Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01001562.1 Corchorus olitorius cultivar O-4 contig01562, 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, 628
Length: 1047
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Found at i:516 original size:25 final size:25
Alignment explanation
Indices: 476--628 Score: 263
Period size: 25 Copynumber: 6.2 Consensus size: 25
466 CTGCTGGGCC
* *
476 GGCCTG-GCGCGGCCCAGGCGTGTG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
500 GGCCTGTGCGTGGCCCAGGCGCGTG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
525 GGCCTGTGCGTGGCCCAGGCGCGTG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
*
550 GCCCTGTGCGTGGCCCAGGCGCGTG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
575 GGCCTGTGCGTGGCCCAGGCGCGTG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
*
600 GGCCTGTGCGTGGCCCAGGCGCGCG
1 GGCCTGTGCGTGGCCCAGGCGCGTG
625 GGCC
1 GGCC
629 AGGCCAGGCT
Statistics
Matches: 123, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 6 0.05
25 117 0.95
ACGTcount: A:0.04, C:0.34, G:0.48, T:0.14
Consensus pattern (25 bp):
GGCCTGTGCGTGGCCCAGGCGCGTG
Found at i:682 original size:6 final size:6
Alignment explanation
Indices: 664--719 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
654 CCAAGCCAGG
* * * *
664 AAAAG- AAAA-A AAAAGA AAAAGGA AAAGGA AGAGGA AATAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAA-GA AAAAGA AAAAGA AAAAGA AAAAGA
711 AAAAGA AAA
1 AAAAGA AAA
720 TAAAATAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
7 5 0.12
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
AAAAGA
Done.