Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011744.1 Corchorus olitorius cultivar O-4 contig11777, 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, 861
Length: 1436
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Found at i:286 original size:154 final size:154
Alignment explanation
Indices: 1--1436 Score: 2344
Period size: 154 Copynumber: 9.4 Consensus size: 154
* * * * *
1 ATTGGGGTTTGCCAAATGGAAGACGATTCAAGACGGAAATAATGGGTCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* *
66 ACAAGTGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGATAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* *
131 GCCATAAACGATGGAAAGAAAAGG
131 GCCATAAACAATGGAAAGAAAAGC
** *
155 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATTAGCCCCGTTAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* *
220 ACAAGTGTTCCAAATGACCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
285 GCCATAAACAATGGAAAGAAAATGC
131 GCCATAAACAATGGAAAGAAAA-GC
* *
310 ATTGGGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* *
375 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGCTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
440 GCCTTAAACAATGGAAAGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
** ** * *
464 ATT-TCGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGATAGGCCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
*
528 ACAAGTGTTCCCAAA-GAGCTATAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
66 ACAAGTGTT-CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA
592 GGCCATAAACAATGGAAAGAAAAGC
130 GGCCATAAACAATGGAAAGAAAAGC
* * * *
617 ATTGAGATTTGCCAAATCGAAGACGATTCAAAATGCAACTAATGGGCCTCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
*
682 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
747 GCCATAAACAATGGAATGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
* *
771 TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* * * *
836 ACAAGTGTTCCAAATGAGCTAAATATTTCACAGTTGACTAATCTAACCAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
901 GCCATAAACAATGGAAAGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
* * *
925 ATTGAGGTTT-CCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAATTA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
989 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
1054 GCCATAAACAATGGAAAGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
1078 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* *
1143 ACAAGTGCTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
1208 GCCATAAACAATGGAAAGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
* * *
1232 TTTGACGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
*
1297 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
*
1362 GCCATAAACAATGGAATGAAAAGC
131 GCCATAAACAATGGAAAGAAAAGC
* * * *
1386 TTTGAGG--TGCCAAATCAAAGACAATTCAAAACGG-ACTAATGGGCCTCGATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATA
Statistics
Matches: 1197, Mismatches: 80, Indels: 13
0.93 0.06 0.01
Matches are distributed among these distances:
151 16 0.01
152 25 0.02
153 286 0.24
154 727 0.61
155 143 0.12
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
GCCATAAACAATGGAAAGAAAAGC
Found at i:741 original size:307 final size:307
Alignment explanation
Indices: 1--1436 Score: 2292
Period size: 307 Copynumber: 4.7 Consensus size: 307
* * * * *
1 ATTGGGGTTTGCCAAATGGAAGACGATTCAAGACGGAAATAATGGGTCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
* * *
66 ACAAGTGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGATAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
* * *
131 GCCATAAACGATGGAAAGAAAAGGATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
131 GCCATAAACAATGGAAAGAAAAGCATT-TGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* * *
196 ATTA-GCCCCGTTAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAAGTTCACAGTGGACTA
195 A-TAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
260 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATGC
259 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA-GC
* *
310 ATTGGGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
*
375 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGCTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
* * ** *
440 GCCTTAAACAATGGAAAGAAAAGCATTTCGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGA
131 GCCATAAACAATGGAAAGAAAAGCATTTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
*
505 TAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCCAAA-GAGCTATAAACTTCACAGTGGACTAA
196 TAGGCCCCGATAGGCCCAAAATAACAAGTGTT-CCAAATGAGCTAAAAACTTCACAGTGGACTAA
569 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
260 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * *
617 ATTGAGATTTGCCAAATCGAAGACGATTCAAAATGCAACTAATGGGCCTCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
682 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
*
747 GCCATAAACAATGGAATGAAAAGC-TTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
131 GCCATAAACAATGGAAAGAAAAGCATTT--GGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * * * *
811 AATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAATATTTCACAGTTGACTA
194 AATAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
876 ATCTAACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
259 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * *
