Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020105.1 Corchorus olitorius cultivar O-4 contig20138, 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: 19546
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Found at i:15641 original size:21 final size:20
Alignment explanation
Indices: 15615--15656 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
15605 CCGCATCTCA
15615 AATTTTTCTCCCGAGAAATC
1 AATTTTTCTCCCGAGAAATC
15635 AATTTTTCTCCCGAGAAATC
1 AATTTTTCTCCCGAGAAATC
15655 AA
1 AA
15657 AAACCAGCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (20 bp):
AATTTTTCTCCCGAGAAATC
Found at i:16527 original size:55 final size:56
Alignment explanation
Indices: 16466--16571 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 56
16456 ATAATGTTAT
*
16466 TGTTCACATTTGA-TTGAAGG-GAAAAAAAATTCCTACAAAAAATAAAAACAATTAC
1 TGTTCACATTTGACTT-AAGGAAAAAAAAAATTCCTACAAAAAATAAAAACAATTAC
*
16521 TGTTCACATTTGACTTAAGGAAAAAAAAAATTCCTACAAACAATAAAAACA
1 TGTTCACATTTGACTTAAGGAAAAAAAAAATTCCTACAAAAAATAAAAACA
16572 GATCAATACC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
55 17 0.36
56 30 0.64
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (56 bp):
TGTTCACATTTGACTTAAGGAAAAAAAAAATTCCTACAAAAAATAAAAACAATTAC
Done.