Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011020.1 Corchorus olitorius cultivar O-4 contig11053, 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, 671
Length: 1119
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Found at i:283 original size:154 final size:153
Alignment explanation
Indices: 2--561 Score: 883
Period size: 154 Copynumber: 3.6 Consensus size: 153
1 A
* *
2 TAATCTCACCAAAATGATTATTGTTAGGCCATAAACAAGGGAAAGAAAAGCATTGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
* *
67 AATCGAAAACGATTCAAAACGGAACTAATGGGTCTCGATA-AGCCCAAAATAACAAGTGTTCCAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGG-CCCGATAGA-CCCAAAATAACAAGTGTTCCAA
* * *
131 ATGAGTTAATAACTTCACAGTGGAC
129 ATGAGCTAAAAACTTCACAGTCGAC
* * * * *
156 AAATCT-ATCCAAAATGATTATAGTTACGCCATAAACAATGAAAAGAAATGCATTGAGGTTAGCC
1 TAATCTCA-CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCC
220 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAA
65 AAATCGAAGACGATTCAAAACGGAACTAATGGGCCC-GATAGACCCAAAATAACAAGTGTTCCAA
285 ATGAGCTAAAAACTTCACAGTCGAC
129 ATGAGCTAAAAACTTCACAGTCGAC
*
310 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
** * *
375 AATCGAAGAATATTCAAAACGGAACCAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAA
66 AATCGAAGACGATTCAAAACGGAACTAATGGG-CCCGATAGACCCAAAATAACAAGTGTTCCAAA
440 TGAGCTAAAAACTTCACAGTCGAC
130 TGAGCTAAAAACTTCACAGTCGAC
* *
464 TAATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCGA
1 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
528 AATCGAAGACGATTCAAAACGGAACTAATGGGCC
66 AATCGAAGACGATTCAAAACGGAACTAATGGGCC
562 ATAAACAATT
Statistics
Matches: 373, Mismatches: 28, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
152 2 0.01
153 39 0.10
154 327 0.88
155 5 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (153 bp):
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
AATCGAAGACGATTCAAAACGGAACTAATGGGCCCGATAGACCCAAAATAACAAGTGTTCCAAAT
GAGCTAAAAACTTCACAGTCGAC
Found at i:570 original size:68 final size:69
Alignment explanation
Indices: 490--630 Score: 230
Period size: 69 Copynumber: 2.1 Consensus size: 69
480 ATTATAATTA
*
490 GGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCGAAATCGAAGACGATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCGAAATCGAAGACGATTCAAAACGGAACT
554 AATG
66 AATG
* ** *
558 GGCCATAAACAATTGAAAGAAAAGCAATGAGGTTTGTTAAATCGAAGACGGTTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCGAAATCGAAGACGATTCAAAACGGAACT
623 AATG
66 AATG
627 GGCC
1 GGCC
631 CCTATAGGCC
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
68 28 0.42
69 39 0.58
ACGTcount: A:0.43, C:0.15, G:0.24, T:0.18
Consensus pattern (69 bp):
GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCGAAATCGAAGACGATTCAAAACGGAACT
AATG
Found at i:722 original size:222 final size:222
Alignment explanation
Indices: 336--783 Score: 788
Period size: 222 Copynumber: 2.0 Consensus size: 222
326 ATTATAGTTA
*
336 GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGAATATTCAAAACGGAACC
1 GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACC
*
401 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
* *
466 ATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGTTTGCGAAAT
131 ATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTGCCAAAT
531 CGAAGACGATTCAAAACGGAACTAATG
196 CGAAGACGATTCAAAACGGAACTAATG
* ** * * *
558 GGCCATAAACAATTGAAAGAAAAGCAATGAGGTTTGTTAAATCGAAGACGGTTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACC
*
623 AATGGGCCCCTATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
*
688 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTGCCAAAT
131 ATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTGCCAAAT
753 CGAAGACGATTCAAAACGGAACTAATG
196 CGAAGACGATTCAAAACGGAACTAATG
780 GGCC
1 GGCC
784 CAGATAGACC
Statistics
Matches: 214, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
222 214 1.00
ACGTcount: A:0.43, C:0.18, G:0.20, T:0.19
