Database and Motifs High-scoring Motif Occurences Debugging Information Results in TSV Format Results in GFF3 Format



FIMO - Motif search tool

FIMO version 5.5.1, (Release date: Sun Jan 29 10:33:12 2023 -0800)

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/fimo-output-format.html.
To get a copy of the FIMO software please access https://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 AND MOTIFS

DATABASE sd_neg.fa
Database contains 50 sequences, 1000 residues

MOTIFS meme_out/meme.txt (DNA)

MOTIF WIDTH BEST POSSIBLE MATCH
AARGGAG 7 AAAGGAG

Random model letter frequencies (--nrdb--):
A 0.275 C 0.225 G 0.225 T 0.275


SECTION I: HIGH-SCORING MOTIF OCCURENCES

Motif ID Alt ID Sequence Name Strand Start End p-value q-value Matched Sequence

DEBUGGING INFORMATION

Command line:

fimo -o fimo_neg meme_out/meme.txt sd_neg.fa

Settings:

output_directory = fimo_neg MEME file name = meme_out/meme.txt sequence file name = sd_neg.fa
background file name = --nrdb-- alphabet = DNA max stored scores = 100000
allow clobber = false compute q-values = true parse genomic coord. = false
text only = false scan both strands = true max strand = false
threshold type = p-value output theshold = 0.0001 pseudocount = 0.1
alpha = 1 verbosity = 2

This information can be useful in the event you wish to report a problem with the FIMO software.


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