Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005795.1 Kokia drynarioides strain JFW-HI SEQ_120068, 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: 3459
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Found at i:2757 original size:18 final size:18
Alignment explanation
Indices: 2734--2789 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 18
2724 GTTGAAAAGG
2734 AAGAAGAGAAAAG-AGAAA
1 AAGAAG-GAAAAGAAGAAA
*
2752 AAGAAGGAAGAGAAGAAA
1 AAGAAGGAAAAGAAGAAA
*
2770 AGGAGAAAGAAAATGAAGAA
1 A--AGAAGGAAAA-GAAGAA
2790 GATTTTGTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.16
18 12 0.39
20 8 0.26
21 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (18 bp):
AAGAAGGAAAAGAAGAAA
Found at i:2759 original size:25 final size:26
Alignment explanation
Indices: 2727--2791 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 26
2717 TATGGGTGTT
2727 GAAAAGGAAGAAGAGAAAA-GAGAAA
1 GAAAAGGAAGAAGAGAAAAGGAGAAA
2752 -AAGAAGGAAG-AGAAGAAAAGGAGAAA
1 GAA-AAGGAAGAAG-AGAAAAGGAGAAA
*
2778 GAAAATGAAGAAGA
1 GAAAAGGAAGAAGA
2792 TTTTGTGCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
24 4 0.12
25 13 0.38
26 13 0.38
27 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (26 bp):
GAAAAGGAAGAAGAGAAAAGGAGAAA
Done.