Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01008744.1 Corchorus olitorius cultivar O-4 contig08771, 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, 693
Length: 1156
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.24
Found at i:500 original size:25 final size:25
Alignment explanation
Indices: 472--528 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
462 TTGTTAGTGG
472 AGATTTGCATCCATAACATGCTGCC
1 AGATTTGCATCCATAACATGCTGCC
497 AGATTTGCATCCATAACATGCTGCC
1 AGATTTGCATCCATAACATGCTGCC
522 AG-TTTGC
1 AGATTTGC
529 GAGACTCCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 5 0.16
25 27 0.84
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (25 bp):
AGATTTGCATCCATAACATGCTGCC
Found at i:1024 original size:21 final size:21
Alignment explanation
Indices: 998--1109 Score: 149
Period size: 21 Copynumber: 5.4 Consensus size: 21
988 TGCTAGAAGT
998 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
1019 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
1040 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
1061 TCATTGGAG-AAGGTTCC-AGA
1 TCATTGGAGCAA-GTTCCAAGC
*
1081 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
1102 TCATTGGA
1 TCATTGGA
1110 AATGCCTAAG
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
20 19 0.23
21 64 0.77
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.