Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01002147.1 Corchorus olitorius cultivar O-4 contig02147, 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, 985
Length: 1643
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Found at i:929 original size:25 final size:24
Alignment explanation
Indices: 892--938 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
882 CTAGAAAATT
892 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
918 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
939 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:1184 original size:21 final size:21
Alignment explanation
Indices: 1161--1261 Score: 159
Period size: 21 Copynumber: 4.8 Consensus size: 21
1151 CAAGTTCCAA
1161 GTTCCAAGCTCATTGGAGCAA-
1 GTTCCAAGCTCATTGGAG-AAG
1182 GTTCCAAGCTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
1203 GTTCCAAGTTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
1224 GTTCCAAGTTCATTGGAGAAG
1 GTTCCAAGCTCATTGGAGAAG
*
1245 GTTTCAAGCTCATTGGA
1 GTTCCAAGCTCATTGGA
1262 ATTGCCTAAG
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
20 2 0.03
21 74 0.97
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.28
Consensus pattern (21 bp):
GTTCCAAGCTCATTGGAGAAG
Done.