Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011082.1 Corchorus olitorius cultivar O-4 contig11115, 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: 2070
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Found at i:435 original size:154 final size:154
Alignment explanation
Indices: 10--2070 Score: 2886
Period size: 154 Copynumber: 13.5 Consensus size: 154
1 GAAACAATC
* * * * * *
10 GCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACCAATGGGCTCCGATAGGCCC-AAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* * *
74 TAACAAGTGTTCCACATGAGCTAAAAAGTTCACAATGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
139 AGGCCATAAACAATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* *
163 GCATTGAGGTTTGCC-AATCGAAGACTATTCAATACGTAACTAATGGGCTCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* * * * *
227 TAACGAGTATTACAAATGAGCTAAAAACTTCGCAGTGGACTAATCTCACGAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
292 AGGCCATAAAAAATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * * * *
316 GCATTGAGGTTTGCCAAACCGAAGACGACTCAAAACGGAACTAATGGGCGCCGATAGCCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
** * * *
381 TAACAAGTGTTCCACGTGATCTATAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
446 AGGCCATAAACAATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * * * *
470 TCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCGGATACGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* *
535 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGAAATAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
600 TGGCCATAAACAATTGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * * *
624 TCATTGAGGTTTGCCAAATTGAAGACGATTCAAAATGGAACTAATGGGCCCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* * *
689 TAACAAGTGTTCCAAATGAGCTAAAAACTTCATAGTGGACTAATCTAAACAAAATGAATTATAGT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG-ATTATAGT
*
754 TAGGCCATAAACAATTGAAAGAAAA
130 TAGGCCATAAACAATGGAAAGAAAA
*
779 GCATTGAGGTTTGCCAAATCGTAA-ACGATTCAATACGTCACTAATGGGCCCCGATAGGCCCAAA
1 GCATTGAGGTTTGCCAAATCG-AAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAA
** * * * *
843 ATAACAAGTGTTCCACGTGATCTATAAAGTTCACAGTGGACTAATCTCACC-AAATTATTATAGT
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
907 TTGGCCATAAACAATGGAAAGAAAA
130 TAGGCCATAAACAATGGAAAGAAAA
* *
932 GCATTGAGGTTTGCCAAATCGAAGACTATTCAATACGTAACTAATGGGCTCCGATAGGCCC-AAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* *
996 T-ACGAGTATTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
1060 AGGCCATAAA-AATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * *
1083 GCATTGAGGTTTGCCAAATCGAAGACGATTCAAAATGGAACTAACTGGTCCCCGAT-GGCCC-AA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAA-TGGGCCCCGATAGGCCCAAA
* * * * * *
1146 AT-AGAAGTGTTCCGAATGAGCTAAAAACTTCATAGACGGACTAATACTAAACAAAATAGATTAT
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG-TGGACTAAT-CTCACCAAAAT-GATTAT
*
1210 AGTTAGGCCAT-AACAATTGAAAG-AAA
127 AGTTAGGCCATAAACAATGGAAAGAAAA
* * *
1236 GCATTGAGGTTTGCCAAATCGTAGACGATTCAATACGTCACTAATGGGCCCTGATA-GCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
*
1300 TAACAAGTGTTCCAAATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1365 TGGCCATAAACAATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* *
1389 GCATTGAGGTTTCCCAAATCGAAGACGATTCAAAACAG-AACTAATGGGCCCCGATAGGCCCAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATAC-GTAACTAATGGGCCCCGATAGGCCCAAA
* * *
1453 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACACTGGACTAATCTCACCAAAATAATTATAAT
65 ATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT
*
1518 TAGGCCATAAAC------AA-ATAA
130 TAGGCCATAAACAATGGAAAGAAAA
* *
1536 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATATGTCACTAATGGGCCCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* * * * * *
1601 TAACAAGTCTTCCAAATGAGCTAAAAACTTCAAAGTGAACTAATCTAAACAAAATGATTATAGGT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
* *
1666 AGGCCATAAACAATGGAAACAAAC
131 AGGCCATAAACAATGGAAAGAAAA
* * * * *
1690 GCATTGAGGCTTGCCAATTCGAAGAAGATTCAATACGTCACCAATGGGCCCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* *
1755 TAACAAGTGTTCCACATGAGCTAAAAAGTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1820 AGGCCATAAACAATGGAAAAAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * *
1844 GCATTGAGGTTTGCCAAATCTAAGACTATTCAATACGTAACTAATGGGCTCCGATAGGCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
* ** *
1909 TAACAAGTATTCTGAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
66 TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
*
1974 AGGCCATAAGCAATGGAAAGAAAA
131 AGGCCATAAACAATGGAAAGAAAA
* * * ** * *
1998 GCATTGAGGTTTGCAAAACCGAAGACGATTCAAAACAAAACTAATGGGCGCCGATAGCCCCAAAA
1 GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
2063 TAACAAGT
66 TAACAAGT
Statistics
Matches: 1695, Mismatches: 187, Indels: 51
0.88 0.10 0.03
Matches are distributed among these distances:
146 1 0.00
147 129 0.08
148 2 0.00
151 147 0.09
152 118 0.07
153 317 0.19
154 849 0.50
155 130 0.08
156 2 0.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
GCATTGAGGTTTGCCAAATCGAAGACGATTCAATACGTAACTAATGGGCCCCGATAGGCCCAAAA
TAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT
AGGCCATAAACAATGGAAAGAAAA
Done.