Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003303.1 Kokia drynarioides strain JFW-HI SEQ_115982, 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: 12948
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Found at i:42 original size:25 final size:23
Alignment explanation
Indices: 2--84 Score: 105
Period size: 23 Copynumber: 3.5 Consensus size: 23
1 A
*
2 CTAATCAGAGAGCACACAAAGTG
1 CTAATCAGAGAGCACACACAGTG
25 CTAATCAGAGAGCACACACAGTG
1 CTAATCAGAGAGCACACACAGTG
*
48 CTAATAACAGAGAGCACGAGAC-GTG
1 CTAAT--CAGAGAGCAC-ACACAGTG
*
73 CTAAACAGAGAG
1 CTAATCAGAGAG
85 TGCTAGTGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
23 34 0.63
25 17 0.31
26 3 0.06
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CTAATCAGAGAGCACACACAGTG
Found at i:562 original size:11 final size:11
Alignment explanation
Indices: 535--564 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
525 TCAATCTCTA
535 ATAATTTTTCT
1 ATAATTTTTCT
546 AT-ATTTTTCT
1 ATAATTTTTCT
556 ATAATTTTT
1 ATAATTTTT
565 AAAAGTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (11 bp):
ATAATTTTTCT
Found at i:4285 original size:23 final size:23
Alignment explanation
Indices: 4248--4301 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
4238 ATTTCACTAT
4248 TTTATAATATATTTA-AAATTAATA
1 TTTATAATATATTTATAAA-TAA-A
*
4272 TTTAT-ATATTTTTATAAATAAA
1 TTTATAATATATTTATAAATAAA
4294 TTTA-AATA
1 TTTATAATA
4302 AATATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 8 0.30
23 11 0.41
24 8 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTATAATATATTTATAAATAAA
Found at i:12495 original size:25 final size:26
Alignment explanation
Indices: 12444--12495 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
12434 GAGGAACACG
*
12444 AAGTGGCGGCACCAATGGAGGGTTTTT
1 AAGTGGCGGCACCAA-GGAGGGGTTTT
*
12471 AAGTGGCGGCACTAA-GAGGGGTTTT
1 AAGTGGCGGCACCAAGGAGGGGTTTT
12496 GCCACTTGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 9 0.39
27 14 0.61
ACGTcount: A:0.23, C:0.13, G:0.38, T:0.25
Consensus pattern (26 bp):
AAGTGGCGGCACCAAGGAGGGGTTTT
Found at i:12741 original size:37 final size:38
Alignment explanation
Indices: 12652--12742 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 38
12642 GGAGACCAAC
*
12652 GAAAATTGAAGAAAAAAAGAAAGAAAAAAGGGAAAGAAA
1 GAAAA-TGAAAAAAAAAAGAAAGAAAAAAGGGAAAGAAA
* * * * *
12691 G-AAATAAATAAAAAAAAG-AAGGAAGAAGGGGAAGAAG
1 GAAAATGAA-AAAAAAAAGAAAGAAAAAAGGGAAAGAAA
12728 GAAAATGAAAAAAAA
1 GAAAATGAAAAAAAA
12743 GGTAATGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
37 25 0.58
38 17 0.40
39 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.05
Consensus pattern (38 bp):
GAAAATGAAAAAAAAAAGAAAGAAAAAAGGGAAAGAAA
Found at i:12913 original size:12 final size:12
Alignment explanation
Indices: 12896--12921 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12886 TTTAAGTATG
12896 ATTAATTTTAAA
1 ATTAATTTTAAA
12908 ATTAATTTTAAA
1 ATTAATTTTAAA
12920 AT
1 AT
12922 ATTTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTAATTTTAAA
Done.