Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009067.1 Kokia drynarioides strain JFW-HI SEQ_123767, 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: 5961
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1128 original size:17 final size:17
Alignment explanation
Indices: 1101--1149 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
1091 GCTTCTCAAA
1101 ATTTT-TAAAAATAATT
1 ATTTTATAAAAATAATT
1117 ATTTTATAAAAAT-ATT
1 ATTTTATAAAAATAATT
1133 ATTTTACATAAAAATAA
1 ATTTT--ATAAAAATAA
1150 ATGAATTTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 13 0.45
17 7 0.24
18 8 0.28
19 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTTTATAAAAATAATT
Found at i:3550 original size:6 final size:6
Alignment explanation
Indices: 3533--3562 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3523 ATCGAATACC
*
3533 CTTTTT CCTTTT CTTTTT CTTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
3563 TAAATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:5342 original size:6 final size:6
Alignment explanation
Indices: 5331--5419 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
5321 TTGGGCCCAA
* * *
5331 TAAATT TAAATT T-ATTT TAAAAT TAAGTT T--ATT CTAAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT -TAAATT TAAATT
5377 T--ATT TGAAATT TAAATT T--ATT ATAAATT TAAATT TAAAATT TA
1 TAAATT T-AAATT TAAATT TAAATT -TAAATT TAAATT T-AAATT TA
5420 TTTAAATAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 22
0.70 0.06 0.23
Matches are distributed among these distances:
4 9 0.14
5 6 0.09
6 35 0.53
7 16 0.24
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (6 bp):
TAAATT
Found at i:5356 original size:17 final size:17
Alignment explanation
Indices: 5331--5412 Score: 119
Period size: 17 Copynumber: 4.8 Consensus size: 17
5321 TTGGGCCCAA
5331 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* * *
5348 TAAAATTAAGTTTATTC
1 TAAATTTAAATTTATTT
5365 TAAATTTAAATTTATTT
1 TAAATTTAAATTTATTT
* *
5382 GAAATTTAAATTTATTA
1 TAAATTTAAATTTATTT
5399 TAAATTTAAATTTA
1 TAAATTTAAATTTA
5413 AAATTTATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (17 bp):
TAAATTTAAATTTATTT
Found at i:5386 original size:11 final size:10
Alignment explanation
Indices: 5368--5426 Score: 52
Period size: 10 Copynumber: 5.8 Consensus size: 10
5358 TTTATTCTAA
5368 ATTTAAATTT
1 ATTTAAATTT
*
5378 ATTTGAA---
1 ATTTAAATTT
5385 ATTTAAATTT
1 ATTTAAATTT
5395 ATTATAAATTT
1 ATT-TAAATTT
5406 AAATTTAAAATTT
1 --ATTT-AAATTT
5419 ATTTAAAT
1 ATTTAAAT
5427 AATGTCCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
7 6 0.15
10 13 0.32
11 11 0.28
12 1 0.03
13 9 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
ATTTAAATTT
Found at i:5416 original size:24 final size:23
Alignment explanation
Indices: 5378--5426 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
5368 ATTTAAATTT
5378 ATTTGAAATTTAAATTTATTATAA
1 ATTTGAAATTTAAATTTATT-TAA
5402 ATTT-AAATTTAAAATTTATTTAA
1 ATTTGAAATTT-AAATTTATTTAA
5425 AT
1 AT
5427 AATGTCCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATTTGAAATTTAAATTTATTTAA
Done.