Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011633.1 Corchorus olitorius cultivar O-4 contig11666, 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, 912
Length: 1521
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.23
Found at i:337 original size:154 final size:154
Alignment explanation
Indices: 1--776 Score: 1225
Period size: 154 Copynumber: 5.0 Consensus size: 154
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* *
66 TAGGCTATAAACAATGGAAAGAAAAAGCATTGAGGTTTTACCAAATCGAAGACGATTCAAAACGG
66 TAGGCCATAAACAATGGAAAG-AAAAGCATTGAGG-TTTGCCAAATCGAAGACGATTCAAAACGG
*
131 AACTAATGGGCCCTGATAGGCCCAAA
129 AACTAATGGGCCCCGATAGGCCCAAA
* * * * *
157 ATAACAAATGTTCCAATTGAGCTAAAAACTTCAAAGTGGACTAATCTTACCAAAATGATTATATT
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
222 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGATTCAAAAC-GAC
66 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-
* *
286 ACTAATGGTCCCCGATAGGTCCAAA
130 ACTAATGGGCCCCGATAGGCCCAAA
* *
311 ATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGT
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* * * * **
376 TAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGTCGATTCAATACGTCA
66 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
*
441 CTAATGGGCCCCGATAGGCACAAA
131 CTAATGGGCCCCGATAGGCCCAAA
*
465 ATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTGGACTAATCTCACCAAAAATGATTATAG
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAAATGATTATAG
*
530 TTGGGCCATAAACAATGGAAAGAAAA-CATTGAGGTTTTGCCAAATCGAAGACGTATTCAAAACG
65 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTGCCAAATCGAAGACG-ATTCAAAACG
594 GAACTAATGGGCCCCGATAGGCCCAAA
128 GAACTAATGGGCCCCGATAGGCCCAAA
* * *
621 ATAACAAGTGTTCAAAATGA-CATAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAG
1 ATAACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* *
685 TTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
65 TTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
750 ACTAATGGGCCCCGATAGGCCCAAA
130 ACTAATGGGCCCCGATAGGCCCAAA
775 AT
1 AT
777 CCAAAATGAT
Statistics
Matches: 571, Mismatches: 42, Indels: 16
0.91 0.07 0.03
Matches are distributed among these distances:
153 2 0.00
154 282 0.49
155 121 0.21
156 166 0.29
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (154 bp):
ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAA
CTAATGGGCCCCGATAGGCCCAAA
Found at i:592 original size:310 final size:308
Alignment explanation
Indices: 1--776 Score: 1243
Period size: 310 Copynumber: 2.5 Consensus size: 308
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
66 TAGGCTATAAACAATGGAAAGAAAAAGCATTGAGGTTTTACCAAATCGAAGACGATTCAAAACGG
66 TAGGCTATAAACAATGGAAAG-AAAAGCATTGAGGTTTT-CCAAATCGAAGACGATTCAAAACGG
* *
131 AACTAATGGGCCCTGATAGGCCCAAAATAACAAATGTTCCAATTGAGCTAAAAACTTCAAAGTGG
129 AACTAATGGGCCCCGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCAAAGTGG
* *
196 ACTAATCTTACCAAAATGATTATATTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCC
194 ACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCC
* *
261 CAAATCGAAGACGATTCAAAAC-GACACTAATGGTCCCCGATAGGTCCAAA
259 CAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCCCAAA
* *
311 ATAACAAATGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATTTCACCAAAATGATTATAGT
1 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
* * **
376 TAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGTCGATTCAATACGTCA
66 TAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAA
* * * *
441 CTAATGGGCCCCGATAGGCACAAAATAACAAGTGTTCCAAATGAGCTAAATACTTCACAGTGGAC
