Database and Motifs | High-scoring Motif Occurences | Debugging Information | Results in TSV Format | Results in GFF3 Format |
FIMO version 5.1.1, (Release date: Wed Jan 29 15:00:42 2020 -0800)
For further information on how to interpret these results please access http://alternate.meme-suite.org//doc/fimo-output-format.html.
To get a copy of the FIMO software please access http://meme-suite.org
If you use FIMO in your research, please cite the following paper:
Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
"FIMO: Scanning for occurrences of a given motif",
Bioinformatics, 27(7):1017-1018, 2011.
[full text]
DATABASE strain.fasta
Database contains 1 sequences, 27544 residues
MOTIFS motifs.meme (DNA)
MOTIF | WIDTH | BEST POSSIBLE MATCH |
---|---|---|
1 | 23 | CTATTATTCTCAACTAAACGAAA |
Random model letter frequencies (--nrdb--):
A 0.282 C 0.222 G 0.229 T 0.267
Motif ID | Alt ID | Sequence Name | Strand | Start | End | p-value | q-value | Matched Sequence |
---|---|---|---|---|---|---|---|---|
1 | MK334045.1 | + | 51 | 73 | 4.62e-14 | 1.09e-09 | CTACTCTTCTCAACTAAACGAAA | |
1 | MK334045.1 | + | 20454 | 20476 | 2.82e-11 | 3.33e-07 | CATTTAGTCTCAACTAAATGAAA | |
1 | MK334045.1 | + | 26110 | 26132 | 1.22e-10 | 9.65e-07 | CATTTAATCTAAACTAAACAAAA | |
1 | MK334045.1 | + | 25176 | 25198 | 3.61e-10 | 2.14e-06 | CTACTCCTCTCAACTATACGAAG | |
1 | MK334045.1 | + | 25421 | 25443 | 1.2e-08 | 5.69e-05 | TTAAATGTCTAAACTAAACGATG | |
1 | MK334045.1 | + | 13344 | 13366 | 7.79e-06 | 0.0307 | CTATTTGCCACAACTATACCAGG | |
1 | MK334045.1 | + | 15910 | 15932 | 5.52e-05 | 0.187 | CAACTATTGCAAACCAAGAGAAG |
Command line:
fimo --oc . --verbosity 1 --thresh 1.0E-4 --norc motifs.meme strain.fasta
Settings:
output_directory = . | MEME file name = motifs.meme | sequence file name = strain.fasta |
background file name = --nrdb-- | alphabet = DNA | max stored scores = 100000 |
allow clobber = true | compute q-values = true | parse genomic coord. = false |
text only = false | scan both strands = false | max strand = false |
threshold type = p-value | output theshold = 0.0001 | pseudocount = 0.1 |
alpha = 1 | verbosity = 1 |
This information can be useful in the event you wish to report a problem with the FIMO software.