Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010086.1 Kokia drynarioides strain JFW-HI SEQ_124867, 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: 46179
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Warning! 64 characters in sequence are not A, C, G, or T
Found at i:1514 original size:31 final size:31
Alignment explanation
Indices: 1479--1539 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1469 AAAATAGTCA
1479 TTGAACTATTCAAAAATTTTCATTTAAGTTT
1 TTGAACTATTCAAAAATTTTCATTTAAGTTT
* * *
1510 TTGAATTATTCCAAAATTTTTATTTAAGTT
1 TTGAACTATTCAAAAATTTTCATTTAAGTT
1540 ACTATTAGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (31 bp):
TTGAACTATTCAAAAATTTTCATTTAAGTTT
Found at i:5993 original size:20 final size:19
Alignment explanation
Indices: 5968--6020 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
5958 TTAAAAAACG
*
5968 TTTTTATATAATTCGTATAA
1 TTTTTATATAATT-GAATAA
*
5988 TTTTTATGTAATTGAATAA
1 TTTTTATATAATTGAATAA
*
6007 TGTTTCATATAATT
1 T-TTTTATATAATT
6021 ATAAAAAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 22 0.79
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (19 bp):
TTTTTATATAATTGAATAA
Found at i:9628 original size:12 final size:12
Alignment explanation
Indices: 9611--9635 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9601 ATATATTGAC
9611 TAAATTTTTTAA
1 TAAATTTTTTAA
9623 TAAATTTTTTAA
1 TAAATTTTTTAA
9635 T
1 T
9636 TATTGTACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAAATTTTTTAA
Found at i:13313 original size:20 final size:20
Alignment explanation
Indices: 13288--13327 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13278 AATGACTGTT
* *
13288 ATTCAAGCCAGTGAAGAGAA
1 ATTCAAGCCACTAAAGAGAA
13308 ATTCAAGCCACTAAAGAGAA
1 ATTCAAGCCACTAAAGAGAA
13328 GACTCTCTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (20 bp):
ATTCAAGCCACTAAAGAGAA
Found at i:14621 original size:6 final size:6
Alignment explanation
Indices: 14611--14647 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
14601 AAAAGGGAAA
*
14611 AAGATA AAGATG AAGATG AAGATG AAGATG AAGATG A
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG A
14648 GAGGTGTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.54, C:0.00, G:0.30, T:0.16
Consensus pattern (6 bp):
AAGATG
Found at i:24032 original size:10 final size:10
Alignment explanation
Indices: 24013--24053 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
24003 TTTATTAAAC
24013 ATTATAAAAAA
1 ATTAT-AAAAA
*
24024 ATTATAAAAT
1 ATTATAAAAA
24034 ATTATAAAAA
1 ATTATAAAAA
24044 ATTA-AAAAA
1 ATTATAAAAA
24053 A
1 A
24054 AAATTAATGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 6 0.21
10 17 0.61
11 5 0.18
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:24037 original size:21 final size:20
Alignment explanation
Indices: 24004--24051 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
23994 ATATATATTT
*
24004 TTATTAAACATTATAAAAAAA
1 TTATAAAACATTAT-AAAAAA
*
24025 TTATAAAATATTATAAAAAA
1 TTATAAAACATTATAAAAAA
24045 TTA-AAAA
1 TTATAAAA
24052 AAAAATTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.16
20 9 0.36
21 12 0.48
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAAAACATTATAAAAAA
Found at i:24053 original size:21 final size:21
Alignment explanation
Indices: 24013--24052 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
24003 TTTATTAAAC
*
24013 ATTATAAAAAAATTATAAAAT
1 ATTATAAAAAAATTAAAAAAT
24034 ATTAT-AAAAAATTAAAAAA
1 ATTATAAAAAAATTAAAAAA
24053 AAAATTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
ATTATAAAAAAATTAAAAAAT
Done.