Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002020.1 Corchorus olitorius cultivar O-4 contig02020, 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, 967
Length: 1612
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Found at i:285 original size:43 final size:43
Alignment explanation
Indices: 237--324 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
227 CTCACTAAGT
*
237 GAGTATGGTACCAAGTGAGTATTTTGTTGGGTGAGTAGGGTAG
1 GAGTATGATACCAAGTGAGTATTTTGTTGGGTGAGTAGGGTAG
280 GAGTATGATACCAAGTGAGTATTTTGTTGGGTGAGTAGGGTAG
1 GAGTATGATACCAAGTGAGTATTTTGTTGGGTGAGTAGGGTAG
323 GA
1 GA
325 ACACGTCACT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.25, C:0.05, G:0.39, T:0.32
Consensus pattern (43 bp):
GAGTATGATACCAAGTGAGTATTTTGTTGGGTGAGTAGGGTAG
Found at i:1185 original size:25 final size:25
Alignment explanation
Indices: 1148--1211 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
1138 GGGAGTCTCC
1148 CAGGTGAGTCTCACCTAGCGCACAG
1 CAGGTGAGTCTCACCTAGCGCACAG
* *
1173 CAGGTGAGCCTCACCTAGCGCATAG
1 CAGGTGAGTCTCACCTAGCGCACAG
1198 CAGGTGAGTCTCAC
1 CAGGTGAGTCTCAC
1212 TGATCAGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.23, C:0.31, G:0.28, T:0.17
Consensus pattern (25 bp):
CAGGTGAGTCTCACCTAGCGCACAG
Done.