Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008715.1 Kokia drynarioides strain JFW-HI SEQ_123397, 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: 13625
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:679 original size:14 final size:16
Alignment explanation
Indices: 660--693 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
650 TTAAATAAAA
660 ATAATATA-AA-TTTT
1 ATAATATATAACTTTT
674 ATAATATATAACTTTT
1 ATAATATATAACTTTT
690 ATAA
1 ATAA
694 AAAAAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
15 2 0.11
16 8 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
ATAATATATAACTTTT
Found at i:684 original size:16 final size:16
Alignment explanation
Indices: 663--693 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
653 AATAAAAATA
663 ATATAAATTTTATAAT
1 ATATAAATTTTATAAT
*
679 ATATAACTTTTATAA
1 ATATAAATTTTATAA
694 AAAAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATAAATTTTATAAT
Found at i:2257 original size:30 final size:33
Alignment explanation
Indices: 2223--2295 Score: 100
Period size: 32 Copynumber: 2.3 Consensus size: 33
2213 AAGTTTCAAT
2223 TCAGTCACTCAA-CTT-TC-AAAAAATAACAAA
1 TCAGTCACTCAATCTTATCAAAAAAATAACAAA
* *
2253 TCAGTCACT-AATGTTATCAAAAAAATGACAAA
1 TCAGTCACTCAATCTTATCAAAAAAATAACAAA
2285 TCAGTCACTCA
1 TCAGTCACTCA
2296 TTAACATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 2 0.05
30 11 0.30
31 2 0.05
32 21 0.57
33 1 0.03
ACGTcount: A:0.47, C:0.22, G:0.07, T:0.25
Consensus pattern (33 bp):
TCAGTCACTCAATCTTATCAAAAAAATAACAAA
Found at i:5463 original size:19 final size:19
Alignment explanation
Indices: 5427--5480 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
5417 ATGTTTCGTT
5427 TTTTAGTTTT-TTAATTTTA
1 TTTTA-TTTTATTAATTTTA
*
5446 TTTTATTTTATTATTTTTA
1 TTTTATTTTATTAATTTTA
* *
5465 TGTTATATT-TTAATTT
1 TTTTATTTTATTAATTT
5481 CGTTTATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 20 0.67
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTAATTTTA
Found at i:7391 original size:23 final size:22
Alignment explanation
Indices: 7349--7397 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 22
7339 TGATCTATTA
*
7349 CATTATGCATTTTAGATAAGTG
1 CATTATGCATGTTAGATAAGTG
7371 CATTCATGCATGTTA-ATTAAGTG
1 CATT-ATGCATGTTAGA-TAAGTG
7394 -ATTA
1 CATTA
7398 CTAAATTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 1 0.04
22 8 0.33
23 15 0.62
ACGTcount: A:0.33, C:0.10, G:0.16, T:0.41
Consensus pattern (22 bp):
CATTATGCATGTTAGATAAGTG
Found at i:8527 original size:10 final size:11
Alignment explanation
Indices: 8509--8537 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
8499 AAACACACCT
8509 AAAAGAGAAAG
1 AAAAGAGAAAG
8520 AAAA-AGAAAG
1 AAAAGAGAAAG
8530 AAAAGAGA
1 AAAAGAGA
8538 CAGCCTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:11242 original size:23 final size:25
Alignment explanation
Indices: 11216--11261 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
11206 CCAATTAGGG
11216 AATTA-TTGTTTAG-ATTTAATTCT
1 AATTATTTGTTTAGAATTTAATTCT
*
11239 AATTATTTTTTTAGAATTTAATT
1 AATTATTTGTTTAGAATTTAATT
11262 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.59
Consensus pattern (25 bp):
AATTATTTGTTTAGAATTTAATTCT
Done.