Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011715.1 Corchorus olitorius cultivar O-4 contig11748, 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, 1000
Length: 1965
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Found at i:425 original size:154 final size:154
Alignment explanation
Indices: 40--1965 Score: 3065
Period size: 154 Copynumber: 12.5 Consensus size: 154
30 TGGAAAGAAA
*
40 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCCT-AAAACATCACAGTGGAC
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGAC
*
104 TAATCTCACCAAAATAGATTATAGTTCGGCCATAAACAATGGAATAGAAAAGCATTGAGGTTTGC
65 TAATCTCACCAAAAT-GATTATAGTTAGGCCATAAACAATGGAA-AGAAAAGCATTGAGGTTTGC
169 CAAATCGAAGACGATTCAAAACCG-AAC
128 CAAATCGAAGACGATTCAAAA-CGTAAC
* * * * * *
196 TAATGGGCCGTCGATAGGCCCAAAATAACAAGTGTTTCGAATAAGCTAAAAACTACACAATGGAC
1 TAATGGGCC-CCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
* *
261 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATTGATAGAAAAGCATTGAGGTTTGCCA
65 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
* *
326 AATCAAAGACGATTCAAAACGGAAC
130 AATCGAAGACGATTCAAAACGTAAC
*
351 TAATGAGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
416 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
481 ATCGAAGAACGATTCAAATACGTCAC
131 ATCGAAG-ACGATTCAAA-ACGTAAC
* * *
507 TAAT-GGCCCCGAAAGGCCTAAAATAACAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGCC
1 TAATGGGCCCCGATAGGCCCAAAATAAC-AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
571 TAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
65 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCA
*
636 AATCGAACACGATTCAAAACCG-AAC
130 AATCGAAGACGATTCAAAA-CGTAAC
* *
661 TAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
726 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
791 ATCGAAGACGATTCAAAACGGAAC
131 ATCGAAGACGATTCAAAACGTAAC
* * *
815 TAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGCCT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
880 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
945 ATCGAAGACGATTCAATACGTCAC
131 ATCGAAGACGATTCAAAACGTAAC
* *
969 TAATGGG-CCCGATAGGCCCAAAATAACAAGTGTTCCCAATGAGCTAAAAACTTCAAAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* * * * **
1033 AATCTAAACAAAATGATTATAGGTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCATGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * * *
1098 TTCGAAGAAGATTCAATACGTTAC
131 ATCGAAGACGATTCAAAACGTAAC
* * * *
1122 TAATGGGCCCCGATAAGCCCAAAATAACAATTGTTCCAAATGAGTTAAAAACATCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* * * *
1187 AATATCACCAAAATAATTATAGTTAGGCCATAAACAATCGAAAGAAAAGTATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* * *
1252 ATCAAAGACGATTCAATACGTCAC
131 ATCGAAGACGATTCAAAACGTAAC
* *
1276 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
1341 AATCTCACCAAAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
1406 ATCGAAGACGATTCAAAACGAAAC
131 ATCGAAGACGATTCAAAACGTAAC
* * * * *
1430 TAATGAGCCCAGATAGGCCCAAAATAACAAGTGTTCCGAATGAGCTACAAACTTCACAATGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
1495 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCTAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
1560 ATCGAAGACGATTCAATACGTCAC
131 ATCGAAGACGATTCAAAACGTAAC
1584 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1649 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
1714 ATCGAAGACGATTCAAAACGGAAC
131 ATCGAAGACGATTCAAAACGTAAC
* * * *
1738 TAATGAGTCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGCAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
* *
1803 AATCTCACTAAAATGATTATAGTTAGG-C-TAAACAATGGAAAGAAAAGCTTTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
1866 ATCGAAGACGATTCAAAACGTCAC
131 ATCGAAGACGATTCAAAACGTAAC
* *
1890 TAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACA
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1955 AATCTCACCAA
66 AATCTCACCAA
Statistics
Matches: 1628, Mismatches: 132, Indels: 24
0.91 0.07 0.01
Matches are distributed among these distances:
152 125 0.08
153 141 0.09
154 1038 0.64
155 113 0.07
156 151 0.09
157 60 0.04
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
ATCGAAGACGATTCAAAACGTAAC
Found at i:1280 original size:615 final size:615
Alignment explanation
Indices: 40--1965 Score: 3121
Period size: 615 Copynumber: 3.1 Consensus size: 615
30 TGGAAAGAAA
*
40 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCCT-AAAACATCACAGTGGAC
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAG-CTAAAAACTTCACAGTGGAC
*
104 TAATCTCACCAAAATAGATTATAGTTCGGCCATAAACAATGGAATAGAAAAGCATTGAGGTTTGC
65 TAATCTCACCAAAAT-GATTATAGTTAGGCCATAAACAATGGAA-AGAAAAGCATTGAGGTTTGC
* * *