925 ATTGAGGTTT-CCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAATTA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
*
989 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
*
1054 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
131 GCCATAAACAATGGAAAGAAAAGCATT-TGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* *
1119 ATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
195 ATAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
1184 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
260 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * *
1232 TTTGACGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
1297 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
* * * *
1362 GCCATAAACAATGGAATGAAAAGC-TTTGAG-GTGCCAAATCAAAGACAATTCAAAACGG-ACTA
131 GCCATAAACAATGGAAAGAAAAGCATTTG-GTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
* *
1424 ATGGGCCTCGATA
195 ATAGGCCCCGATA
Statistics
Matches: 1048, Mismatches: 70, Indels: 22
0.92 0.06 0.02
Matches are distributed among these distances:
305 16 0.02
306 29 0.03
307 442 0.42
308 410 0.39
309 151 0.14
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (307 bp):
ATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAA
TAGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
Found at i:1017 original size:461 final size:462
Alignment explanation
Indices: 1--1436 Score: 2339
Period size: 461 Copynumber: 3.1 Consensus size: 462
* * * * * * *
1 ATTGGGGTTTGCCAAATGGAAGACGATTCAAGACGGAAATAATGGGTCCCGATAGGCCCAAAATA
1 ATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATA
* *
66 ACAAGTGTTCCAAGTGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGATAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
* *
131 GCCATAAACGATGGAAAGAAAAGGATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
131 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
** * * *
196 ATTAGCCCCGTTAGGCCCAAAATAACAAGTGTTCCAAATGACCTAAAAAGTTCACAGTGGACTAA
196 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* * *
261 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAATGCATTGGGGTTTGCCAAA
261 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA-GCTTTGAGGTTTGCCAAA
*
326 TCGAAGACGATTCAAAACAGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
325 TCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATG
* *
391 AGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGCTAGGCCTTAAACAATGGAA
390 AGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAA
456 AGAAAAGC
455 AGAAAAGC
** * ** *
464 ATT-TCGTTTGCCAAATCGAAGACGATTCAAAACGTCACTGAT-AGGCCCCGATAGGCCCAAAAT
1 ATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGA-GCCCCGATAGGCCCAAAAT
*
527 AACAAGTGTTCCCAAA-GAGCTATAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
65 AACAAGTGTT-CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
591 AGGCCATAAACAATGGAAAGAAAAGCATTGAGATTTGCCAAATCGAAGACGATTCAAAATGCAAC
129 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAAC
*
656 TAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
194 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
721 AATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAATGAAAAGCTTTGAGGTTTGCCAA
259 AATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
*
786 ATCGAAGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAAT
324 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAAT
* * * * *
851 GAGCTAAATATTTCACAGTTGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAATGGA
389 GAGCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGA
916 AAGAAAAGC
454 AAGAAAAGC
*
925 ATTGAGGTTT-CCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAATTA
1 ATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATA
989 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
66 ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
1054 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
131 GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
*
1119 ATGGGCCCCGATAGGCCCAAAATAACAAGTGCTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
196 ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
*
1184 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGACGTTTGCCAAAT
261 TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
*
1249 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATATGCCCAAAATAACAAGTGTTCCAAATGA
326 CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
*
1314 GCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAT
391 GCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1379 GAAAAGC
456 GAAAAGC
* * * *
1386 TTTGAGG--TGCCAAATC-AAAGACAATTCAAAACGG-ACTAATGGGCCTCGATA
1 ATTGAGGTTTGCCAAATCGAAA-ACGATTCAAAACGGAACTAATGAGCCCCGATA
Statistics
Matches: 902, Mismatches: 64, Indels: 18
0.92 0.07 0.02
Matches are distributed among these distances:
459 19 0.02
460 25 0.03
461 576 0.64
462 275 0.30
463 7 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (462 bp):
ATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCCAAAATA
ACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTA
ATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
TCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAAAT
CGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCACAGTGGACTAATCTCACTAAAATGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGC
Done.