Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011662.1 Corchorus olitorius cultivar O-4 contig11695, 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: 2154
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Found at i:435 original size:154 final size:155
Alignment explanation
Indices: 1--2142 Score: 3248
Period size: 153 Copynumber: 14.0 Consensus size: 155
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
*
66 GTATTCCAAATGAGCT-AAAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
129 TAAACAATGGAAAGAAAAGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
** * *
154 AGGTTT-CCAAATCGAAGACGATTCAAAACGAAACTAATGATCCCCGATAGAG--AAAAATAACA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAG-GCCCAAAATAACA
216 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * *
281 ATACACAATGTAAAGAAAAGCATTG-
130 ATAAACAATGGAAAGAAAAGCATCGA
* * ** *
306 AGGTTTGCCAAATCGAAGATGATTCAAAACTTCACTAATAATCCCCAATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
*
371 GTGTTCCAAATGAGGTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* *
436 TACACAATGGAAAGAAAGGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
461 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* *
526 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTGACTAAAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * *
591 CACACAATGGAAAGAAAAGAATTG-
131 TAAACAATGGAAAGAAAAGCATCGA
*
615 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCGAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* *
680 GTATTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
744 TAAACAATGGAAAGAAAAGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
* ** * *
769 ATGTTT-CCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGAG--AAAAATAACA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAG-GCCCAAAATAACA
*
831 AGTGTTCCAAATGAGCTAAAAACTTACACAGTTGACTAATCTCACCAAAATGATTATA-TGTAGG
65 AGTGTTCCAAATGAGCTAAAAACTT-CACAGTGGACTAATCTCACCAAAATGATTATAGT-TAGG
* *
895 CCATAAACAATTGAAAGAAAGGCATCGA
128 CCATAAACAATGGAAAGAAAAGCATCGA
*
923 AGG-ATGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
*
987 GTTTTCCAAATGAGCT-AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAAGGCC
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTT-AGGCC
* * *
1051 ATACACAATGTAAAGAAAAGCATTG-
130 ATAAACAATGGAAAGAAAAGCATCGA
* * **
1076 AGGTTTGCCAAATCGAAGATGATTCAAAACTTCACTAATAATCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* * * * *
1141 ATGTTCCAAAAGAGCTAAAATCTTCACAGTGGACTAATGTCACCAAACTGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* ** * *
1206 TACACAGCGTAAAGAAAAGCATTG-
131 TAAACAATGGAAAGAAAAGCATCGA
* * **
1230 AGGTTTGCCAAATCGAAGATGATTCAAAACTTCACTAATAAT-CCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
*
1294 GTGTTCCAAATGAGCTAAAAACTTCACTGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
*
1359 TAAACAATGGAAAGAAAGGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
*
1384 AGG-TTGCCAAATCTAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* *
1448 GTTTTCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACC-AAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1512 TAAACAATGGAAAGAAAAGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
** *
1537 AGGTTT-CCAAATCGAAGACGATTCAAAACGAAACTAATGGGT-TCCGATAGAG--CAAAATAAC
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT-GGTCCCCGATAG-GCCCAAAATAAC
* * *
1598 AAGTGTTCCAAATGAGCTAAAAACTTCACAATAGACTAATCTCACCAAAATGATTATAATTAGGC
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
*
1663 CATAAACAATGGAAAGAAAGGCATCGA
129 CATAAACAATGGAAAGAAAAGCATCGA
* *
1690 AGG-TTGCCAAATCGAAGACGATTCAAAACGTCAGTAATGGTCCCCAATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* *
1754 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC-CCCAAATGATTATAGTTATGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
1818 TAAACAATGGAAAGAAAAGCATCGA
131 TAAACAATGGAAAGAAAAGCATCGA
* **
1843 AGGTTT-CCAAATCGAAGACGATTCAAAATGAAACTAATGGGT-CCCGATAGAG--CAAAATAAC
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAAT-GGTCCCCGATAG-GCCCAAAATAAC
*
1904 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGTTTATA-TGTAGG
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGT-TAGG
*
1968 CCATAAACAATGGAAAGAAAGGCATCGA
128 CCATAAACAATGGAAAGAAAAGCATCGA
1996 AGG-TTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
1 AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
* *
2060 GTTTTCCATATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
66 GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* *
2125 TACACAATGTAAAGAAAA
131 TAAACAATGGAAAGAAAA
2143 CCATTGAGGT
Statistics
Matches: 1814, Mismatches: 136, Indels: 77
0.89 0.07 0.04
Matches are distributed among these distances:
151 25 0.01
152 223 0.12
153 684 0.38
154 675 0.37
155 207 0.11
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (155 bp):
AGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGTCCCCGATAGGCCCAAAATAACAA
GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
TAAACAATGGAAAGAAAAGCATCGA
Done.