Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01006998.1 Kokia drynarioides strain JFW-HI SEQ_121604, 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: 42207
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Found at i:1021 original size:2 final size:2
Alignment explanation
Indices: 1014--1045 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1004 ATTCTTTCCA
1014 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1046 TAATAAACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8211 original size:50 final size:53
Alignment explanation
Indices: 8143--8244 Score: 129
Period size: 53 Copynumber: 2.0 Consensus size: 53
8133 ATATTTATCG
* * * *
8143 ATACTTTTAAACAATTTTA-GTTTA-ATTTTTA-ATTTTTTAATAAATTATAT
1 ATACATTTAAACAATTTTACATCTATATTTATATATTTTTTAATAAATTATAT
* *
8193 ATACATTTAAATATTTTTACATCTATATTTATATATTTTTTAATAAATTATA
1 ATACATTTAAACAATTTTACATCTATATTTATATATTTTTTAATAAATTATA
8245 CATTACTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
50 16 0.37
51 3 0.07
52 6 0.14
53 18 0.42
ACGTcount: A:0.39, C:0.05, G:0.01, T:0.55
Consensus pattern (53 bp):
ATACATTTAAACAATTTTACATCTATATTTATATATTTTTTAATAAATTATAT
Found at i:9767 original size:20 final size:20
Alignment explanation
Indices: 9703--9773 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
9693 ATATAGAAAT
9703 TAAAAAAAT-TAAAA-ATAGA
1 TAAAAAAATATAAAATATA-A
* *
9722 GAAAAAAATATAAAATTACAA
1 TAAAAAAATATAAAA-TATAA
* *
9743 AAAAAAAATATAAAATATAT
1 TAAAAAAATATAAAATATAA
*
9763 TAAAAACATAT
1 TAAAAAAATAT
9774 TAGAATATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 8 0.19
20 17 0.40
21 15 0.36
22 2 0.05
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (20 bp):
TAAAAAAATATAAAATATAA
Found at i:10204 original size:17 final size:17
Alignment explanation
Indices: 10182--10269 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
10172 TTTTTTTACT
*
10182 AATTTTAATATCTTTGC
1 AATTTTAATATTTTTGC
**
10199 AATTTTAAATATTTTTAA
1 AATTTT-AATATTTTTGC
10217 AATTTTAA-A-TTTT--
1 AATTTTAATATTTTTGC
*
10230 AATTTT-ATAATTTTTCC
1 AATTTTAAT-ATTTTTGC
*
10247 TATTTTAATATTTTTGC
1 AATTTTAATATTTTTGC
10264 AATTTT
1 AATTTT
10270 TAAAGATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
12 1 0.02
13 6 0.10
14 1 0.02
15 8 0.14
16 1 0.02
17 25 0.43
18 16 0.28
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (17 bp):
AATTTTAATATTTTTGC
Found at i:10221 original size:65 final size:65
Alignment explanation
Indices: 10159--10279 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 65
10149 TGTAATTTTA
* *
10159 TAAAATTT-TCTTAT-TTTTTTACTAATTTTAATATCTTTGCAA-TTTTAAATATTTTTAAAATT
1 TAAAATTTATCTTATAATTTTTACT-ATTTTAATATCTTTGCAATTTTTAAAGATTTTTAAAATT
10221 T
65 T
* * * *
10222 TAAATTTTAATTTTATAATTTTTCCTATTTTAATATTTTTGCAATTTTTAAAGATTTT
1 TAAAATTT-ATCTTATAATTTTTACTATTTTAATATCTTTGCAATTTTTAAAGATTTT
10280 AAGGGTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
63 7 0.15
65 22 0.46
66 19 0.40
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (65 bp):
TAAAATTTATCTTATAATTTTTACTATTTTAATATCTTTGCAATTTTTAAAGATTTTTAAAATTT
Found at i:11164 original size:30 final size:28
Alignment explanation
Indices: 11118--11176 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
11108 TAAATTTGTA
11118 AAAAGTTATTAAAATTTATAAGAATATTAAAT
1 AAAAGTTA-TAAAATTTA-AA-AATA-TAAAT
11150 AAAAGTTA-AAAATTTAAAAATATAAAT
1 AAAAGTTATAAAATTTAAAAATATAAAT
11177 TACTAGAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 5 0.19
28 4 0.15
29 2 0.07
30 8 0.30
32 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (28 bp):
AAAAGTTATAAAATTTAAAAATATAAAT
Found at i:14666 original size:7 final size:7
Alignment explanation
Indices: 14654--14682 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
14644 CTGTCCATTC
14654 TCTCTCT
1 TCTCTCT
14661 TCTCTCT
1 TCTCTCT
14668 TCTCTCT
1 TCTCTCT
14675 TCTCTCT
1 TCTCTCT
14682 T
1 T
14683 GGCTTGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTCTCT
Done.