Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011152.1 Kokia drynarioides strain JFW-HI SEQ_126126, 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: 17720
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:564 original size:16 final size:16
Alignment explanation
Indices: 545--576 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
535 TTTATTCTTA
545 TTTCATCTTTATTTAT
1 TTTCATCTTTATTTAT
*
561 TTTCATGTTTATTTAT
1 TTTCATCTTTATTTAT
577 GTTTATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTCATCTTTATTTAT
Found at i:16330 original size:50 final size:52
Alignment explanation
Indices: 16273--16395 Score: 178
Period size: 50 Copynumber: 2.4 Consensus size: 52
16263 TTTAGATATG
*
16273 ATGTTTTAAATAAATATAAACATTTATTTAATTTG-TTTTGTTTAA-ATCTA
1 ATGTTTTAAATAAATATAAACATTTATTTAACTTGTTTTTGTTTAAGATCTA
*
16323 ATGTTTTAAATAAATATAAATATTTATTTAACTTGTTTTTGTTTAAGATCTA
1 ATGTTTTAAATAAATATAAACATTTATTTAACTTGTTTTTGTTTAAGATCTA
* * *
16375 GTGTTTTTACATAAACATAAA
1 ATG-TTTTAAATAAATATAAA
16396 TGTTTGTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
50 33 0.51
51 10 0.15
52 7 0.11
53 15 0.23
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (52 bp):
ATGTTTTAAATAAATATAAACATTTATTTAACTTGTTTTTGTTTAAGATCTA
Found at i:16799 original size:84 final size:83
Alignment explanation
Indices: 16647--17234 Score: 566
Period size: 84 Copynumber: 7.0 Consensus size: 83
16637 TAACAAATAC
* * * * *
16647 TTTGA-TTTGTTTCCAACCAAGAATT-AAGTGAATAATTTTGTTTCAGGATTTATTCCTGTCGTT
1 TTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGTT
* * **
16710 TAACAGATTTTATTATTTT
66 CAACAGATTTGATT-TGAT
* * * *
16729 TTTAATTTTGTTTCCAAAATAAGAA-TAAGTTGAATAAATCTGTTTCAGGATTTATTCCCGCCGT
1 TTTGATTTTGTTTCC-AAACAAGAATTAAATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGT
*
16793 TCAACAGATTTTATTCT-ATT
65 TCAACAGATTTGATT-TGA-T
* * * *
16813 TTTTATTTTGTTTCCAAAGAGGAATTAAAATTAAATAATTCTGTTTTCAGGATTTATTCCCGCCG
1 TTTGATTTTGTTTCCAAACAAGAATT-AAATTGAATAATTCTG-TTTCAGGATTTATTCCCGCCG
**
16878 TTCAACTTATTTGATTTGAT
64 TTCAACAGATTTGATTTGAT
* *
16898 TTTGATTTTGTTTTCAAACAAGAATTAAAATTAAATAATTCT-TATTC-GAGATTTATTCCCGCC
1 TTTGATTTTGTTTCCAAACAAGAATT-AAATTGAATAATTCTGT-TTCAG-GATTTATTCCCGCC
* *
16961 GTTCAACAAATTTGATTAGAT
63 GTTCAACAGATTTGATTTGAT
* * *** **
16982 TTTGATTTTGATTCCAAACAAGAATTAAAATTGAATAATTTTGTTTC-GGAATTTATTTATGTTG
1 TTTGATTTTGTTTCCAAACAAGAATT-AAATTGAATAATTCTGTTTCAGG-ATTTATTCCCGCCG
* *
17046 TTAAATAGATTTGATTTGAT
64 TTCAACAGATTTGATTTGAT
* * * * *
17066 TTTGATTTTGCTTCCAAATAAGAATT-AATTGAATAATTATGTTTC-GAGATTTATTCTCGTCGT
1 TTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTGTTTCAG-GATTTATTCCCGCCGT
*
17129 TTAACAGATTTGATTTGAT
65 TCAACAGATTTGATTTGAT
* * * * * * *
17148 TTTGATTTTGTTTCAAAACAAGAAAT-AATTAAATAATTCTGTTTCAAGATTTAATCCTGCCATT
1 TTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGTT
*
17212 CAACAGAATTGATTTTGAT
66 CAACAGATTTGA-TTTGAT
17231 TTTG
1 TTTG
17235 TTTCAGAATT
Statistics
Matches: 427, Mismatches: 64, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
82 112 0.26
83 31 0.07
84 195 0.46
85 54 0.13
86 35 0.08
ACGTcount: A:0.31, C:0.11, G:0.13, T:0.45
Consensus pattern (83 bp):
TTTGATTTTGTTTCCAAACAAGAATTAAATTGAATAATTCTGTTTCAGGATTTATTCCCGCCGTT
CAACAGATTTGATTTGAT
Done.