Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009029.1 Kokia drynarioides strain JFW-HI SEQ_123727, 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: 13190
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:9182 original size:123 final size:124
Alignment explanation
Indices: 8958--9326 Score: 546
Period size: 123 Copynumber: 3.0 Consensus size: 124
8948 ATTCTGCTAT
* * *
8958 ATTTCCTTTTATTTAATATCTCATATTAAAATGAAAATATAT-CTTTAGAGAAATATATGGAAGG
1 ATTTCCTTTTATATAATATCTCATATTAAAATGGAAATAT-TCCTTTAAAGAAATATATGGAAGG
*
9022 TTTATTAAAACATTATATCCTTTCCAAAATGATATTAACTTCCCT-GTTTTTAATATTCA
65 TTTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCCTGGTTTTTAATATTCA
* * * * * *
9081 ATTTTCTTTTATATAATATCTCATATTTAAATGGAAATATTCCATGAAAGAAATATATAGAAGAT
1 ATTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGT
* * *
9146 TTATTAAAACATTATATCCTTTTCAAAAAGATATTAACTTCCATGGTTTTTTAATATTTA
66 TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCCTGG-TTTTTAATATTCA
* *
9206 ATTTCCTTTTATATAATATCTCAAATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAAGGT
1 ATTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGT
* *
9271 TTATTAAAACATTATATCATTTCCAAAAGGATATTAACTT-CCTGGTTTTTAATATT
66 TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCCTGGTTTTTAATATT
9327 TAACGAAATC
Statistics
Matches: 218, Mismatches: 25, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
122 1 0.00
123 106 0.49
124 5 0.02
125 106 0.49
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (124 bp):
ATTTCCTTTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATGGAAGGT
TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCCTGGTTTTTAATATTCA
Found at i:9256 original size:125 final size:123
Alignment explanation
Indices: 8958--9329 Score: 543
Period size: 125 Copynumber: 3.0 Consensus size: 123
8948 ATTCTGCTAT
* *
8958 ATTTCCTTTTATTTAATATCTCATATTAAAA-TGAAAATATAT-CTTTAGAGAAATATATGGAAG
1 ATTTCCTTTTATATAATATCTCATATTAAAATTG-AAATAT-TCCTTTAAAGAAATATATGGAAG
* *
9021 GTTTATTAAAACATTATATCCTTTCCAAAATGATATTAACTTCCCT-GTTTTTAATATTCA
64 GTTTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTT-CCTGGTTTTTAATATTTA
* * * * * * *
9081 ATTTTCTTTTATATAATATCTCATATTTAAATGGAAATATTCCATGAAAGAAATATATAGAAGAT
1 ATTTCCTTTTATATAATATCTCATATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAAGGT
*
9146 TTATTAAAACATTATATCCTTTTCAAAAAGATATTAACTTCCATGGTTTTTTAATATTTA
66 TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCC-TGG-TTTTTAATATTTA
*
9206 ATTTCCTTTTATATAATATCTCAAATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAAGGT
1 ATTTCCTTTTATATAATATCTCATATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAAGGT
* *
9271 TTATTAAAACATTATATCATTTCCAAAAGGATATTAACTTCCTGGTTTTTAATATTTA
66 TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCTGGTTTTTAATATTTA
9329 A
1 A
9330 CGAAATCTTT
Statistics
Matches: 221, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
122 3 0.01
123 105 0.48
124 5 0.02
125 108 0.49
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (123 bp):
ATTTCCTTTTATATAATATCTCATATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAAGGT
TTATTAAAACATTATATCCTTTCCAAAAAGATATTAACTTCCTGGTTTTTAATATTTA
Done.