Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005898.1 Kokia drynarioides strain JFW-HI SEQ_120240, 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: 6754
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Found at i:2908 original size:18 final size:17
Alignment explanation
Indices: 2872--2909 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2862 GCAAATGTCT
2872 TTAAAATAATAACAAAA
1 TTAAAATAATAACAAAA
2889 TTAACAATAA-AACAAGAA
1 TTAA-AATAATAACAA-AA
2907 TTA
1 TTA
2910 TATAACATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.66, C:0.08, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAAAATAATAACAAAA
Found at i:4429 original size:68 final size:68
Alignment explanation
Indices: 4318--4452 Score: 216
Period size: 68 Copynumber: 2.0 Consensus size: 68
4308 GTTGTTTTTG
* *
4318 CATTAATCACGAATAAACGCACCGCACATCTAAACCAACATTAAATATGTTGAAATTTCTCTTTT
1 CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
4383 AAA
66 AAA
* * * *
4386 CATTAATCACGAATAAACACACTGTATATCTAAACCAATATTAAATATGTTAAAATTTCTCTTTT
1 CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
4451 AA
66 AA
4453 TGAAATTGAC
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 61 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.33
Consensus pattern (68 bp):
CATTAATCACGAATAAACACACCGCACATCTAAACCAACATTAAATATGTTAAAATTTCTCTTTT
AAA
Done.