Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010930.1 Corchorus olitorius cultivar O-4 contig10962, 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: 1847
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Found at i:859 original size:154 final size:154
Alignment explanation
Indices: 558--1298 Score: 1221
Period size: 154 Copynumber: 4.8 Consensus size: 154
548 ATTCGTATCA
* * *
558 AATGGGCCGCGATAGGCCCAAAATAACAACTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTA
1 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
623 ATTTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* *
688 TCGACGACGATTGAAAACGGAACT
131 TCGAAGACGATTCAAAACGGAACT
* * * * *
712 AATTGGCCCCGTTATGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAACTTCACAGTCGACTA
1 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * *
777 ATCTGACCAAAATGATTATAGTTTGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCACA
66 ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
*
842 TCGAAGAAGATTCAAAACGGAACT
131 TCGAAGACGATTCAAAACGGAACT
866 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
1 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* * * *
931 ATCTCACCAAAAAGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTACCAAA
66 ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
* **
996 TCGAAGACGATTCAAAATGTCACT
131 TCGAAGACGATTCAAAACGGAACT
1020 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
1 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
* *
1085 ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCCTTGAGGTTTGCCAAA
66 ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
**
1150 TCGAAGACGATTCAAAACGTCACT
131 TCGAAGACGATTCAAAACGGAACT
* *
1174 AATGGGCCGCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTA
1 AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
*
1239 ATTTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
66 ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTG
1299 ATGCGCCAAG
Statistics
Matches: 548, Mismatches: 39, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
154 548 1.00
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (154 bp):
AATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA
ATCTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAA
TCGAAGACGATTCAAAACGGAACT
Done.