Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003780.1 Kokia drynarioides strain JFW-HI SEQ_116759, 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: 17058
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:5182 original size:7 final size:7
Alignment explanation
Indices: 5166--5194 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
5156 CAAAAACCAC
5166 AAAA-AA
1 AAAAGAA
5172 AAAAGAA
1 AAAAGAA
5179 AAAAGAA
1 AAAAGAA
5186 AAAAGAA
1 AAAAGAA
5193 AA
1 AA
5195 GAAAAGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:5187 original size:14 final size:13
Alignment explanation
Indices: 5166--5199 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5156 CAAAAACCAC
5166 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
5179 AAAAGAAAAAAGAA
1 AAAA-AAAAAAGAA
5193 AAGAAAA
1 AA-AAAA
5200 GAAATCAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.21
14 13 0.68
15 2 0.11
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:13135 original size:4 final size:4
Alignment explanation
Indices: 13126--13166 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
13116 ACGCAGCATG
* * *
13126 TACA TACA TATA TACA TGCA TACA TACA CACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T
13167 CCATGCATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.24, G:0.02, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:13173 original size:88 final size:88
Alignment explanation
Indices: 13058--13230 Score: 283
Period size: 88 Copynumber: 2.0 Consensus size: 88
13048 CAACCAATAT
* * * *
13058 TACATACATACATACGTTCATATATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
1 TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
*
13123 ATGTACATACATATATACATGCA
66 ATGTACATACATACATACATGCA
* *
13146 TACATACACACATACATACATCCATGCATGGCAATACCATATGAAAATGGTGTAATAAACGTAGC
1 TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
13211 ATGTACATACATACATACAT
66 ATGTACATACATACATACAT
13231 ACATGCATGG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 78 1.00
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.26
Consensus pattern (88 bp):
TACATACACACATACATACATACATGCATGGCAATACCATATGAAAATGGTGTAATAAACGCAGC
ATGTACATACATACATACATGCA
Found at i:16064 original size:18 final size:18
Alignment explanation
Indices: 16041--16077 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16031 AAGAAAGTCC
16041 TGATTCTCCTTACTGAAA
1 TGATTCTCCTTACTGAAA
16059 TGATTCTCCTTACTGAAA
1 TGATTCTCCTTACTGAAA
16077 T
1 T
16078 CTGTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
TGATTCTCCTTACTGAAA
Found at i:16287 original size:21 final size:19
Alignment explanation
Indices: 16247--16288 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
16237 ACATCATAAT
*
16247 CAAATAAGTTAACAAGTTA
1 CAAATAAATTAACAAGTTA
16266 CAAACTAAATTAACATAGTTA
1 CAAA-TAAATTAACA-AGTTA
16287 CA
1 CA
16289 TTGAAAACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.26
Consensus pattern (19 bp):
CAAATAAATTAACAAGTTA
Done.