131 CTAATGGGCCCCGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCAAAGTGGAC
* *
506 TAATCTCACCAAAAATGATTATAGTTGGGCCATAAACAATGGAAAGAAAA-CATTGAGGTTTTGC
196 TAATCTCACC-AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG-TTTCC
570 CAAATCGAAGACGTATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
259 CAAATCGAAGACG-ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
* * *
621 ATAACAAGTGTTCAAAATGA-CATAAAAACTTCACAATGGACTAATCTCATCAAAATGATTATAG
1 ATAACAAGTGTTCCAAATGAGC-TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAG
* * * *
685 TTAGTCCATAAATAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA
65 TTAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGA
750 ACTAATGGGCCCCGATAGGCCCAAAAT
130 ACTAATGGGCCCCGATAGGCCCAAAAT
777 CCAAAATGAT
Statistics
Matches: 429, Mismatches: 32, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
308 99 0.23
309 72 0.17
310 256 0.60
311 2 0.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.23
Consensus pattern (308 bp):
ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
TAGGCTATAAACAATGGAAAGAAAAGCATTGAGGTTTTCCAAATCGAAGACGATTCAAAACGGAA
CTAATGGGCCCCGATAGGCCCAAAATAACAAATGTTCCAAATGAGCTAAAAACTTCAAAGTGGAC
TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTCCCA
AATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAA
Found at i:815 original size:108 final size:108
Alignment explanation
Indices: 671--885 Score: 326
Period size: 108 Copynumber: 2.0 Consensus size: 108
661 CTAATCTCAT
* * *
671 CAAAATGATTATAGTTAGTCCATAAATAATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAAG
1 CAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTAG-GGTTTGCCAAATCAAAG
735 ACGATTCAAAACGGAACTAATGGGCCCCGATAGG-CCCAAAATC
65 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGACCCAAAATC
*
778 CAAAATGATTATAGTTACGTCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCGAATCAAAG
1 CAAAATGATTATAGTTA-GTCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCAAATCAAAG
** **
843 ACGATTCAAAACGTCACTAATGGGCCTTGATAGGACCCAAAAT
65 ACGATTCAAAACGGAACTAATGGGCCCCGATAGGACCCAAAAT
886 AACAAGTGTT
Statistics
Matches: 97, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
107 17 0.18
108 71 0.73
109 9 0.09
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.21
Consensus pattern (108 bp):
CAAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCAAATCAAAGA
CGATTCAAAACGGAACTAATGGGCCCCGATAGGACCCAAAATC
Found at i:982 original size:262 final size:262
Alignment explanation
Indices: 517--1031 Score: 804
Period size: 262 Copynumber: 2.0 Consensus size: 262
507 AATCTCACCA
* * * *
517 AAAATGATTATAGTTGGGCCATAAACAATGGAAAGAAAACATTGAGGTTTTGCCAAATCGAAGAC
1 AAAATGATTATAGTTCGGCCATAAACAATGAAAAGAAAACATTGAGGGTTTGCCAAATCAAAGAC
582 GTATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGACATAAA
66 GTATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGACATAAA
* * *
647 AACTTCACAATGGACTAATCTCATCAAAATGATTATAGTTAGTCCATAAATAATGGAAAGAAAAG
131 AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* *
712 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
196 CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGAAAGGCCCAAAAT
777 CC
261 CC
* *
779 AAAATGATTATAGTTACGTCCATAAACAATGAAAAGAAAAGCATT-AGGGTTTGCCGAATCAAAG
1 AAAATGATTATAGTT-CGGCCATAAACAATGAAAAGAAAA-CATTGAGGGTTTGCCAAATCAAAG
** ** *
843 ACG-ATTCAAAACGTCACTAATGGGCCTTGATAGGACCCAAAATAACAAGTGTTCCAAATGAGC-
64 ACGTATTCAAAACGGAACTAATGGGCCCCGATAGG-CCCAAAATAACAAGTGTTCAAAATGA-CA
* *
906 T-AAAACTTCACAGTTGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
127 TAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
