Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009627.1 Kokia drynarioides strain JFW-HI SEQ_124343, 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: 3643
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Found at i:2775 original size:39 final size:40
Alignment explanation
Indices: 2676--2775 Score: 166
Period size: 40 Copynumber: 2.5 Consensus size: 40
2666 TTAAATAGGG
2676 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGTT
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGTT
*
2716 TTTTAATGTGTCTTATTTTGATACATATTTAATAGTTG-T
1 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGTT
* *
2755 TTTTAAGGTGTCTAAGTTTGA
1 TTTTAATGTGTCTTAGTTTGA
2776 GACAAATTAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
39 19 0.34
40 37 0.66
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.54
Consensus pattern (40 bp):
TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGTT
Found at i:2857 original size:32 final size:32
Alignment explanation
Indices: 2821--2883 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
2811 AGCCGAAATT
* * *
2821 AATTAGCTGATTAATGTGTTTTAGGTACATGC
1 AATTAGCTGATTAATATATTTCAGGTACATGC
*
2853 AATTAGTTGATTAATATATTTCAGGTACATG
1 AATTAGCTGATTAATATATTTCAGGTACATG
2884 TATGGATGGC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (32 bp):
AATTAGCTGATTAATATATTTCAGGTACATGC
Done.