Consensus pattern (222 bp):
GGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAGAAGATTCAAAACGGAACC
AATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
ATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATTGCCAAAT
CGAAGACGATTCAAAACGGAACTAATG
Found at i:909 original size:376 final size:376
Alignment explanation
Indices: 183--931 Score: 1268
Period size: 376 Copynumber: 2.0 Consensus size: 376
173 TTATAGTTAC
* *
183 GCCATAAACAATGAAAAGAAATGCATTGAGGTTAGCCAAATCGAAGACGATTCAAAACGGAACTA
1 GCCATAAACAATGAAAAGAAAAGCAATGAGGTTAGCCAAATCGAAGACGATTCAAAACGGAACTA
*
248 ATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAA
66 ATGGGCCCAGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAA
*
313 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGTTTGCCAAAT
131 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGATTGCCAAAT
* * *
378 CGAAGAATATTCAAAACGGAACCAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGA
196 CGAAGAAGATTCAAAACGGAACCAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATGA
443 GCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAA
261 GCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAA
* * *
508 GAAAAGCATTGAGTTTGCGAAATCGAAGACGATTCAAAACGGAACTAATGG
326 GAAAAGCATTGAGTTTGCCAAATCGAAAACGATTCAAAACGAAACTAATGG
* ** *
559 GCCATAAACAATTG-AAAGAAAAGCAATGAGGTTTGTTAAATCGAAGACGGTTCAAAACGGAACT
1 GCCATAAACAA-TGAAAAGAAAAGCAATGAGGTTAGCCAAATCGAAGACGATTCAAAACGGAACT
** *
623 AATGGGCCCCTATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
65 AATGGGCCCAGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
*
688 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GATTGCCAAA
130 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGATTGCCAAA
* *
752 TCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATG
195 TCGAAGAAGATTCAAAACGGAACCAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATG
*
817 AGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
260 AGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAA
*
882 AGAAAAGCATTTAGGTTTGCCAAATCGAAAACGATTCAAAACGAAACTAA
325 AGAAAAGCATTGA-GTTTGCCAAATCGAAAACGATTCAAAACGAAACTAA
932 CGGGTCTCGA
Statistics
Matches: 349, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
375 145 0.42
376 202 0.58
377 2 0.01
ACGTcount: A:0.43, C:0.19, G:0.18, T:0.20
Consensus pattern (376 bp):
GCCATAAACAATGAAAAGAAAAGCAATGAGGTTAGCCAAATCGAAGACGATTCAAAACGGAACTA
ATGGGCCCAGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAA
TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAATGAGGATTGCCAAAT
CGAAGAAGATTCAAAACGGAACCAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATGA
GCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAATTAGGCCATAAACAATGGAAA
GAAAAGCATTGAGTTTGCCAAATCGAAAACGATTCAAAACGAAACTAATGG
Found at i:1005 original size:154 final size:154
Alignment explanation
Indices: 558--1119 Score: 887
Period size: 154 Copynumber: 3.7 Consensus size: 154
548 GGAACTAATG
* * ** *
558 GGCCATAAACAATTGAAAGAAAAGCAATGAGGTTTGTTAAATCGAAGACGGTTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
** *
623 AATGGGCCCCTATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
688 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
*
712 GGCCATAAACAATGGAAAGAAAAGCATTGA-GATTGCCAAATCGAAGACGATTCAAAACGGAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
*
776 AATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
841 ATCTCACCAAAATGATTATAGTTA
131 ATCTCACCAAAATGATTATAGTTA
* * *
865 GGCCATAAACAATGGAAAGAAAAGCATTTAGGTTTGCCAAATCGAAAACGATTCAAAACGAAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
* * * *
930 AACGGGTCTC-GATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACT
66 AATGGG-CCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACT
994 AATCT-ATCCAAAATGATTATAGTTA
130 AATCTCA-CCAAAATGATTATAGTTA
* * * *
1019 CGCCATAAACAATGAAAAGAAATGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTAACT
