Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012621.1 Kokia drynarioides strain JFW-HI SEQ_127630, 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: 6522
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Found at i:292 original size:41 final size:40
Alignment explanation
Indices: 185--375 Score: 186
Period size: 41 Copynumber: 4.6 Consensus size: 40
175 ACTTGGTGTA
*** * *
185 TGAATAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAA-AT
1 TGAATAAGGAAGACTCATGTCTCGAAATGAGAAT-A-AATTT
*
226 TGTATAAATGGAAGACTCATGTCTCGAAATGAGAATAAGATTT
1 TGAAT-AA-GGAAGACTCATGTCTCGAAATGAGAATAA-ATTT
* * * *
269 TGACTAAGGAAGAATCATGTCTCGAAATGAGAACAATATTA
1 TGAATAAGGAAGACTCATGTCTCGAAATGAGAATAA-ATTT
* * *
310 TGAATAAAGAAGACTCGTGTCTTGAAATGAGAATGAAATTT
1 TGAATAAGGAAGACTCATGTCTCGAAATGAGAAT-AAATTT
*
351 TGATTAAGGAAGACTCATGTCTCGA
1 TGAATAAGGAAGACTCATGTCTCGA
376 GTTGAGAACA
Statistics
Matches: 122, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
41 87 0.71
42 8 0.07
43 27 0.22
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (40 bp):
TGAATAAGGAAGACTCATGTCTCGAAATGAGAATAAATTT
Found at i:343 original size:82 final size:82
Alignment explanation
Indices: 236--419 Score: 235
Period size: 82 Copynumber: 2.2 Consensus size: 82
226 TGTATAAATG
236 GAAGACTCATGTCTCGAAATGAGAAT-AAGATTTTGACTAAGGAAGAATCATGTCTCGAAATGAG
1 GAAGACTCATGTCTCGAAATGAGAATGAA-ATTTTGACTAAGGAAGAATCATGTCTCGAAATGAG
300 AACAATATTATGAATAAA
65 AACAATATTATGAATAAA
* * * * **
318 GAAGACTCGTGTCTTGAAATGAGAATGAAATTTTGATTAAGGAAGACTCATGTCTCGAGTTGAGA
1 GAAGACTCATGTCTCGAAATGAGAATGAAATTTTGACTAAGGAAGAATCATGTCTCGAAATGAGA
* * **
383 ACAAGAATATGGTTAAA
66 ACAATATTATGAATAAA
* *
400 GGAAGACTTATGACTCGAAA
1 -GAAGACTCATGTCTCGAAA
420 GAGCATAAGG
Statistics
Matches: 86, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
82 69 0.80
83 17 0.20
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (82 bp):
GAAGACTCATGTCTCGAAATGAGAATGAAATTTTGACTAAGGAAGAATCATGTCTCGAAATGAGA
ACAATATTATGAATAAA
Found at i:382 original size:41 final size:42
Alignment explanation
Indices: 189--419 Score: 184
Period size: 41 Copynumber: 5.5 Consensus size: 42
179 GGTGTATGAA
*** * **
189 TAAGGAAGACTCATGTCTCGGGTTGAGCATG-AGAAATTGTAT
1 TAAGGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTG-AT
* *
231 AAATGGAAGACTCATGTCTCGAAATGAGAAT-AAGATTTTGAC
1 TAA-GGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTGAT
* * * * *
273 TAAGGAAGAATCATGTCTCGAAATGAGAA-CAATATTATGAA
1 TAAGGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTGAT
* * *
314 TAAAGAAGACTCGTGTCTTGAAATGAGAATGAA-ATTTTGAT
1 TAAGGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTGAT
** * * * *
355 TAAGGAAGACTCATGTCTCGAGTTGAGAA-CAAGAATATGGT
1 TAAGGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTGAT
* *
396 TAAAGGAAGACTTATGACTCGAAA
1 T-AAGGAAGACTCATGTCTCGAAA
420 GAGCATAAGG
Statistics
Matches: 150, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
40 2 0.01
41 94 0.63
42 25 0.17
43 29 0.19
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.26
Consensus pattern (42 bp):
TAAGGAAGACTCATGTCTCGAAATGAGAATGAAGATTTTGAT
Found at i:4785 original size:19 final size:19
Alignment explanation
Indices: 4761--4822 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
4751 ATGGCAAAAT
4761 AATATATATAAAGAATAAA
1 AATATATATAAAGAATAAA
* *
4780 AATATA-AT-ACGCATTAAA
1 AATATATATAAAG-AATAAA
*
4798 AATATATATAAAGAATAGA
1 AATATATATAAAGAATAAA
4817 AATATA
1 AATATA
4823 ATATGTAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 2 0.06
18 13 0.37
19 18 0.51
20 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.27
Consensus pattern (19 bp):
AATATATATAAAGAATAAA
Found at i:4840 original size:37 final size:37
Alignment explanation
Indices: 4761--4843 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 37
4751 ATGGCAAAAT
*
4761 AATATATATAAAGAATAAAAATATAATACGCATTAAA
1 AATATATATAAAGAATAAAAATATAATACGCAATAAA
* * * *
4798 AATATATATAAAGAATAGAAATATAATATGTAATATA
1 AATATATATAAAGAATAAAAATATAATACGCAATAAA
*
4835 TATATATAT
1 AATATATAT
4844 TGAATAATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (37 bp):
AATATATATAAAGAATAAAAATATAATACGCAATAAA
Found at i:4975 original size:40 final size:39
Alignment explanation
Indices: 4893--4979 Score: 110
Period size: 39 Copynumber: 2.3 Consensus size: 39
4883 AAAATATTTA
*
4893 ATATATATAAAGTAAAAATAAACTAAGTATTGTAAAGAT
1 ATATATATAAAGTAAAAATAAACTAAATATTGTAAAGAT
4932 ATATATATAAAGAATAAAAAT-AAC-AGAATATTG-AAAG-T
1 ATATATATAAAG--TAAAAATAAACTA-AATATTGTAAAGAT
4970 ATATATATAA
1 ATATATATAA
4980 GTGCTGGGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
38 11 0.25
39 17 0.39
40 9 0.20
41 7 0.16
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (39 bp):
ATATATATAAAGTAAAAATAAACTAAATATTGTAAAGAT
Found at i:5076 original size:29 final size:29
Alignment explanation
Indices: 5019--5078 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
5009 GTTATTTTGG
*
5019 TGCAAGAAAAGTAAATGTATAAATTTAAA
1 TGCAAGAAAAGTAAATGTATAAATGTAAA
* *
5048 TGCAAGAAAA-TAAATTTGTAAATAGTAAA
1 TGCAAGAAAAGTAAATGTATAAAT-GTAAA
5077 TG
1 TG
5079 GGAAGAGTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.53, C:0.03, G:0.15, T:0.28
Consensus pattern (29 bp):
TGCAAGAAAAGTAAATGTATAAATGTAAA
Done.