Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006867.1 Kokia drynarioides strain JFW-HI SEQ_121466, 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: 8373
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Found at i:1999 original size:24 final size:24
Alignment explanation
Indices: 1972--2022 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1962 TAATATTTGA
*
1972 AATTGAGTTCTATCTTAAAAATGC
1 AATTGAATTCTATCTTAAAAATGC
1996 AATTGAATTCTATCTTAAAAATGC
1 AATTGAATTCTATCTTAAAAATGC
2020 AAT
1 AAT
2023 GTGTCTTACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (24 bp):
AATTGAATTCTATCTTAAAAATGC
Found at i:7543 original size:18 final size:18
Alignment explanation
Indices: 7522--7588 Score: 73
Period size: 18 Copynumber: 3.7 Consensus size: 18
7512 CATTTTGGGC
7522 TTAAATTTAATTTAAAGT
1 TTAAATTTAATTTAAAGT
** *
7540 TTAAACTTTTCTTTTAAGT
1 TTAAA-TTTAATTTAAAGT
*
7559 TTAAAATTAATTTAAA-T
1 TTAAATTTAATTTAAAGT
7576 TTAAAATTTAATT
1 TT-AAATTTAATT
7589 AATTAAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 21 0.54
19 15 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (18 bp):
TTAAATTTAATTTAAAGT
Found at i:7578 original size:17 final size:18
Alignment explanation
Indices: 7524--7588 Score: 69
Period size: 17 Copynumber: 3.6 Consensus size: 18
7514 TTTTGGGCTT
7524 AAATTTAATTTAAAGTTTA
1 AAATTTAATTTAAA-TTTA
* ** *
7543 AACTTTTCTTTTAAGTTTA
1 AA-ATTTAATTTAAATTTA
7562 AAA-TTAATTTAAATTTA
1 AAATTTAATTTAAATTTA
7579 AAATTTAATT
1 AAATTTAATT
7589 AATTAAAAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
17 14 0.39
18 6 0.17
19 8 0.22
20 8 0.22
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATTTAATTTAAATTTA
Found at i:7660 original size:21 final size:21
Alignment explanation
Indices: 7636--7686 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
7626 ATCCAAATTA
7636 GGCCCAAATGCTAACCTAAAT
1 GGCCCAAATGCTAACCTAAAT
7657 GGCCCAAATGCTAACCTAAAT
1 GGCCCAAATGCTAACCTAAAT
7678 GGCCCAAAT
1 GGCCCAAAT
7687 CGGCCCAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (21 bp):
GGCCCAAATGCTAACCTAAAT
Found at i:8321 original size:12 final size:12
Alignment explanation
Indices: 8304--8373 Score: 60
Period size: 12 Copynumber: 6.1 Consensus size: 12
8294 TCAAAATGTC
8304 ATTAATAATATT
1 ATTAATAATATT
8316 ATTAAT--TATT
1 ATTAATAATATT
8326 ATGGTAATAATA--
1 AT--TAATAATATT
*
8338 A-TAATAATAAT
1 ATTAATAATATT
* *
8349 ATTACTAATATC
1 ATTAATAATATT
8361 ATTAATAATATT
1 ATTAATAATATT
8373 A
1 A
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
9 8 0.17
10 6 0.13
11 1 0.02
12 29 0.63
14 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (12 bp):
ATTAATAATATT
Done.