1 GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
*
1084 AATGGGCCCAGATAGGCCCCAAATAACAAGTGTTCC
66 AATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCC
Statistics
Matches: 376, Mismatches: 28, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
153 147 0.39
154 227 0.60
155 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
GGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACT
AATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
ATCTCACCAAAATGATTATAGTTA
Found at i:1027 original size:529 final size:531
Alignment explanation
Indices: 28--1091 Score: 1742
Period size: 529 Copynumber: 2.0 Consensus size: 531
18 ATTATTGTTA
*
28 GGCCATAAACAAGGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACT
1 GGCCATAAACAAGGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACT
* * * * * *
93 AATGGGTCTCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGTTAATAACTTCACAGTGGACAA
66 AATGGGCCCCGATAAGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACAA
* *
158 ATCTATCCAAAATGATTATAGTTACGCCATAAACAATGAAAAGAAATGCATTGAGGTTAGCCAAA
131 ATCTATCCAAAATGATTATAGTTACGCCATAAACAATGAAAAGAAAAGCATTGAGATTAGCCAAA
223 TCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATG
196 TCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATG
288 AGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
261 AGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
* * *
353 AGAAAAGCAATGAGGTTTGCCAAATCGAAGAATATTCAAAACGGAACCAATGGGCCCCGATAGGC
326 AGAAAAGCAATGAGGTTTGCCAAATCGAAGAAGATTCAAAACGAAACCAACGGGCCCCGATAGGC
418 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATT
391 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATT
* * *
483 ATAATTAGGCCATAAACAATGGAAAGAAAAGCATTGA-GTTTGCGAAATCGAAGACGATTCAAAA
456 ATAATTACGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
547 CGGAACTAATG
521 CGGAACTAATG
** ** * *
558 GGCCATAAACAATTGAAAGAAAAGCAATGAGGTTTGTTAAATCGAAGACGGTTCAAAACGGAACT
1 GGCCATAAACAAGGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACT
* * *
623 AATGGGCCCCTATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTA
66 AATGGGCCCCGATAAGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACAA
* *
688 ATCTCA-CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGATT-GCCAA
131 ATCT-ATCCAAAATGATTATAGTTACGCCATAAACAATGAAAAGAAAAGCATTGAGATTAGCCAA
751 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAAT
195 ATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAAT
816 GAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
260 GAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
* * * * *
881 AAGAAAAGCATTTAGGTTTGCCAAATCGAA-AACGATTCAAAACGAAACTAACGGGTCTCGATAG
325 AAGAAAAGCAATGAGGTTTGCCAAATCGAAGAA-GATTCAAAACGAAACCAACGGGCCCCGATAG
* *
945 GCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCT-ATCCAAAATG
389 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCA-CCAAAATG
* *
1009 ATTATAGTTACGCCATAAACAATGAAAAGAAATGCATTGAGGTTTGCCAAATCGAAGACGATTCA
453 ATTATAATTACGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCA
*
1074 AAACGTAACTAATG
518 AAACGGAACTAATG
1088 GGCC
1 GGCC
1092 CAGATAGGCC
Statistics
Matches: 494, Mismatches: 36, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
528 3 0.01
529 284 0.57
530 206 0.42
531 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (531 bp):
GGCCATAAACAAGGGAAAGAAAAGCAATGAGGTTTGCCAAATCGAAAACGATTCAAAACGGAACT
AATGGGCCCCGATAAGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACAA
ATCTATCCAAAATGATTATAGTTACGCCATAAACAATGAAAAGAAAAGCATTGAGATTAGCCAAA
TCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGACCCAAAATAACAAGTGTTCCAAATG
AGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
AGAAAAGCAATGAGGTTTGCCAAATCGAAGAAGATTCAAAACGAAACCAACGGGCCCCGATAGGC
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTCGACTAATCTCACCAAAATGATT
ATAATTACGCCATAAACAATGAAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAA
CGGAACTAATG
Done.