Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007005.1 Kokia drynarioides strain JFW-HI SEQ_121611, 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: 12281
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:2018 original size:4 final size:4
Alignment explanation
Indices: 2011--2060 Score: 50
Period size: 4 Copynumber: 12.5 Consensus size: 4
2001 ATACATGGAC
* *
2011 AATA AATA AATA AATA AAT- AATA CAACA ATTA AATA AA-A AATA TAATA
1 AATA AATA AATA AATA AATA AATA -AATA AATA AATA AATA AATA -AATA
2059 AA
1 AA
2061 AATGATGATA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 6 0.16
4 25 0.66
5 7 0.18
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:2279 original size:13 final size:13
Alignment explanation
Indices: 2230--2284 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2220 AAAAGTACTA
2230 AAAATGAACAAAAT
1 AAAA-GAACAAAAT
* * *
2244 -AAACAATAAATT
1 AAAAGAACAAAAT
*
2256 AAAATAA-AAAAT
1 AAAAGAACAAAAT
2268 AAAAGAACAAAAT
1 AAAAGAACAAAAT
2281 AAAA
1 AAAA
2285 ACAAACAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
12 16 0.48
13 17 0.52
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (13 bp):
AAAAGAACAAAAT
Found at i:2456 original size:24 final size:24
Alignment explanation
Indices: 2406--2458 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2396 ATAAGCAAAT
*
2406 TAAAGGCATAAATTAAAAAAGGGAA
1 TAAAGGCATAAATTAAAAAA-GAAA
*
2431 TAAAGGCTTAAATTAAAACAA-AAA
1 TAAAGGCATAAATTAAAA-AAGAAA
2455 TAAA
1 TAAA
2459 AATGCAGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.24
25 17 0.68
26 2 0.08
ACGTcount: A:0.62, C:0.06, G:0.13, T:0.19
Consensus pattern (24 bp):
TAAAGGCATAAATTAAAAAAGAAA
Found at i:4248 original size:16 final size:15
Alignment explanation
Indices: 4195--4251 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
4185 AAAGAACTCT
*
4195 TTAAAATTAAATAAAA
1 TTAAAAATAAA-AAAA
*
4211 ATAAAAATAAAAACAA
1 TTAAAAATAAAAA-AA
4227 TTTTAAAAATAAACAAAA
1 --TTAAAAATAAA-AAAA
4245 TTAAAAA
1 TTAAAAA
4252 ATTCAGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 2 0.06
16 18 0.53
18 12 0.35
19 2 0.06
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
TTAAAAATAAAAAAA
Found at i:4492 original size:32 final size:33
Alignment explanation
Indices: 4438--4504 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 33
4428 CGTTGCGGGT
*
4438 ACAAAACTCAAAATCATCCCCACCCCACGACCC
1 ACAAAACTCAAAATCATCCCCACCCCACCACCC
* *
4471 ACAAGACT-AAAATCATTCCCACCCCACCACCC
1 ACAAAACTCAAAATCATCCCCACCCCACCACCC
4503 AC
1 AC
4505 GTGAGTTCCC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
32 24 0.77
33 7 0.23
ACGTcount: A:0.39, C:0.48, G:0.03, T:0.10
Consensus pattern (33 bp):
ACAAAACTCAAAATCATCCCCACCCCACCACCC
Found at i:5150 original size:20 final size:20
Alignment explanation
Indices: 5113--5173 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
5103 TTATTATATT
* * *
5113 ATGCGAGGTGGGCGGGGATG
1 ATGCGAGGCGAGCAGGGATG
5133 ATGCGAGGCGAGCAGGGATG
1 ATGCGAGGCGAGCAGGGATG
*
5153 -TGGCGAGGCGAGTAGGGATG
1 AT-GCGAGGCGAGCAGGGATG
5173 A
1 A
5174 GGCGGGTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.03
20 34 0.97
ACGTcount: A:0.21, C:0.11, G:0.54, T:0.13
Consensus pattern (20 bp):
ATGCGAGGCGAGCAGGGATG
Found at i:5177 original size:20 final size:20
Alignment explanation
Indices: 5127--5177 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5117 GAGGTGGGCG
*
5127 GGGATGATGCGAGGCGAGCA
1 GGGATGAGGCGAGGCGAGCA
* *
5147 GGGATGTGGCGAGGCGAGTA
1 GGGATGAGGCGAGGCGAGCA
5167 GGGATGAGGCG
1 GGGATGAGGCG
5178 GGTACAAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.12, G:0.55, T:0.12
Consensus pattern (20 bp):
GGGATGAGGCGAGGCGAGCA
Found at i:5740 original size:43 final size:46
Alignment explanation
Indices: 5641--5745 Score: 110
Period size: 43 Copynumber: 2.4 Consensus size: 46
5631 TATTGACTCT
* ** *
5641 AAAATTTTTTTATATTTTTAAATTCATTTTTATTTTTTAAAATTTA
1 AAAAATTTTTTATATTTTTAAATTCATTTTTATTTTAAAAAATATA
* *
5687 AAAAAGTTTTTAT-TTTTT-TATTC-TTTTTATTTTAAAAAATATA
1 AAAAATTTTTTATATTTTTAAATTCATTTTTATTTTAAAAAATATA
* *
5730 TATAATTTTTTA-ATTT
1 AAAAATTTTTTATATTT
5746 CTTTGTTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
43 29 0.59
44 4 0.08
45 5 0.10
46 11 0.22
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (46 bp):
AAAAATTTTTTATATTTTTAAATTCATTTTTATTTTAAAAAATATA
Found at i:7133 original size:22 final size:20
Alignment explanation
Indices: 7097--7137 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
7087 TATATTGATT
7097 ATAAATAGGATTAATTAAGG
1 ATAAATAGGATTAATTAAGG
7117 ATAAATAAGTGATTAATTAAG
1 ATAAAT-AG-GATTAATTAAG
7138 TTAATCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 2 0.11
22 11 0.58
ACGTcount: A:0.51, C:0.00, G:0.17, T:0.32
Consensus pattern (20 bp):
ATAAATAGGATTAATTAAGG
Found at i:8916 original size:21 final size:21
Alignment explanation
Indices: 8890--8941 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
8880 GTTCATAGTA
8890 GTATCAGTAGTCTGAGTACTT
1 GTATCAGTAGTCTGAGTACTT
8911 GTATCAGTAGTCTGAGTACTT
1 GTATCAGTAGTCTGAGTACTT
8932 GTATCAGTAG
1 GTATCAGTAG
8942 AAGTTGTAGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (21 bp):
GTATCAGTAGTCTGAGTACTT
Found at i:9477 original size:53 final size:53
Alignment explanation
Indices: 9397--9502 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
9387 AATGATTTAG
9397 AAGTACATGCCATATGAACCTGTAATAGTGTGATATAGATGGATTCGATCTAA
1 AAGTACATGCCATATGAACCTGTAATAGTGTGATATAGATGGATTCGATCTAA
*
9450 AAGTACATGCCATATGAACTTGTAATAGTGTGATATAGATGGATTCGATCTAA
1 AAGTACATGCCATATGAACCTGTAATAGTGTGATATAGATGGATTCGATCTAA
9503 CTATTGTTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (53 bp):
AAGTACATGCCATATGAACCTGTAATAGTGTGATATAGATGGATTCGATCTAA
Done.