970 AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGAAAGGC
192 AAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGAAAGGC
1032 TTAAAATAAC
Statistics
Matches: 231, Mismatches: 18, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
262 160 0.69
263 66 0.29
264 5 0.02
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (262 bp):
AAAATGATTATAGTTCGGCCATAAACAATGAAAAGAAAACATTGAGGGTTTGCCAAATCAAAGAC
GTATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCAAAATGACATAAA
AACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
CATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCACGAAAGGCCCAAAAT
CC
Found at i:1005 original size:154 final size:153
Alignment explanation
Indices: 777--1344 Score: 786
Period size: 154 Copynumber: 3.7 Consensus size: 153
767 GGCCCAAAAT
* * * *
777 CCAAAATGATTATAGTTACGTCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCGAATCAAA
1 CCAAAATCATTATAGTTA-GGCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCAAATCGAA
** *
842 GACGATTCAAAACGTCACTAATGGGCCTTGATAGGACCCAAAATAACAAGTGTTCCAAATGAGCT
65 GACGATTCAAAACGGAACTAATGGGCCTCGATAGG-CCCAAAATAACAAGTGTTCCAAATGAGCT
*
907 AAAACTTCACAGTTGACTAATCTCA
129 AAAACTTCACAGTGGACTAATCTCA
* *
932 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GAGGTTTGCCAAATCGAA
1 CCAAAATCATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTAG-GGTTTGCCAAATCGAA
* * **
996 GACGATTCAAAACGGAACTAATGGGCCACGAAAGGCTTAAAATAACAAGTGTTCCAAATGAGCTA
65 GACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
1061 AGAACTTCACAGTGGACTAATCTCA
130 A-AACTTCACAGTGGACTAATCTCA
* ** * * *
1086 TCAAAATCATTATAACTAGGCCATAAACAACT-TAAAGAAAAAC-TTTGAGGTTTGCCAAATCGA
1 CCAAAATCATTATAGTTAGGCCATAAACAA-TGAAAAGAAAAGCATTAG-GGTTTGCCAAATCGA
* * *
1149 AGACAATTC-AAACGGAACTAATGCGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
64 AGACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCT
1213 AAAACTTCACAGTGGACTAATCTCA
129 AAAACTTCACAGTGGACTAATCTCA
* * * *
1238 CCAATATCATTATAGTTAGTCCATAAACAATGAAAAGAAAAGAATTAGGGTTTGCCGAATCGAAG
1 CCAAAATCATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCAAATCGAAG
*
1303 ACGATTCAAAA-GGTCACTAATGGGCCTCGATAGGCCCAAAAT
66 ACGATTCAAAACGG-AACTAATGGGCCTCGATAGGCCCAAAAT
1345 CCAAAATGAT
Statistics
Matches: 367, Mismatches: 38, Indels: 18
0.87 0.09 0.04
Matches are distributed among these distances:
151 1 0.00
152 80 0.22
153 115 0.31
154 152 0.41
155 19 0.05
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (153 bp):
CCAAAATCATTATAGTTAGGCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCAAATCGAAG
ACGATTCAAAACGGAACTAATGGGCCTCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAA
AACTTCACAGTGGACTAATCTCA
Found at i:1432 original size:107 final size:107
Alignment explanation
Indices: 1246--1451 Score: 367
Period size: 107 Copynumber: 1.9 Consensus size: 107
1236 CACCAATATC
*
1246 ATTATAGTTAGTCCATAAACAATGAAAAGAAAAGAATTAGGGTTTGCCGAATCGAAGACGATTCA
1 ATTATAGTTAGTCCATAAACAATGAAAAGAAAAGAATTAGGGTTTGCCGAATCGAAGACGACTCA
*
1311 AAAGGTCACTAATGGGCCTCGATAGGCCCAAAATCCAAAATG
66 AAACGTCACTAATGGGCCTCGATAGGCCCAAAATCCAAAATG
* * *
1353 ATTATAGTTAGTCCATAAACAATGAAAAGAAAAGCATTAGGGTTTGCCGAATTGAAGATGACTCA
1 ATTATAGTTAGTCCATAAACAATGAAAAGAAAAGAATTAGGGTTTGCCGAATCGAAGACGACTCA
1418 AAACGTCACTAATGGGCCTCGATAGGCCCAAAAT
66 AAACGTCACTAATGGGCCTCGATAGGCCCAAAAT
1452 AACAAGTGTT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
107 94 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.22
Consensus pattern (107 bp):
ATTATAGTTAGTCCATAAACAATGAAAAGAAAAGAATTAGGGTTTGCCGAATCGAAGACGACTCA
AAACGTCACTAATGGGCCTCGATAGGCCCAAAATCCAAAATG
Done.