Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007179.1 Corchorus olitorius cultivar O-4 contig07204, 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, 694
Length: 1157
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.25
Found at i:1058 original size:76 final size:74
Alignment explanation
Indices: 889--1157 Score: 423
Period size: 74 Copynumber: 3.6 Consensus size: 74
879 AGGACGGACA
* * *
889 GGGGTGCCAGTCTCGGCGCTCAGCCGTTAGGTGAGCAGCGTCTGCATGGACGCTGTCTCACTAAT
1 GGGGTGCCAGTCTAGGCACTCAGCCGTTAGGTGAGCAGCGTCTGCATGGACGCTGTCTCACAAAT
*
954 GGACGAACG
66 AGACGAACG
*
963 GGGGTGCCAGTCTAGGCACTCAGCCGTTAAGTGAGCAGCGTCTGCATGGACGCTTTGTCTCACAA
1 GGGGTGCCAGTCTAGGCACTCAGCCGTTAGGTGAGCAGCGTCTGCATGGACGC--TGTCTCACAA
1028 ATAGACGAACG
64 ATAGACGAACG
* * *
1039 GGGGTGCTAGTCTAGGCACTCAGCCGTTGGGTGAGCAGCGTCTGCATGGTCGCTGTCTCACAAAT
1 GGGGTGCCAGTCTAGGCACTCAGCCGTTAGGTGAGCAGCGTCTGCATGGACGCTGTCTCACAAAT
1104 AGACGAACG
66 AGACGAACG
1113 GGGGTGCCAGTCTAGGCACTCAGCCGTT-GCGTGAGCAGTCGTCTG
1 GGGGTGCCAGTCTAGGCACTCAGCCGTTAG-GTGAGCAG-CGTCTG
Statistics
Matches: 181, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
73 1 0.01
74 106 0.59
75 6 0.03
76 68 0.38
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (74 bp):
GGGGTGCCAGTCTAGGCACTCAGCCGTTAGGTGAGCAGCGTCTGCATGGACGCTGTCTCACAAAT
AGACGAACG
Done.