Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017112.1 Corchorus olitorius cultivar O-4 contig17145, 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: 5168
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Found at i:2710 original size:26 final size:26
Alignment explanation
Indices: 2676--2738 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
2666 GGGCTAGCCC
2676 GCGCCTGGCCTGGGCGCTTGGGCCAT
1 GCGCCTGGCCTGGGCGCTTGGGCCAT
*
2702 GCGCTTGGCCTGGGCGCTTGGGCC--
1 GCGCCTGGCCTGGGCGCTTGGGCCAT
*
2726 GCGCCAGGCCTGG
1 GCGCCTGGCCTGG
2739 CCCAAGAGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 11 0.32
26 23 0.68
ACGTcount: A:0.03, C:0.35, G:0.44, T:0.17
Consensus pattern (26 bp):
GCGCCTGGCCTGGGCGCTTGGGCCAT
Found at i:2718 original size:13 final size:13
Alignment explanation
Indices: 2676--2722 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
2666 GGGCTAGCCC
*
2676 GCGCCTGGCCTGG
1 GCGCTTGGCCTGG
2689 GCGCTTGGGCCAT--
1 GCGCTT-GGCC-TGG
2702 GCGCTTGGCCTGG
1 GCGCTTGGCCTGG
2715 GCGCTTGG
1 GCGCTTGG
2723 GCCGCGCCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
11 1 0.03
12 4 0.14
13 19 0.66
14 4 0.14
15 1 0.03
ACGTcount: A:0.02, C:0.32, G:0.45, T:0.21
Consensus pattern (13 bp):
GCGCTTGGCCTGG
Done.