Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008952.1 Kokia drynarioides strain JFW-HI SEQ_123648, 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: 3831
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.34
Found at i:3380 original size:24 final size:24
Alignment explanation
Indices: 3353--3432 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
3343 GCGATATGAT
*
3353 ATGGAAGACTTGGTGATATCATTA
1 ATGGAAGACTTGGTGATATCTTTA
*
3377 ATGGAAGACTTGGTGAAATCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
*
3401 ATGGAAGACTTGGTGATTTCTTTA
1 ATGGAAGACTTGGTGATATCTTTA
3425 ATGGAAGA
1 ATGGAAGA
3433 GCTTACGTCT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.34
Consensus pattern (24 bp):
ATGGAAGACTTGGTGATATCTTTA
Found at i:3512 original size:36 final size:36
Alignment explanation
Indices: 3425--3516 Score: 96
Period size: 36 Copynumber: 2.6 Consensus size: 36
3415 GATTTCTTTA
* * *
3425 ATGGAAGAGCTTACGTCTCGGTTAGAGTGTAAGGTT
1 ATGGAAGTGCTTACGTCTCGATTAGAGTGTAAGATT
* * * **
3461 ATGTG-ATTTCATACGTCTCGATTAGAGTGTATTATT
1 ATG-GAAGTGCTTACGTCTCGATTAGAGTGTAAGATT
3497 ATGGAAGTGCTTACGTCTCG
1 ATGGAAGTGCTTACGTCTCG
3517 GTTAAGCGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
35 1 0.02
36 41 0.95
37 1 0.02
ACGTcount: A:0.24, C:0.13, G:0.27, T:0.36
Consensus pattern (36 bp):
ATGGAAGTGCTTACGTCTCGATTAGAGTGTAAGATT
Done.