Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005862.1 Kokia drynarioides strain JFW-HI SEQ_120182, 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: 3403
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:78 original size:31 final size:31
Alignment explanation
Indices: 19--80 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
9 ATAAACGCCG
*
19 CTATTGCTTTACCTTTTGCGGCGCTTATGGA
1 CTATTGCTTTACCTTTTGCGGCACTTATGGA
* *
50 CTATTGCTTTACCTTTTGCGGTATTTATGGA
1 CTATTGCTTTACCTTTTGCGGCACTTATGGA
81 AAAACGCCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.15, C:0.19, G:0.21, T:0.45
Consensus pattern (31 bp):
CTATTGCTTTACCTTTTGCGGCACTTATGGA
Found at i:3080 original size:28 final size:28
Alignment explanation
Indices: 2989--3080 Score: 66
Period size: 28 Copynumber: 3.3 Consensus size: 28
2979 ATTTTTGGTG
*
2989 TAAAGAAT-ATATTTTTTATGTAAAGAAAA
1 TAAA-AATAATATTTTTT-TATAAAGAAAA
* * * *
3018 CAGAAA-AATATTGTTGTA-AAGAGAAAA
1 TAAAAATAATATTTTTTTATAA-AGAAAA
*
3045 GT-ATAATAATATTTTTTTATAAAGAAAA
1 -TAAAAATAATATTTTTTTATAAAGAAAA
3073 TAAAAATA
1 TAAAAATA
3081 TTACATTAAC
Statistics
Matches: 46, Mismatches: 11, Indels: 13
0.66 0.16 0.19
Matches are distributed among these distances:
26 2 0.04
27 10 0.22
28 30 0.65
29 4 0.09
ACGTcount: A:0.54, C:0.01, G:0.11, T:0.34
Consensus pattern (28 bp):
TAAAAATAATATTTTTTTATAAAGAAAA
Done.