Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013081.1 Corchorus olitorius cultivar O-4 contig13114, 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: 3044
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Found at i:471 original size:51 final size:51
Alignment explanation
Indices: 415--518 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
405 ACTAACCCTT
415 ATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAA
1 ATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAA
466 ATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAA
1 ATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAA
517 AT
1 AT
519 TGAGGATTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.38
Consensus pattern (51 bp):
ATATATACTATATATTATTTTTAGTGACAATGGAAATTACTTAAAGGCCAA
Found at i:1552 original size:19 final size:19
Alignment explanation
Indices: 1525--1568 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1515 GGCTTATGAG
* *
1525 CCGGCTTGGCCGGTCCGAA
1 CCGGTTTGGCCGGGCCGAA
*
1544 CCGGTTTGGTCGGGCCGAA
1 CCGGTTTGGCCGGGCCGAA
1563 CCGGTT
1 CCGGTT
1569 GACCCGGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.32, G:0.39, T:0.20
Consensus pattern (19 bp):
CCGGTTTGGCCGGGCCGAA
Done.