Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012733.1 Kokia drynarioides strain JFW-HI SEQ_127744, 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: 7806
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Warning! 12 characters in sequence are not A, C, G, or T
Found at i:265 original size:30 final size:30
Alignment explanation
Indices: 229--327 Score: 105
Period size: 30 Copynumber: 3.3 Consensus size: 30
219 TAAACCTAGC
229 TAATTAATTACCAAAATATAATATAAAAAA
1 TAATTAATTACCAAAATATAATATAAAAAA
* ****
259 TAATTAATTATC-AAA-ATAATAT-CCCCA
1 TAATTAATTACCAAAATATAATATAAAAAA
*
286 TCATATTATTTACCAAAATATAATATAAAAAA
1 T-A-ATTAATTACCAAAATATAATATAAAAAA
318 TAATTAATTA
1 TAATTAATTA
328 TGAAAATAAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
27 2 0.04
28 8 0.15
29 11 0.21
30 21 0.40
31 8 0.15
32 2 0.04
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (30 bp):
TAATTAATTACCAAAATATAATATAAAAAA
Found at i:274 original size:16 final size:16
Alignment explanation
Indices: 229--278 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
219 TAAACCTAGC
*
229 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
245 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
259 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
275 TAAT
1 TAAT
279 ATCCCCATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:299 original size:59 final size:59
Alignment explanation
Indices: 231--364 Score: 241
Period size: 59 Copynumber: 2.3 Consensus size: 59
221 AACCTAGCTA
*
231 ATTAATTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
*
290 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATGAAAATAATATCCCCATCAT
1 ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
*
349 ATTATTTACTAAAATA
1 ATTATTTACCAAAATA
365 GTACAAAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 72 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (59 bp):
ATTATTTACCAAAATATAATATAAAAAATAATTAATTATCAAAATAATATCCCCATCAT
Found at i:302 original size:29 final size:29
Alignment explanation
Indices: 261--364 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
251 ATAAAAAATA
*
261 ATTAATTATCAAAATAATATCCCCATCAT
1 ATTAATTACCAAAATAATATCCCCATCAT
* ** **
290 ATTATTTACCAAAATATAATAT--AAAAAAT
1 ATTAATTACC-AAA-ATAATATCCCCATCAT
**
319 AATTAATTATGAAAATAATATCCCCATCAT
1 -ATTAATTACCAAAATAATATCCCCATCAT
* *
349 ATTATTTACTAAAATA
1 ATTAATTACCAAAATA
365 GTACAAAATA
Statistics
Matches: 54, Mismatches: 16, Indels: 10
0.68 0.20 0.12
Matches are distributed among these distances:
28 7 0.13
29 27 0.50
30 13 0.24
31 7 0.13
ACGTcount: A:0.50, C:0.13, G:0.01, T:0.36
Consensus pattern (29 bp):
ATTAATTACCAAAATAATATCCCCATCAT
Found at i:1699 original size:43 final size:43
Alignment explanation
Indices: 1629--1713 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
1619 ATTAACATGT
* *
1629 TAAATTATATTACTTGACTCGTGTTAATATGATTG-CATGTTAC
1 TAAATTATATTACTTGAATCGTATTAATAT-ATTGACATGTTAC
* * *
1672 TAAATTATATTATTTTAATCTTATTAATATATTGACATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATATTGACATGTTA
1714 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGAATCGTATTAATATATTGACATGTTAC
Found at i:2333 original size:45 final size:45
Alignment explanation
Indices: 2266--2402 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 45
2256 GCATAGCTCA
*
2266 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
2311 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * * *
2356 TCAAGGGC-AGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
1 TCAA-GCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
2401 TC
1 TC
2403 TATTCCAATA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 81 0.98
46 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Found at i:4250 original size:43 final size:43
Alignment explanation
Indices: 4180--4264 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
4170 ATTAACATGT
* *
4180 TAAATTATATTACTTGACTCGTGTTAATATGATTG-CATGTTAC
1 TAAATTATATTACTTGAATCGTATTAATAT-ATTGACATGTTAC
* * *
4223 TAAATTATATTATTTTAATCTTATTAATATATTGACATGTTA
1 TAAATTATATTACTTGAATCGTATTAATATATTGACATGTTA
4265 TTAATTGTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
42 4 0.11
43 32 0.89
ACGTcount: A:0.34, C:0.08, G:0.09, T:0.48
Consensus pattern (43 bp):
TAAATTATATTACTTGAATCGTATTAATATATTGACATGTTAC
Found at i:4858 original size:45 final size:45
Alignment explanation
Indices: 4791--4927 Score: 195
Period size: 45 Copynumber: 3.0 Consensus size: 45
4781 GCATAGCTCA
*
4791 TCAAGCCAAGGATATCAACCTCAGTTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
*
4836 TCAAGCCAAGGATATCAGCCTCAATTTGACGAGCCACCGCAATAC
1 TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
* * * * *
4881 TCAAGGGC-AGGATATCAGGCTGAGTTTGACGAGCCATCGCGATAC
1 TCAA-GCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
4926 TC
1 TC
4928 TATTCCAATA
Statistics
Matches: 83, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
45 81 0.98
46 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (45 bp):
TCAAGCCAAGGATATCAGCCTCAGTTTGACGAGCCACCGCAATAC
Done.