Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013548.1 Kokia drynarioides strain JFW-HI SEQ_128574, 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: 14765
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.33
Warning! 169 characters in sequence are not A, C, G, or T
Found at i:486 original size:17 final size:18
Alignment explanation
Indices: 450--542 Score: 84
Period size: 17 Copynumber: 5.3 Consensus size: 18
440 AATAATTTTT
*
450 TTTAAATTTGAAAATAAA
1 TTTAAATTTCAAAATAAA
* *
468 TTTAAACTT-AAATTAAA
1 TTTAAATTTCAAAATAAA
* *
485 TTTAAA-TTCAAGACAAA
1 TTTAAATTTCAAAATAAA
502 TTTAAATTT-AAAATAAA
1 TTTAAATTTCAAAATAAA
* ** *
519 TTCAAATTTTTAAACAAA
1 TTTAAATTTCAAAATAAA
537 TTTAAA
1 TTTAAA
543 GGGAGTTTGG
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
16 2 0.03
17 38 0.62
18 21 0.34
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (18 bp):
TTTAAATTTCAAAATAAA
Found at i:524 original size:23 final size:23
Alignment explanation
Indices: 480--527 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
470 TAAACTTAAA
* *
480 TTAAATTTAAATTCAAGACAAAT
1 TTAAATTTAAAATAAAGACAAAT
**
503 TTAAATTTAAAATAAATTCAAAT
1 TTAAATTTAAAATAAAGACAAAT
526 TT
1 TT
528 TTAAACAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATTTAAAATAAAGACAAAT
Found at i:2015 original size:27 final size:27
Alignment explanation
Indices: 1985--2045 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
1975 CCAAGAATTC
*
1985 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
**
2012 TATTAAAGGGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
2039 TCATTAA
1 T-ATTAA
2046 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Found at i:5995 original size:16 final size:17
Alignment explanation
Indices: 5958--5996 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
5948 TGAATTTAAG
5958 AAAT-GAAAGAGTAGTT
1 AAATGGAAAGAGTAGTT
5974 --ATGGAAAGAGTA-TT
1 AAATGGAAAGAGTAGTT
5988 AAATGGAAA
1 AAATGGAAA
5997 AGTGCACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (17 bp):
AAATGGAAAGAGTAGTT
Found at i:7260 original size:27 final size:27
Alignment explanation
Indices: 7230--7290 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
7220 CCAAGAATTC
*
7230 TATTAAAAAGAGGATCGAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
**
7257 TATTAAAGGGAGGATCAAAGGAAACAA
1 TATTAAAAAGAGGATCAAAGGAAACAA
7284 TCATTAA
1 T-ATTAA
7291 TTGAAAATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.52, C:0.08, G:0.21, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAGGATCAAAGGAAACAA
Found at i:11240 original size:16 final size:17
Alignment explanation
Indices: 11203--11241 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
11193 TGAATTTAAG
11203 AAAT-GAAAGAGTAGTT
1 AAATGGAAAGAGTAGTT
11219 --ATGGAAAGAGTA-TT
1 AAATGGAAAGAGTAGTT
11233 AAATGGAAA
1 AAATGGAAA
11242 AGTGCACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (17 bp):
AAATGGAAAGAGTAGTT
Done.