Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013562.1 Kokia drynarioides strain JFW-HI SEQ_128588, 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: 44957
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:5977 original size:20 final size:21
Alignment explanation
Indices: 5936--5978 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5926 TAATTTACTT
5936 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
5957 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
5977 TA
1 TA
5979 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:6503 original size:16 final size:16
Alignment explanation
Indices: 6458--6507 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
6448 TAAACCTAAC
*
6458 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
6474 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
6488 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
6504 TAAT
1 TAAT
6508 ATCACCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:6574 original size:30 final size:30
Alignment explanation
Indices: 6540--6634 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
6530 AAATGGTACA
* *
6540 AAATAAATATTTATTTTGTACCATTTTAGT
1 AAATAAATATATATTTTGTACTATTTTAGT
* * * * *
6570 AAAT-AATA-GTGTGTGGATACTATTTTGGT
1 AAATAAATATATATTTTG-TACTATTTTAGT
*
6599 ATATAAATATATATTTTGTACTATTTTAGT
1 AAATAAATATATATTTTGTACTATTTTAGT
6629 AAATAA
1 AAATAA
6635 CTCATTTTGG
Statistics
Matches: 49, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
28 4 0.08
29 17 0.35
30 24 0.49
31 4 0.08
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (30 bp):
AAATAAATATATATTTTGTACTATTTTAGT
Found at i:8424 original size:45 final size:45
Alignment explanation
Indices: 8360--8494 Score: 180
Period size: 45 Copynumber: 3.0 Consensus size: 45
8350 ATAGCTCATT
8360 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATACTC
* * * *
8405 AAGCCAAAGATATCAGCCTCAATTTGACGAGTCATCGTAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATACTC
** * * * *
8450 AAGTGAAGGATATCAGGCTGAGTTTGACGAGCCACTGCAATACTC
1 AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATACTC
8495 TACTCCTCCC
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (45 bp):
AAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGTAATACTC
Found at i:8512 original size:21 final size:21
Alignment explanation
Indices: 8486--8526 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
8476 ACGAGCCACT
*
8486 GCAATACTCTACTCCTCCCGG
1 GCAATACTATACTCCTCCCGG
8507 GCAATACTATACTCCTCCCG
1 GCAATACTATACTCCTCCCG
8527 AGAAAATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.41, G:0.12, T:0.24
Consensus pattern (21 bp):
GCAATACTATACTCCTCCCGG
Found at i:8781 original size:14 final size:14
Alignment explanation
Indices: 8759--8805 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
8749 TATTAAACCC
*
8759 TAAAACCTAAACTA
1 TAAACCCTAAACTA
*
8773 TAACCCCTAAACT-
1 TAAACCCTAAACTA
*
8786 TAAAACCCTAAATTA
1 T-AAACCCTAAACTA
8801 TAAAC
1 TAAAC
8806 ACTAGACTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:8814 original size:28 final size:28
Alignment explanation
Indices: 8759--8839 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 28
8749 TATTAAACCC
* * *
8759 TAAAA-CCTAAACTATAACCCCTAAACT
1 TAAAACCCTAAACTATAAACACTAGACT
*
8786 TAAAACCCTAAATTATAAACACTAGACT
1 TAAAACCCTAAACTATAAACACTAGACT
* **
8814 TAAAACTCTAAACCGTAAACACTAGA
1 TAAAACCCTAAACTATAAACACTAGA
8840 TTGATTAAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 5 0.11
28 40 0.89
ACGTcount: A:0.49, C:0.25, G:0.04, T:0.22
Consensus pattern (28 bp):
TAAAACCCTAAACTATAAACACTAGACT
Found at i:12816 original size:4 final size:4
Alignment explanation
Indices: 12796--12840 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
12786 AACACATTAC
* * *
12796 CTTT CCTT CCTT C-TT CTTT CTTT GTTT CTTT CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CTTT CT
12841 CGTTTATTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:26509 original size:20 final size:20
Alignment explanation
Indices: 26472--26512 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
26462 CGAATTCAAT
* **
26472 TAAATATTTTAATTATAATA
1 TAAATAGTTTAAACATAATA
26492 TAAATAGTTTAAACATAATA
1 TAAATAGTTTAAACATAATA
26512 T
1 T
26513 CTTTTATTGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TAAATAGTTTAAACATAATA
Done.