Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005480.1 Kokia drynarioides strain JFW-HI SEQ_119535, 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: 10587
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Warning! 19 characters in sequence are not A, C, G, or T
Found at i:1700 original size:10 final size:10
Alignment explanation
Indices: 1678--1708 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1668 AAATTTAAAG
1678 AGAAAAAGCAA
1 AGAAAAAG-AA
1689 AGAAAAAGAA
1 AGAAAAAGAA
1699 AGAAAAAGAA
1 AGAAAAAGAA
1709 GAGGGAAGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.60
11 8 0.40
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.00
Consensus pattern (10 bp):
AGAAAAAGAA
Found at i:5496 original size:23 final size:23
Alignment explanation
Indices: 5470--5554 Score: 86
Period size: 23 Copynumber: 3.8 Consensus size: 23
5460 AAGCCTAAAC
*
5470 CCTTTTAAAACCTAAACCCAAAT
1 CCTTTTAAAACCTAAACCCAAAA
* *
5493 CC-TTTAAAA-TTAAATCCAATAA
1 CCTTTTAAAACCTAAACCCAA-AA
* *
5515 CCTTTTTAAACCTAAACCCAAAC
1 CCTTTTAAAACCTAAACCCAAAA
*
5538 CCTTTAAAAACC-AAACC
1 CCTTTTAAAACCTAAACC
5555 AAACCCAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
21 8 0.16
22 15 0.30
23 19 0.38
24 8 0.16
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (23 bp):
CCTTTTAAAACCTAAACCCAAAA
Found at i:5501 original size:22 final size:22
Alignment explanation
Indices: 5473--5554 Score: 78
Period size: 22 Copynumber: 3.7 Consensus size: 22
5463 CCTAAACCCT
*
5473 TTTAAAACCTAAACCCAAATCC
1 TTTAAAACCTAAACCCAAAACC
* *
5495 TTTAAAA-TTAAATCCAATAACC
1 TTTAAAACCTAAACCCAA-AACC
* *
5517 TTTTTAAACCTAAACCCAAACCC
1 -TTTAAAACCTAAACCCAAAACC
5540 TTTAAAAACC-AAACC
1 TTT-AAAACCTAAACC
5555 AAACCCAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 8 0.17
22 18 0.38
23 14 0.29
24 8 0.17
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (22 bp):
TTTAAAACCTAAACCCAAAACC
Found at i:5530 original size:24 final size:23
Alignment explanation
Indices: 5470--5542 Score: 69
Period size: 24 Copynumber: 3.2 Consensus size: 23
5460 AAGCCTAAAC
* *
5470 CCTTTTAAAACCTAAACCCAAAT
1 CCTTTTTAAACCTAAACCCAAAA
** *
5493 CC--TTTAAAATTAAATCCAATAA
1 CCTTTTTAAACCTAAACCCAA-AA
*
5515 CCTTTTTAAACCTAAACCCAAAC
1 CCTTTTTAAACCTAAACCCAAAA
5538 CCTTT
1 CCTTT
5543 AAAAACCAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
21 13 0.34
22 3 0.08
23 8 0.21
24 14 0.37
ACGTcount: A:0.41, C:0.29, G:0.00, T:0.30
Consensus pattern (23 bp):
CCTTTTTAAACCTAAACCCAAAA
Found at i:5634 original size:7 final size:7
Alignment explanation
Indices: 5622--5684 Score: 56
Period size: 7 Copynumber: 9.1 Consensus size: 7
5612 CGAACCCGAC
5622 CCATTGA
1 CCATTGA
5629 CCATTGA
1 CCATTGA
* *
5636 TCGTTGA
1 CCATTGA
**
5643 CTGTTGA
1 CCATTGA
* *
5650 TCGTTGA
1 CCATTGA
*
5657 -CTTTGA
1 CCATTGA
5663 CCATTGA
1 CCATTGA
5670 CCATTGA
1 CCATTGA
5677 CCATTGA
1 CCATTGA
5684 C
1 C
5685 TTTTTTCGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
6 5 0.11
7 42 0.89
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (7 bp):
CCATTGA
Found at i:8525 original size:25 final size:25
Alignment explanation
Indices: 8497--8544 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
8487 AGACAGCCTG
*
8497 GGTTGGTATATGCGATTAGGGATAA
1 GGTTGGTATATGCGACTAGGGATAA
*
8522 GGTTTGTATATGCGACTAGGGAT
1 GGTTGGTATATGCGACTAGGGAT
8545 GAGCCTAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.35, T:0.33
Consensus pattern (25 bp):
GGTTGGTATATGCGACTAGGGATAA
Done.