Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011932.1 Corchorus olitorius cultivar O-4 contig11965, 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: 3797
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Found at i:350 original size:154 final size:154
Alignment explanation
Indices: 1--3797 Score: 5661
Period size: 154 Copynumber: 24.9 Consensus size: 154
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * **
66 AGGCCATAAACAATGGAAACAAAAGCATCGAGG-TTGCCAAATCGAAAACGATTCAAAACGAAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* * *
130 TAATGGCCCCCGA-AAGCCTAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
*
153 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
218 AGGCCATAAACAATCGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
283 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
307 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * ** *
372 AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAA
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
437 TAATGGGCCCCGATAGGCCAAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
461 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTAGACTAATCTCACAAAAATAATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
526 AGGCCATAAACAATCGAAAGGAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
591 TAATGGGCCCCTATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * * * * *
615 TAACAAGTGTTCCAAATGAGCTAATAACTTCAAAGTGGACTAATCTAAACAAAATGATTACAGGT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * * * *
680 AGGCCATAAACAATGGAAACAAAAGCATAGAGGATTGCCAATTCGAAGAAGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
745 TAATGGGCCCCGATAGGCCTAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
769 TAAAAAGTGTTCCAAATGAGCTAAAAAGTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
834 AGGCCATAAACAATGGAAAGAAAAGCATTAAGGTTTGCAAAATCGAAGACGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
**
899 TAATAAGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
*
923 TAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * ** *
987 AGGCCATAAACAAT-GAAA-AGAA--A---A-----G-C--ATCGAAGACGATTCAAAATGAAAT
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
1037 TAATGGACCCCGATAGAG--CAAAA
131 TAATGGGCCCCGATAG-GCCCAAAA
* *
1060 TAACAAGTGTACCAAATGAGCTAAAAATTTCACAGTGGACTAATCTCACC-AAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * **
1124 AGGCCATAAACAAT-GAAA-AGAA--A---A-----G-C--ATCGAAGACGATTCAAAATGAAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
1174 TAATGGACCCCGATAGAG--CAAAA
131 TAATGGGCCCCGATAG-GCCCAAAA
* *
1197 TAACAAGTGTACCAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * **
1262 AGGCCATAAACAATGGAAACAAAAGCATCGAGG-TTGCCAAATCGAAAACGATTCAAAACGAAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* * *
1326 TAATGGCCCCCGA-AAGCCTAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
1349 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1414 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
1479 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
1503 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
1568 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTCTGCGAAATCGAAGACGATTCAAAACAG-AA
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC-GTCA
1632 CTAATGGGCCCCGATAGGCCCAAAA
130 CTAATGGGCCCCGATAGGCCCAAAA
* * *
1657 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACAAAAATAATTACAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1722 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
1787 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * * * *
1811 TAACAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATCTAAACAAAATGATTACAGGT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * * * * *
1876 AGGCCATAAACAATGGAAACAAAAGCATAGAGGATTGCCAATTCAAAGAAGATTCAATACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
1941 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* *
1965 TAAAAAGGGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
2030 AGCCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
2095 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
2119 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
2184 AGGCCATAAACAATCGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
2249 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
2273 TAACAAGTGTTCCAAATGAGTTAAAAACTTCATAGTGGACTAATCTCAGCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * * * ** *
2338 AGCCCATAAACAATGGAAACAAAAGCATCGAGGGTTGCCAAATCGATGACGATTCAAAACGAAAT
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
2403 TAATGGCCCCCGGA-AGGCCTAAAA
131 TAATGGGCCCC-GATAGGCCCAAAA
*
2427 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAATAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
2492 AGGCCATAAATAATCGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
2557 TAATGGGCCCCGGA-AGGCCTAAAA
131 TAATGGGCCCC-GATAGGCCCAAAA
2581 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* ** * **
2646 AGGCCATAAACAATCGAAAGAAAAATATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGAAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
2711 TAATGGGCCCCGGA-AAGCCTAAAA
131 TAATGGGCCCC-GATAGGCCCAAAA
*
2735 TAACAAGTGTTCCAAATAAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* ** * ** *
2800 AGGCCATAAACAATCGAAAGAAAAATATTGAGGTTTCCCAAATCGAAGACGATTCAAAACGGAAA
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
2865 TAATGGGCCTCGGA-AGGCCTAAAA
131 TAATGGGCC-CCGATAGGCCCAAAA
* * *
2889 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGTCTAATCTCACCAAAATGATTATAATA
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * *
2954 AGGCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGATGACGATTCAGAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* *
3019 TAATGGGCCCCGAAAGGCCTAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
3043 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * *
3108 AGGCCATAAATAATCGAAAGAAAAGCATTGAGCTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
3173 TAATGGGCCCCGATAGGCCCAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* *
3197 TAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCAGCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * * **
3262 AGCCCATAAACAATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAATGGAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
* * *
3327 TAATTGGCTCCGA-ATGGCCTAAAA
131 TAATGGGCCCCGATA-GGCCCAAAA
*
3351 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAATCTCACCAAAATGATTATAAT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACT-AATCTCACCAAAATGATTATAGT
* ** * *
3416 TAGGCCATAAACAATGGAAAGAACAGCATCAAGGGTTGCCAAATCGATGACGATTCAAAACGTCG
65 TAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTC-
* *
3481 AACTAATGGGCCCCGAAAGGCCTAAAA
129 -ACTAATGGGCCCCGATAGGCCCAAAA
3508 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
3573 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
*
3638 TAATGGGCCCCGATAGGCCTAAAA
131 TAATGGGCCCCGATAGGCCCAAAA
* * *
3662 TAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTTAGCAAAATGATTATAGTT
1 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* * * * **
3727 AGCCCATAAACGATGGAAAGAAAAGCATCGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAAC
66 AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
3792 TAATGG
131 TAATGG
Statistics
Matches: 3354, Mismatches: 259, Indels: 62
0.91 0.07 0.02
Matches are distributed among these distances:
137 186 0.06
138 60 0.02
139 5 0.00
140 3 0.00
141 1 0.00
142 1 0.00
145 1 0.00
146 1 0.00
149 2 0.00
150 2 0.00
151 4 0.00
152 230 0.07
153 112 0.03
154 2519 0.75
155 82 0.02
156 81 0.02
157 63 0.02
158 1 0.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (154 bp):
TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCAC
TAATGGGCCCCGATAGGCCCAAAA
Done.