Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000025.1 Kokia drynarioides strain JFW-HI SEQ_31641, 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: 3154
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Found at i:2926 original size:4 final size:4
Alignment explanation
Indices: 2913--2959 Score: 69
Period size: 4 Copynumber: 11.8 Consensus size: 4
2903 AAAATTGAAG
*
2913 GAAA -AAA GAAA GAAA AAAGA GAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA GAA
2960 GAAGGAAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
3 3 0.08
4 33 0.85
5 3 0.08
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:2930 original size:13 final size:13
Alignment explanation
Indices: 2914--2987 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
2904 AAATTGAAGG
2914 AAAAAAGAAAGAA
1 AAAAAAGAAAGAA
*
2927 AAAAGAGAAAG-A
1 AAAAAAGAAAGAA
*
2939 AAGAAAGAAAGAA
1 AAAAAAGAAAGAA
*
2952 AGAAAGAAGAAGGAA
1 A-AAA-AAGAAAGAA
* ** *
2967 GAAGGAGAAGGAA
1 AAAAAAGAAAGAA
2980 AAAAAAGA
1 AAAAAAGA
2988 TAATATATTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
12 10 0.21
13 25 0.53
14 4 0.09
15 8 0.17
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAGAA
Done.