Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000639.1 Kokia drynarioides strain JFW-HI SEQ_111608, 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: 7862
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.33
Warning! 21 characters in sequence are not A, C, G, or T
Found at i:515 original size:6 final size:6
Alignment explanation
Indices: 494--554 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
484 TTCTATTTAT
*
494 TTTAAA CTTAAA -TTAAA TTTAAA TTTTGAAA --TAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTT-AAA TTTAAA TTTAAA TTTAAA
*
541 -ATAAA TTTAAA TTT
1 TTTAAA TTTAAA TTT
555 TTAAGCAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
4 3 0.07
5 10 0.22
6 27 0.59
7 3 0.07
8 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:528 original size:18 final size:18
Alignment explanation
Indices: 501--587 Score: 113
Period size: 18 Copynumber: 4.9 Consensus size: 18
491 TATTTTAAAC
*
501 TTAAATTAAATTTAAATT
1 TTAAAATAAATTTAAATT
*
519 TTGAAATAAATTTAAA-T
1 TTAAAATAAATTTAAATT
536 TTAAAATAAATTTAAATT
1 TTAAAATAAATTTAAATT
* ** *
554 TTTAAGCAAATTTAATTT
1 TTAAAATAAATTTAAATT
572 TTAAAATAAATTTAAA
1 TTAAAATAAATTTAAA
588 GGGAGTATGG
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.28
18 41 0.72
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (18 bp):
TTAAAATAAATTTAAATT
Found at i:540 original size:35 final size:35
Alignment explanation
Indices: 494--587 Score: 125
Period size: 35 Copynumber: 2.7 Consensus size: 35
484 TTCTATTTAT
* * *
494 TTTAAACTTAAATTAAATTTAAATTTTGAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTTGAAACAAA
* *
529 TTTAAATTTAAAATAAATTTAAATTTTTAAGCAAA
1 TTTAAATTTAAAATAAATTTAAATTTTGAAACAAA
*
564 TTTAATTTTTAAAATAAATTTAAA
1 TTTAA-ATTTAAAATAAATTTAAA
588 GGGAGTATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 35 0.67
36 17 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (35 bp):
TTTAAATTTAAAATAAATTTAAATTTTGAAACAAA
Found at i:5532 original size:47 final size:47
Alignment explanation
Indices: 5480--5574 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
5470 TGTCGGTAAA
5480 ACCATTCGGTGTATAAATATATATAAAAAATCTTAATTTACAAATTT
1 ACCATTCGGTGTATAAATATATATAAAAAATCTTAATTTACAAATTT
5527 ACCATTCGGTGTATAAATATATATAAAAAATCTTAATTTACAAATTT
1 ACCATTCGGTGTATAAATATATATAAAAAATCTTAATTTACAAATTT
5574 A
1 A
5575 TACTTAAAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (47 bp):
ACCATTCGGTGTATAAATATATATAAAAAATCTTAATTTACAAATTT
Found at i:6869 original size:31 final size:32
Alignment explanation
Indices: 6818--6885 Score: 111
Period size: 31 Copynumber: 2.1 Consensus size: 32
6808 ATGTATTTAT
*
6818 TTTTAAATATATATGATTAAATTAAAATTAAAA
1 TTTTAAATATACAT-ATTAAATTAAAATTAAAA
6851 TTTTAAATATACAT-TTAAATTAAAATTAAAA
1 TTTTAAATATACATATTAAATTAAAATTAAAA
6882 TTTT
1 TTTT
6886 TTACGTGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 21 0.62
33 13 0.38
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (32 bp):
TTTTAAATATACATATTAAATTAAAATTAAAA
Found at i:7110 original size:83 final size:83
Alignment explanation
Indices: 6971--7139 Score: 293
Period size: 83 Copynumber: 2.0 Consensus size: 83
6961 TATCTGGAAT
* *
6971 GGTAGTATGAACTATTGTATGATGATAGCCTACATAGACTGCTCATAAAGGTGTAGGGCCCCGTT
1 GGTAGTATGAACTATTGTATGATGATAGCCTACAGAGACTGCTCATAAAGGTGTAGGGCCCAGTT
7036 AAGAAAATAATTGTAGTG
66 AAGAAAATAATTGTAGTG
* * *
7054 GGTAGTATGAATTATTGTATGATGATAGCGTACAGAGACTGCTCATAAAGGTGTAGGGCGCAGTT
1 GGTAGTATGAACTATTGTATGATGATAGCCTACAGAGACTGCTCATAAAGGTGTAGGGCCCAGTT
7119 AAGAAAATAATTGTAGTG
66 AAGAAAATAATTGTAGTG
7137 GGT
1 GGT
7140 TGAATCACTT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.29
Consensus pattern (83 bp):
GGTAGTATGAACTATTGTATGATGATAGCCTACAGAGACTGCTCATAAAGGTGTAGGGCCCAGTT
AAGAAAATAATTGTAGTG
Found at i:7629 original size:16 final size:17
Alignment explanation
Indices: 7592--7636 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
7582 ATTTATTAAA
7592 ATAAT-ATTTAAATCAT
1 ATAATAATTTAAATCAT
7608 ATAATAATTTAAAT-ACT
1 ATAATAATTTAAATCA-T
7625 A-AATAATTTAAA
1 ATAATAATTTAAA
7637 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
ATAATAATTTAAATCAT
Done.