Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009903.1 Corchorus olitorius cultivar O-4 contig09935, 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: 2722
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Found at i:96 original size:40 final size:39
Alignment explanation
Indices: 1--99 Score: 112
Period size: 39 Copynumber: 2.5 Consensus size: 39
* * * *
1 AGGATCCTTGCTTTATCAGTCAATTTCAGAATCCTGTTC
1 AGGATCCTGGCTTTATCAGTCAATTTCAAAATCATATTC
*
40 AGGATCCTTGCTTTATCAGTCAATTTCAAAAATCATATTC
1 AGGATCCTGGCTTTATCAGTCAATTTC-AAAATCATATTC
80 AGGA-CCAGTGGC-TTATCAGT
1 AGGATCC--TGGCTTTATCAGT
100 TGATTTCAGC
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
39 29 0.55
40 21 0.40
41 3 0.06
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.35
Consensus pattern (39 bp):
AGGATCCTGGCTTTATCAGTCAATTTCAAAATCATATTC
Found at i:2008 original size:2 final size:2
Alignment explanation
Indices: 2003--2048 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1993 ATATATATAC
2003 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
2045 GT GT
1 GT GT
2049 ACATGTACCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Done.