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]

• There were 328 motif occurences with a p-value less than 0.001. The full set of motif occurences can be seen in the TSV (tab-delimited values) output file fimo.tsv, the GFF3 file fimo.gff which may be suitable for uploading to the UCSC Genome Table Browser (assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format), or the XML file fimo.xml.
• The p-value of a motif occurrence is defined as the probability of a random sequence of the same length as the motif matching that position of the sequence with as good or better a score.
• The score for the match of a position in a sequence to a motif is computed by summing the appropriate entries from each column of the position-dependent scoring matrix that represents the motif.
• The q-value of a motif occurrence is defined as the false discovery rate if the occurrence is accepted as significant.
• The table is sorted by increasing p-value.

Command line:

fimo --oc fimo_neg -motif RGTRTATWATAGCGCMYRTTK -thresh 0.001 meme_out/meme.txt NEGATIVE.fasta

Settings:

  

    
output_directory = fimo_neg
    
MEME file name = meme_out/meme.txt
    
sequence file name = NEGATIVE.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 = true
    
max strand = false
  
  

    
threshold type = p-value
    
output theshold = 0.001
    
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.