Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008789.1 Kokia drynarioides strain JFW-HI SEQ_123472, 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: 3201
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.35
Found at i:252 original size:69 final size:69
Alignment explanation
Indices: 165--304 Score: 262
Period size: 69 Copynumber: 2.0 Consensus size: 69
155 AAAAGTGGCC
* *
165 CAAGAGTATACCATGCTAGAGTATTACAAGCCTATTCACATATATACACAAAAGCATGAATAGAC
1 CAAGAGTATACCATGCTAGAGTACTACAAGCCTATTCACATACATACACAAAAGCATGAATAGAC
230 TATA
66 TATA
234 CAAGAGTATACCATGCTAGAGTACTACAAGCCTATTCACATACATACACAAAAGCATGAATAGAC
1 CAAGAGTATACCATGCTAGAGTACTACAAGCCTATTCACATACATACACAAAAGCATGAATAGAC
299 TATA
66 TATA
303 CA
1 CA
305 TCCACAAGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.44, C:0.21, G:0.13, T:0.23
Consensus pattern (69 bp):
CAAGAGTATACCATGCTAGAGTACTACAAGCCTATTCACATACATACACAAAAGCATGAATAGAC
TATA
Found at i:2396 original size:66 final size:66
Alignment explanation
Indices: 2286--2422 Score: 165
Period size: 66 Copynumber: 2.1 Consensus size: 66
2276 GGGGAAATAA
*
2286 GGAGAGAGTTAGCTTTACGCTTCACTTTTGGGACATGCTTGACTCTATAAGTC-T-TTTGGTGTG
1 GGAGAGAGTTAGCTTTACGCTTCACTTTTGAGACATGCTTGACTC--TAAGTCATATTTGGTGTG
2349 TTT
64 TTT
* * * *
2352 GGAGAGTGTTAG-TTATATGCTTCACTTTTGAGATATG-TTCGACTCTGAGTCATATTTGGTGTG
1 GGAGAGAGTTAGCTT-TACGCTTCACTTTTGAGACATGCTT-GACTCTAAGTCATATTTGGTGTG
2415 TTT
64 TTT
2418 GGAGA
1 GGAGA
2423 TTCGTATATT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
64 5 0.08
65 5 0.08
66 52 0.84
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (66 bp):
GGAGAGAGTTAGCTTTACGCTTCACTTTTGAGACATGCTTGACTCTAAGTCATATTTGGTGTGTT
T
Found at i:2532 original size:23 final size:23
Alignment explanation
Indices: 2499--2696 Score: 272
Period size: 23 Copynumber: 8.6 Consensus size: 23
2489 ATTAAATGTG
*
2499 TTAAATATTAATGTGTTTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
2522 TTAAATGTTAATATGATTTATGC
1 TTAAATATTAATGTGATTTATGC
*
2545 TTACAA-GTTAATGTGATTTATGC
1 TTA-AATATTAATGTGATTTATGC
*
2568 TTAAATATTAATGTGATTTGTGC
1 TTAAATATTAATGTGATTTATGC
*
2591 TTAAATATTAATGTAATTTATGC
1 TTAAATATTAATGTGATTTATGC
* * *
2614 TTAAATGTTAATATGATTTATGT
1 TTAAATATTAATGTGATTTATGC
*
2637 TTACATATTAATGTGATTTATGC
1 TTAAATATTAATGTGATTTATGC
* *
2660 TTAAATATTAATGTAATTTGTGC
1 TTAAATATTAATGTGATTTATGC
2683 TTAAATATTAATGT
1 TTAAATATTAATGT
2697 TAAAACGTAT
Statistics
Matches: 154, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
22 2 0.01
23 150 0.97
24 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.13, T:0.48
Consensus pattern (23 bp):
TTAAATATTAATGTGATTTATGC
Done.