Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007708.1 Kokia drynarioides strain JFW-HI SEQ_122339, 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: 4810
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.38
Found at i:4518 original size:12 final size:12
Alignment explanation
Indices: 4503--4557 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
4493 TTTTTTTTAC
4503 TGTTTTGGTTGT
1 TGTTTTGGTTGT
*
4515 TGTTTT-GCTGT
1 TGTTTTGGTTGT
* * *
4526 TATTTT-TTTAT
1 TGTTTTGGTTGT
*
4537 TGTTTTGGTTGC
1 TGTTTTGGTTGT
4549 TGTTTTGGT
1 TGTTTTGGT
4558 ATTTTTTTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
11 16 0.48
12 17 0.52
ACGTcount: A:0.04, C:0.04, G:0.25, T:0.67
Consensus pattern (12 bp):
TGTTTTGGTTGT
Found at i:4632 original size:12 final size:12
Alignment explanation
Indices: 4576--4633 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
4566 ACTGTTTTGA
4576 TGTTGTTATTTT
1 TGTTGTTATTTT
4588 T-TCTGTTATTTT
1 TGT-TGTTATTTT
* *
4600 TGTTGCTGTTTT
1 TGTTGTTATTTT
4612 TGTTG----TTT
1 TGTTGTTATTTT
4620 TGTTGTTATTTT
1 TGTTGTTATTTT
4632 TG
1 TG
4634 CGGCTGCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
8 8 0.21
11 1 0.03
12 28 0.74
13 1 0.03
ACGTcount: A:0.05, C:0.03, G:0.19, T:0.72
Consensus pattern (12 bp):
TGTTGTTATTTT
Done.