Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004044.1 Kokia drynarioides strain JFW-HI SEQ_117186, 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: 3236
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Found at i:641 original size:11 final size:11
Alignment explanation
Indices: 627--688 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
617 AAAGAGCAAA
*
627 AGAAGAATAAG
1 AGAAGAAGAAG
* *
638 AGAACAA-ATG
1 AGAAGAAGAAG
648 GAGAAGAAGAAG
1 -AGAAGAAGAAG
*
660 AAAAGAAGAAG
1 AGAAGAAGAAG
*
671 AGGAGAAGAAG
1 AGAAGAAGAAG
682 AAGAAGA
1 -AGAAGA
689 GAAAATGGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
10 2 0.05
11 31 0.77
12 7 0.17
ACGTcount: A:0.63, C:0.02, G:0.32, T:0.03
Consensus pattern (11 bp):
AGAAGAAGAAG
Found at i:654 original size:25 final size:25
Alignment explanation
Indices: 610--691 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 25
600 ACTGGGTAGT
* *
610 AGAAGA-AA-AAGAGCAAAAGAAGA
1 AGAAGAGAACAAGAGGAGAAGAAGA
*
633 ATAAGAGAACAA-ATGGAGAAGAAGA
1 AGAAGAGAACAAGA-GGAGAAGAAGA
* *
658 AGAAAAGAAGAAGAGGAGAAGAAGA
1 AGAAGAGAACAAGAGGAGAAGAAGA
683 AGAAGAGAA
1 AGAAGAGAA
692 AATGGAAGGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 5 0.10
24 3 0.06
25 39 0.81
26 1 0.02
ACGTcount: A:0.65, C:0.02, G:0.30, T:0.02
Consensus pattern (25 bp):
AGAAGAGAACAAGAGGAGAAGAAGA
Found at i:657 original size:3 final size:3
Alignment explanation
Indices: 649--688 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
639 GAACAAATGG
*
649 AGA AGA AGA AGA A-A AGA AGA AG- AGG AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
689 GAAAATGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:669 original size:17 final size:17
Alignment explanation
Indices: 610--688 Score: 70
Period size: 17 Copynumber: 4.5 Consensus size: 17
600 ACTGGGTAGT
* *
610 AGAAGAAAAAGAGCAAA
1 AGAAGAAGAAGAGAAAA
*
627 AGAAGAATAAGAGAACAA
1 AGAAGAAGAAGAGAA-AA
*
645 ATGGAGAAGAAGA-AGAAA
1 A-GAAGAAGAAGAGA-AAA
* *
663 AGAAGAAGAGGAGAAGA
1 AGAAGAAGAAGAGAAAA
680 AGAAGAAGA
1 AGAAGAAGA
689 GAAAATGGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 33 0.65
18 8 0.16
19 10 0.20
ACGTcount: A:0.65, C:0.03, G:0.30, T:0.03
Consensus pattern (17 bp):
AGAAGAAGAAGAGAAAA
Found at i:690 original size:14 final size:14
Alignment explanation
Indices: 649--691 Score: 68
Period size: 14 Copynumber: 3.1 Consensus size: 14
639 GAACAAATGG
*
649 AGAAGAAGAAGAAA
1 AGAAGAAGAAGAGA
*
663 AGAAGAAGAGGAGA
1 AGAAGAAGAAGAGA
677 AGAAGAAGAAGAGA
1 AGAAGAAGAAGAGA
691 A
1 A
692 AATGGAAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AGAAGAAGAAGAGA
Found at i:691 original size:11 final size:11
Alignment explanation
Indices: 648--688 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
638 AGAACAAATG
648 GAGAAGAAGAA
1 GAGAAGAAGAA
*
659 GAAAAGAAGAA
1 GAGAAGAAGAA
*
670 GAGGAGAAGAA
1 GAGAAGAAGAA
681 GAAGAAGA
1 G-AGAAGA
689 GAAAATGGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 20 0.80
12 5 0.20
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (11 bp):
GAGAAGAAGAA
Done.