Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008370.1 Kokia drynarioides strain JFW-HI SEQ_123037, 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: 21938
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.34
Found at i:1491 original size:44 final size:45
Alignment explanation
Indices: 1406--1545 Score: 185
Period size: 44 Copynumber: 3.0 Consensus size: 45
1396 ATAAAAATTT
*
1406 AAATTTTATAAATTTATAAATATATATAAATATATAAAAGAACTA
1 AAATTTTATAAATTTATAAATAAATATAAATATATAAAAGAACTA
*
1451 AAATTTTATAAGTTTATAAA-AAATATAAATATATAAAAGAACTA
1 AAATTTTATAAATTTATAAATAAATATAAATATATAAAAGAACTA
* *
1495 CAAA-TTAATAAATTTATAAAATAATATGTATAAATATATAAAAGAAATA
1 -AAATTTTATAAATTTAT-AAATAA-A--TATAAATATATAAAAGAACTA
1544 AA
1 AA
1546 TTCACAACTA
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
44 34 0.40
45 25 0.30
46 2 0.02
47 1 0.01
48 2 0.02
49 20 0.24
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (45 bp):
AAATTTTATAAATTTATAAATAAATATAAATATATAAAAGAACTA
Found at i:6384 original size:19 final size:18
Alignment explanation
Indices: 6356--6400 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
6346 CTCTTGCAAT
* *
6356 TCAA-TCTCAACTCTCTC
1 TCAATTCTCAAATATCTC
6373 TCACATTCTCAAATATCTC
1 TCA-ATTCTCAAATATCTC
6392 TCAATTCTC
1 TCAATTCTC
6401 CCTTAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 7 0.29
19 14 0.58
ACGTcount: A:0.27, C:0.36, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAATTCTCAAATATCTC
Found at i:8294 original size:32 final size:32
Alignment explanation
Indices: 8198--8275 Score: 129
Period size: 32 Copynumber: 2.4 Consensus size: 32
8188 AGTAACTCTC
* * *
8198 CATTAACTTTTATTCCCTCACCCAAGGTGGTA
1 CATTAACTTGTATTCCATCACCCAAGTTGGTA
8230 CATTAACTTGTATTCCATCACCCAAGTTGGTA
1 CATTAACTTGTATTCCATCACCCAAGTTGGTA
8262 CATTAACTTGTATT
1 CATTAACTTGTATT
8276 GCGTCACTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.37
Consensus pattern (32 bp):
CATTAACTTGTATTCCATCACCCAAGTTGGTA
Found at i:8743 original size:18 final size:18
Alignment explanation
Indices: 8722--8776 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
8712 TAAAATTTTG
8722 TAAATTTATAAAAGTATA
1 TAAATTTATAAAAGTATA
* *
8740 TAAATATATAAAAGAACTA
1 TAAATTTATAAAAGTA-TA
* *
8759 TAATTTTATAAAATTATA
1 TAAATTTATAAAAGTATA
8777 AGAAACTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (18 bp):
TAAATTTATAAAAGTATA
Found at i:8794 original size:26 final size:28
Alignment explanation
Indices: 8736--8797 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
8726 TTTATAAAAG
*
8736 TATAT-AAATATATAAAAGAACTATAAT
1 TATATAAAATATATAAAAGAACTATAAA
* *
8763 TTTATAAAAT-TATAAGA-AACTATAAA
1 TATATAAAATATATAAAAGAACTATAAA
8789 TATATAAAA
1 TATATAAAA
8798 GAAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 16 0.53
27 10 0.33
28 4 0.13
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (28 bp):
TATATAAAATATATAAAAGAACTATAAA
Found at i:10713 original size:12 final size:12
Alignment explanation
Indices: 10696--10721 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10686 AAATTAATTT
10696 ATATATTTTTAA
1 ATATATTTTTAA
10708 ATATATTTTTAA
1 ATATATTTTTAA
10720 AT
1 AT
10722 TTTAATTTAT
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATATATTTTTAA
Found at i:10723 original size:20 final size:20
Alignment explanation
Indices: 10681--10724 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
10671 TATTTAACCC
*
10681 TTTTTAAATTAATTTATATA
1 TTTTTAAATTAATTTATAAA
*
10701 TTTTTAAA-TATATTTTTAAA
1 TTTTTAAATTA-ATTTATAAA
10721 TTTT
1 TTTT
10725 AATTTATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAAATTAATTTATAAA
Found at i:10974 original size:24 final size:24
Alignment explanation
Indices: 10929--10975 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
10919 AGTTAGTAGT
* *
10929 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGAATTGATTAGC
*
10953 ATAATATATTTTGAATTGATTAG
1 ATAATATATTTAGAATTGATTAG
10976 AATTAGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (24 bp):
ATAATATATTTAGAATTGATTAGC
Done.