Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014032.1 Corchorus capsularis cultivar CVL-1 contig14053, 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: 9950
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:1295 original size:20 final size:20
Alignment explanation
Indices: 1254--1295 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1244 CCTCACATCA
*
1254 TTCTAGCCGTTGGAGCCTTT
1 TTCTAGCCGTTGGAGCCCTT
1274 TTCTAGCCGTTGG-GCACCTT
1 TTCTAGCCGTTGGAGC-CCTT
1294 TT
1 TT
1296 TCCACTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.10, C:0.26, G:0.24, T:0.40
Consensus pattern (20 bp):
TTCTAGCCGTTGGAGCCCTT
Found at i:8490 original size:49 final size:49
Alignment explanation
Indices: 8435--8534 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
8425 AACCAAGCCC
8435 AATAATAATTTGGGTATTTTGTTATGTAGTTGGATTTAATATTTTAATT
1 AATAATAATTTGGGTATTTTGTTATGTAGTTGGATTTAATATTTTAATT
* *
8484 AATAATAATTTGGGTATTTTGTTATTTAGTTGGGTTTAATATTTTAATT
1 AATAATAATTTGGGTATTTTGTTATGTAGTTGGATTTAATATTTTAATT
8533 AA
1 AA
8535 GATTTATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (49 bp):
AATAATAATTTGGGTATTTTGTTATGTAGTTGGATTTAATATTTTAATT
Done.