Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023136.1 Corchorus olitorius cultivar O-4 contig23169, 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: 6376
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3841 original size:15 final size:14
Alignment explanation
Indices: 3822--3849 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3812 GACATAGAGT
3822 TTTTTTCCCGCAGC
1 TTTTTTCCCGCAGC
3836 TTTTTTCCCGCAGC
1 TTTTTTCCCGCAGC
3850 ATAAGGCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.36, G:0.14, T:0.43
Consensus pattern (14 bp):
TTTTTTCCCGCAGC
Found at i:5304 original size:21 final size:21
Alignment explanation
Indices: 5278--5390 Score: 158
Period size: 21 Copynumber: 5.4 Consensus size: 21
5268 TGCTAGAAGT
5278 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
5299 TCATTGGAGCAAGTTCCAAGC
1 TCATTGGAGCAAGTTCCAAGC
* *
5320 TCATTGGAGCAGGTTCCAAGT
1 TCATTGGAGCAAGTTCCAAGC
*
5341 TCATTGGAG-AAGGTTCCAAGA
1 TCATTGGAGCAA-GTTCCAAGC
*
5362 TCATTGGAG-AAGGTTTCAAGC
1 TCATTGGAGCAA-GTTCCAAGC
5383 TCATTGGA
1 TCATTGGA
5391 AATGCCTAAG
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 84 0.99
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (21 bp):
TCATTGGAGCAAGTTCCAAGC
Done.