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGG-CCCGATAGGCCCAAAA
*
505 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTT
192 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
570 AGTCCATAAAAAATGGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGAC
257 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * * *
620 AATTCAAAACGGAACTAATGGG-CCCAATAGGCCCAAAATAACAAGTGTACCAAATGAGCTAAGA
1 GATTCAAAACGTAACTAATGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * *
684 ACATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGACATAAACAACTTAAAAAAA-CT
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGAAAAAAAGCT
** *
748 TTGAGGTTTGCCAAATCGAAGGTGATTGAAAACGGAACTAATAGGCCCGATAGGCCCAAAATAAC
131 TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCGATAGGCCCAAAATAAC
*
813 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCTCCAAAATGATTATAGTTAGGC
196 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
*
878 CATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATCGAAGAC
261 CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * * *
924 GATTCAAAATGTTAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTAT-CAAATGAGCTAAG
1 GATTCAAAACGTAACTAATGGGACCCGATAGGCCCAAAATAACAAGTGT-TCCAAATGAGCTAAA
* * * * *
988 AACATCATAGTAGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTTAAAAAAAAC
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGAAAAAAAGC
**
1053 TTTGAGGTTTGCCAAATCGAAGGTGATTCAAAACGGAACTAATAGGCCCGATAGGCCCAAAATAA
130 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCGATAGGCCCAAAATAA
*
1118 CAAGTAGTTCCGAATGAGC-AACAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
195 CAAGT-GTTCCAAATGAGCTAA-AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
*
1182 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGAC
258 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
* * * * *
1231 GATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTCTTCCAAATGAGATAAAA
1 GATTCAAAACGTAACTAATGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
*
1296 AGTTCACAGTGGACTAATCT
66 ACTTCACAGTGGACTAATCT
Statistics
Matches: 928, Mismatches: 68, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
304 141 0.15
305 141 0.15
306 77 0.08
307 259 0.28
308 21 0.02
309 288 0.31
310 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (306 bp):
GATTCAAAACGTAACTAATGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACTGAAAAAAAGCT
TTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCGATAGGCCCAAAATAAC
AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
CATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAC
Found at i:961 original size:458 final size:461
Alignment explanation
Indices: 3--1315 Score: 1951
Period size: 458 Copynumber: 2.9 Consensus size: 461
1 GT
** *
3 GATTCAAAACGGAACTAATGGGCTACGATATGCCCAAAATTACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * * *
68 ACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGTCCATATATAATGGAAAGAAAAGC
66 ACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
* * * *
133 TTTAAGGTTTGCCACATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCTAAAATA
131 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGG-CCCGATAGGCCCAAAATA
* *
198 ACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATTATTACAGTTAG
195 ACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* *
263 TCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
260 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
*
328 ATGGGTACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGGGGACTA
325 ATGGG-ACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * * * *
393 ATCTCACCAAAATGATTGTAGTTAGTCCATAAATAATGGAAAGAAAAGCTTTTAGGTTTGCCAAA
389 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAA
458 TCGAAGAC
454 TCGAAGAC
*
466 GATTCAAAACGGAACTAATGGGCCCCAATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
531 ACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
66 ACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
* *
596 TTTGAGGTTTGCCAAATCGAAGACAATTCAAAACGGAACTAATGGGCCCAATAGGCCCAAAATAA
131 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCGATAGGCCCAAAATAA
* * *
661 CAAGTGTACCAAATGAGCTAAGAACATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
196 CAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * ** * **
726 ACATAAACAACT-TAAA-AAAA-CTTTGAGGTTTGCCAAATCGAAGGTGATTGAAAACGGAACTA
261 CCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTA
*
788 ATAGG-CCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
325 ATGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
852 TCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAAT
390 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAAT
917 CGAAGAC
455 CGAAGAC
* ** * * *
924 GATTCAAAATGTTAGTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTAT-CAAATGAGCTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGT-TCCAAATGAGCTAAA
* * * * *
988 AACATCATAGT-AGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA-AAA
65 AACTTCACAGTGA-ACTAATCTCACCAAAATGATTATAGTTAGTCCATAAA-AAATGGAAAGAAA
* ** *
1050 AACTTTGAGGTTTGCCAAATCGAAGGTGATTCAAAACGGAACTAATAGGCCCGATAGGCCCAAAA
128 AGCTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCGATAGGCCCAAAA
* *
1115 TAACAAGTAGTTCCGAATGAGC-AACAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
193 TAACAAGT-GTTCCAAATGAGCTAA-AAACATCACAGTGGACTAATCTCACCAAAATGATTATAG
* *
1179 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTC
256 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC
* * * *
1244 ACTAATGGGCCCCGATAGGCCCAAAATAACAAGTCTTCCAAATGAGATAAAAAGTTCACAGTGGA
321 ACTAATGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGA
1309 CTAATCT
386 CTAATCT
Statistics
Matches: 766, Mismatches: 74, Indels: 22
0.89 0.09 0.03
Matches are distributed among these distances:
457 74 0.10
458 291 0.38
459 8 0.01
460 78 0.10
461 63 0.08
462 86 0.11
463 166 0.22
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (461 bp):
GATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAA
ACTTCACAGTGAACTAATCTCACCAAAATGATTATAGTTAGTCCATAAAAAATGGAAAGAAAAGC
TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCGATAGGCCCAAAATAA
CAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
CCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAA
TGGGACCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAATC
GAAGAC
Done.