Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009386.1 Kokia drynarioides strain JFW-HI SEQ_124093, 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: 6551
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.35
Found at i:122 original size:9 final size:9
Alignment explanation
Indices: 108--141 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
98 TAAAGAAAAG
108 AAAAGAAAC
1 AAAAGAAAC
117 AAAAGAAAC
1 AAAAGAAAC
126 AAAAGAAAC
1 AAAAGAAAC
135 AAAAGAA
1 AAAAGAA
142 GGAATAGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAGAAAC
Found at i:606 original size:17 final size:18
Alignment explanation
Indices: 584--619 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
574 TAAATGAGTT
584 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
601 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
619 A
1 A
620 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:2610 original size:28 final size:28
Alignment explanation
Indices: 2573--2641 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
2563 GGCAAAATAA
*
2573 TTTTCAGAACACAT-CTCGTC-AATTTTAT
1 TTTTCAGAACACATACTC-TCAAATTAT-T
* *
2601 TTTTCAGAACCCATATTCTCAAATTATT
1 TTTTCAGAACACATACTCTCAAATTATT
2629 TTTTCAGAACACA
1 TTTTCAGAACACA
2642 ACACATCAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 28 0.80
29 7 0.20
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.41
Consensus pattern (28 bp):
TTTTCAGAACACATACTCTCAAATTATT
Found at i:2652 original size:27 final size:26
Alignment explanation
Indices: 2573--2656 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 26
2563 GGCAAAATAA
* *
2573 TTTTCAGAACACATCTCGTCAATTTTAT
1 TTTTCAGAACACAACTC-TCAATTAT-T
* *
2601 TTTTCAGAACCCATATTCTCAAATTATT
1 TTTTCAGAACACA-ACTCTC-AATTATT
*
2629 TTTTCAGAACACAACACATCAATTATT
1 TTTTCAGAACACAACTC-TCAATTATT
2656 T
1 T
2657 AGATATATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
27 10 0.22
28 29 0.63
29 7 0.15
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (26 bp):
TTTTCAGAACACAACTCTCAATTATT
Found at i:5197 original size:19 final size:19
Alignment explanation
Indices: 5173--5211 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5163 ACAATCTCTT
*
5173 ATTTTTAACTATAACTAAA
1 ATTTTTAACTATAAATAAA
*
5192 ATTTTTAATTATAAATAAA
1 ATTTTTAACTATAAATAAA
5211 A
1 A
5212 AAATATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTTTAACTATAAATAAA
Found at i:6290 original size:29 final size:29
Alignment explanation
Indices: 6248--6314 Score: 125
Period size: 29 Copynumber: 2.3 Consensus size: 29
6238 AGAGTTAAAT
*
6248 TATACAATTTCTAATTCAATTATTATACA
1 TATACAGTTTCTAATTCAATTATTATACA
6277 TATACAGTTTCTAATTCAATTATTATACA
1 TATACAGTTTCTAATTCAATTATTATACA
6306 TATACAGTT
1 TATACAGTT
6315 GGGTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (29 bp):
TATACAGTTTCTAATTCAATTATTATACA
Done.