Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002154.1 Kokia drynarioides strain JFW-HI SEQ_114103, 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: 4617
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Found at i:3875 original size:82 final size:82
Alignment explanation
Indices: 3772--3935 Score: 285
Period size: 82 Copynumber: 2.0 Consensus size: 82
3762 AACCTTTCTT
* *
3772 GCATGTAACATTTAACTTACCTTAATGCCACCACATCACACATTCATTCTCATATTC-CAACTTA
1 GCATGTAACATTTAACTTACCTTAATGCCACCACAACACACATTAATTCTCATA-TCGCAACTTA
3836 CCTCAATGGTAGATTTTA
65 CCTCAATGGTAGATTTTA
*
3854 GCATGTAACATTTAACTTACCTTAATGTCACCACAACACACATTAATTCTCATATCGCAACTTAC
1 GCATGTAACATTTAACTTACCTTAATGCCACCACAACACACATTAATTCTCATATCGCAACTTAC
3919 CTCAATGGTAGATTTTA
66 CTCAATGGTAGATTTTA
3936 CATTTTCATC
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
81 2 0.03
82 76 0.97
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.34
Consensus pattern (82 bp):
GCATGTAACATTTAACTTACCTTAATGCCACCACAACACACATTAATTCTCATATCGCAACTTAC
CTCAATGGTAGATTTTA
Found at i:4299 original size:25 final size:23
Alignment explanation
Indices: 4241--4411 Score: 134
Period size: 23 Copynumber: 7.3 Consensus size: 23
4231 TGCTGGGTAA
4241 CAGAGGGCACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* * *
4264 CAGAAGACACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
4287 AACAGAGGGCACACAAAGTGCTGAT
1 --CAGAGGGCACACAAAGTGCTAAT
*
4312 CAGAGGGCACACAACA-TGCTAAA
1 CAGAGGGCACACAA-AGTGCTAAT
* ** * *
4335 CAAAAAGCACACACAGTGCTAAA
1 CAGAGGGCACACAAAGTGCTAAT
* *
4358 CAGAGAGCACACACAGTGCTGAAT
1 CAGAGGGCACACAAAGTGCT-AAT
* *
4382 -AGAGAGCACGA-AACGTGCTAAAT
1 CAGAGGGCAC-ACAAAGTGCT-AAT
4405 -AGAGGGC
1 CAGAGGGC
4412 GCGCTAGTGT
Statistics
Matches: 122, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
22 1 0.01
23 98 0.80
24 4 0.03
25 19 0.16
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:4316 original size:71 final size:69
Alignment explanation
Indices: 4241--4379 Score: 176
Period size: 71 Copynumber: 2.0 Consensus size: 69
4231 TGCTGGGTAA
* * *
4241 CAGAGGGCACACAA-AGTGCTAATC-AGAAG-ACACACGAAGTGCTAATAACAGAGGGCACACAA
1 CAGAGGGCACACAACA-TGCTAAACAAAAAGCACACAC--AGTGCT-A-AACAGAGAGCACACAA
4303 AGTGCTGAT
61 AGTGCTGAT
*
4312 CAGAGGGCACACAACATGCTAAACAAAAAGCACACACAGTGCTAAACAGAGAGCACACACAGTGC
1 CAGAGGGCACACAACATGCTAAACAAAAAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGC
4377 TGA
66 TGA
4380 ATAGAGAGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
69 22 0.36
70 1 0.02
71 27 0.44
72 5 0.08
73 6 0.10
ACGTcount: A:0.42, C:0.24, G:0.23, T:0.11
Consensus pattern (69 bp):
CAGAGGGCACACAACATGCTAAACAAAAAGCACACACAGTGCTAAACAGAGAGCACACAAAGTGC
TGAT
Found at i:4332 original size:48 final size:48
Alignment explanation
Indices: 4238--4333 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
4228 AAGTGCTGGG
*
4238 TAACAGAGGGCACACAAAGTGCTAATCAGAAGACACACGAAGTGCTAA
1 TAACAGAGGGCACACAAAGTGCTAATCAGAAGACACACGAAATGCTAA
* * *
4286 TAACAGAGGGCACACAAAGTGCTGATCAGAGGGCACAC-AACATGCTAA
1 TAACAGAGGGCACACAAAGTGCTAATCAGAAGACACACGAA-ATGCTAA
4334 ACAAAAAGCA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 2 0.05
48 41 0.95
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (48 bp):
TAACAGAGGGCACACAAAGTGCTAATCAGAAGACACACGAAATGCTAA
Done.