Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011663.1 Corchorus olitorius cultivar O-4 contig11696, 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, 958
Length: 1597
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Found at i:1190 original size:154 final size:154
Alignment explanation
Indices: 1--1597 Score: 2245
Period size: 153 Copynumber: 10.3 Consensus size: 154
* * * *
1 GATTCAAAACGGAACTAATGAGCCCCGATAGGCACAAGAT-AAAAGTGTTCTAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
* * *
65 ACTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCA-AAACAATGGAAAGAAAAGA
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
** *
129 ATCAAGGATTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
153 GATTCAAAACGGAACTAATGGGCCCCGATAGG-ACTAAAATAAAAAGTGTTCC-AA-TATGCTAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCAC-AAAATAAAAAGTGTTCCAAATTA-GCTAA
* * *
215 AAACATCACAATGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
64 AAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAA
280 GCATAT-AGGGTTGCCAAATCGAAGAC
129 GCAT-TGAGGGTTGCCAAATCGAAGAC
* * *
306 GATTCAAAACGGAAATAATGAGCCCCGATAGGCACAAAATAAAAAGTGCTCCAAATTAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
*
371 ACTTCACAGT-GACTAATCTCACCAAAATGATTGTAGTTAGGCCATAAACAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
435 ATTGAGGTTTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
** * *
459 GATTCAAAACGGAACTAATGGGCCCCGATAGGCTTAAAATAACAAGTGTTCCAAA-TATGCTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTA-GCTAAA
* *
523 AACATCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGGCCATAAACAATGGAAAGAAAA-
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
*
587 CATTGAGGTTTGCCAAATCGAAGAC
130 CATTGAGGGTTGCCAAATCGAAGAC
* * * *
612 GATTCAAAACGGAACTAATGGGCCCCGATCGGCCCAAAATAACAAGTGTTCCAAA-TATGCTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTA-GCTAAA
* * *
676 AACATCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAATAGAAAG-AAAG
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
740 CATTGAGGGTTGCCAAATCGAAGAC
130 CATTGAGGGTTGCCAAATCGAAGAC
* * * * * *
765 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCGAATGAGCTAAGA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
* * * *
830 ACATCACAGTGGACTCATTTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
895 ATTGAGGGTTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
* * * * *
919 GATTCAAAACGGAACTAATAGGCCCCGTTAAG-ACCAAAATAAAAAAAGTGTTCTAAATGAGCTA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCA-CAAAAT--AAAAAGTGTTCCAAATTAGCTA
* *
983 AAAACTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
63 AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
* *
1048 AGCATAT-ATGGTTGCCAAATCGAAAAC
128 AGCAT-TGAGGGTTGCCAAATCGAAGAC
* * * *
1075 TATTCAGAACAGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
*
1140 ACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
1204 ATTGAGGGTTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
*** *
1228 GATTCAAAACGGAACTAATGGGCCCCGATAGATTCAAAATAAAAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCT-AAA
*
1293 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAG
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
1357 CAATTAGAGGGTTGCCAAATCGAAGAAC
130 C-ATT-GAGGGTTGCCAAATCGAAG-AC
* * ** * *
1385 GATTCAAAACGGAACTAATAGGTCCTCGATATTCCGCAAAATAACAAAGTGTTCCAAATGAAGCT
1 GATTCAAAACGGAACTAAT-GGGCCCCGATA-GGCACAAAATAA-AAAGTGTTCCAAAT-TAGCT
1450 AAAAACTTCCAACACGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
62 AAAAACTT-C-ACA-GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1515 GAAAAGCATTGAGGGTTGCCAAATCGAAGAC
124 GAAAAGCATTGAGGGTTGCCAAATCGAAGAC
* * * * *
1546 GATTCAAAACAGAACTAA-GGGTCCTCGATATGCCCAAAATAACAAGTGTTCC
1 GATTCAAAACGGAACTAATGGG-CCCCGATAGGCACAAAATAAAAAGTGTTCC
Statistics
Matches: 1315, Mismatches: 97, Indels: 60
0.89 0.07 0.04
Matches are distributed among these distances:
151 3 0.00
152 91 0.07
153 590 0.45
154 281 0.21
155 5 0.00
156 150 0.11
157 23 0.02
158 18 0.01
159 20 0.02
160 30 0.02
161 24 0.02
162 21 0.02
163 54 0.04
164 5 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
ATTGAGGGTTGCCAAATCGAAGAC
Done.