169 CAAATCGAAGACGATTCAAAACCGAACTAATGGGCCGTCGATAGGCCCAAAATAACAAGTGTTTC
128 CAAATCGAAGACGATTCAAAACGGAACTAATGGGCC-TCAATAGGCCCAAAATAACAAGTGTTCC
* *
234 GAATAAGCTAAAAACTACACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
192 GAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * * ** *
299 TTGATAGAAAAGCATTGAGGTTTGCCAAATCAAAGACGATTCAAAACGGAACTAATGAGCCCCGA
257 TGGAAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATG-GGCCCGA
364 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
321 TAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
429 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAACGAT
386 TGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAA-GAT
* *
494 TCAAATACGTCACTAAT-GGCCCCGA-AAGGCCTAAAATAACAAAGTGTTCCAAATGAGCTAAAA
450 TC-AATACGTAACTAATGGGCCCCGATAA-GCCCAAAATAAC-AAGTGTTCCAAATGAGCTAAAA
* * *
557 ACTTCACAGTGGCCTAATCTCACCAAAATGATTATAGTTAGGCAATAAACAATGGAAAGAAAAGC
512 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGT
* *
622 ATTGAGGTTTGCCAAATCGAACACGATTCAAAACCG-AAC
577 ATTGAGGTTTGCCAAATCGAAGACGATTCAAAA-CGTCAC
* *
661 TAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTACAAATGAGCTAAAAACTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
726 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
*
791 ATCGAAGACGATTCAAAACGGAACTAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCAAAT
131 ATCGAAGACGATTCAAAACGGAACTAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCGAAT
* *
856 GAGCTAAAAACTTCACAGTGGCCTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
196 GAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
921 AAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGGCCCGATAGGC
261 AAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGGCCCGATAGGC
* * * *
986 CCAAAATAACAAGTGTTCCCAATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATT
326 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * ** *
1051 ATAGGTAGGCCATAAACAATGGAAACAAAAGCATTGAGGCATGCCAATTCGAAGAAGATTCAATA
391 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAATA
* * * *
1116 CGTTACTAATGGGCCCCGATAAGCCCAAAATAACAATTGTTCCAAATGAGTTAAAAACATCACAG
456 CGTAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * *
1181 TGGACTAATATCACCAAAATAATTATAGTTAGGCCATAAACAATCGAAAGAAAAGTATTGAGGTT
521 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGAGGTT
* *
1246 TGCCAAATCAAAGACGATTCAATACGTCAC
586 TGCCAAATCGAAGACGATTCAAAACGTCAC
* *
1276 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAACTGAGCTAAAAAGTTCACAGTGGACT
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
*
1341 AATCTCACCAAAATGATTATAGTTAGGTCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
66 AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
* *
1406 ATCGAAGACGATTCAAAACGAAACTAATGAGCC-CAGATAGGCCCAAAATAACAAGTGTTCCGAA
131 ATCGAAGACGATTCAAAACGGAACTAATGGGCCTCA-ATAGGCCCAAAATAACAAGTGTTCCGAA
*
1470 TGAGCTACAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
195 TGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGG
1535 AAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGGCCCCGATAG
260 AAAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGG-CCCGATAG
1600 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
324 GCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGA
*
1665 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAA
389 TTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAA
* * * * * * *
1730 AACGGAACTAATGAGTCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCGC
454 TACGTAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCAC
*
1795 AGTGGACTAATCTCACTAAAATGATTATAGTTAGG-C-TAAACAATGGAAAGAAAAGCT-TTGAG
519 AGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG-TATTGAG
1857 GTTTGCCAAATCGAAGACGATTCAAAACGTCAC
583 GTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
1890 TAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACA
1 TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
1955 AATCTCACCAA
66 AATCTCACCAA
Statistics
Matches: 1212, Mismatches: 86, Indels: 21
0.92 0.07 0.02
Matches are distributed among these distances:
614 130 0.11
615 426 0.35
616 238 0.20
617 125 0.10
618 136 0.11
619 55 0.05
620 29 0.02
621 73 0.06
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.21
Consensus pattern (615 bp):
TAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT
AATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAA
ATCGAAGACGATTCAAAACGGAACTAATGGGCCTCAATAGGCCCAAAATAACAAGTGTTCCGAAT
GAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
AAGAAAAGCATTGAGGTTTGCTAAATCGAAGACGATTCAATACGTCACTAATGGGCCCGATAGGC
CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGAAGATTCAATA
CGTAACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGTATTGAGGTT
TGCCAAATCGAAGACGATTCAAAACGTCAC
Done.