Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010091.1 Kokia drynarioides strain JFW-HI SEQ_124872, 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: 17310
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:902 original size:18 final size:17
Alignment explanation
Indices: 854--903 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
844 TGAGGCAGAT
*
854 GAAGAAGAAAGAAAAGAA
1 GAAGAA-AAAGAAGAGAA
*
872 GAAGAAAAAGAAGGGAA
1 GAAGAAAAAGAAGAGAA
889 GGAAGAAAAAGAAGA
1 -GAAGAAAAAGAAGA
904 TGTTGCCCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
GAAGAAAAAGAAGAGAA
Found at i:5193 original size:24 final size:23
Alignment explanation
Indices: 5160--5210 Score: 84
Period size: 24 Copynumber: 2.2 Consensus size: 23
5150 ATTCATCTCT
*
5160 TATTAATTTGCTCTGACATTTTA
1 TATTAATTTGCACTGACATTTTA
5183 TATTACATTTGCACTGACATTTTA
1 TATTA-ATTTGCACTGACATTTTA
5207 TATT
1 TATT
5211 CTTAACCTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (23 bp):
TATTAATTTGCACTGACATTTTA
Found at i:6143 original size:28 final size:28
Alignment explanation
Indices: 6111--6170 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
6101 TCCACAAAAT
6111 AAGGCAAATTATGTGCTTGTCAAAGTGC
1 AAGGCAAATTATGTGCTTGTCAAAGTGC
*
6139 AAGGCAAATTATGTGTTTGTCAAAGTGC
1 AAGGCAAATTATGTGCTTGTCAAAGTGC
6167 AAGG
1 AAGG
6171 ATGAAGTGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (28 bp):
AAGGCAAATTATGTGCTTGTCAAAGTGC
Found at i:9479 original size:24 final size:24
Alignment explanation
Indices: 9446--9492 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9436 GTCAAGAGTA
*
9446 AAAATTGTCAGTGCAAATGTAATAC
1 AAAATTGTCAGAGCAAAT-TAATAC
9471 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
9493 AAAGATGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
24 12 0.57
25 4 0.19
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAC
Found at i:11052 original size:2 final size:2
Alignment explanation
Indices: 11039--11072 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
11029 TTGTATAATA
* *
11039 AT AT AC AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11073 TCTTTCATCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12151 original size:3 final size:3
Alignment explanation
Indices: 12143--12203 Score: 83
Period size: 3 Copynumber: 20.7 Consensus size: 3
12133 GAGGCAATTC
12143 CTT CTT CTT CTT CTT CTT CTT CTT C-T CTT CTT -TT CTCT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T CTT CTT
12187 C-T CTT GCTT CTT CTT CT
1 CTT CTT -CTT CTT CTT CT
12204 ACTACAATAC
Statistics
Matches: 53, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
2 6 0.11
3 41 0.77
4 6 0.11
ACGTcount: A:0.00, C:0.34, G:0.02, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:12712 original size:7 final size:7
Alignment explanation
Indices: 12700--12725 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12690 GCGACTTTCT
12700 TTTTCCC
1 TTTTCCC
12707 TTTTCCC
1 TTTTCCC
12714 TTTTCCC
1 TTTTCCC
12721 TTTTC
1 TTTTC
12726 TTTCTTTGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (7 bp):
TTTTCCC
Done.