Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013802.1 Kokia drynarioides strain JFW-HI SEQ_128830, 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: 4906
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Found at i:1701 original size:39 final size:39
Alignment explanation
Indices: 1657--1768 Score: 224
Period size: 39 Copynumber: 2.9 Consensus size: 39
1647 GGTTTTAATG
1657 TGTCTTAGTTTGATACATATTTAATAGTTGTTTTACGTA
1 TGTCTTAGTTTGATACATATTTAATAGTTGTTTTACGTA
1696 TGTCTTAGTTTGATACATATTTAATAGTTGTTTTACGTA
1 TGTCTTAGTTTGATACATATTTAATAGTTGTTTTACGTA
1735 TGTCTTAGTTTGATACATATTTAATAGTTGTTTT
1 TGTCTTAGTTTGATACATATTTAATAGTTGTTTT
1769 TAATGTGTCT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.25, C:0.07, G:0.15, T:0.53
Consensus pattern (39 bp):
TGTCTTAGTTTGATACATATTTAATAGTTGTTTTACGTA
Found at i:1868 original size:32 final size:32
Alignment explanation
Indices: 1832--1894 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1822 AGCCGAAAAT
* *
1832 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
*
1864 AATTAGCTGATTAATATATTTTAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
1895 ATGGTTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Done.