FIMO Results

FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

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 aa_memeout/aa_peaks.fa
  
  Database contains 486 sequences, 200874 residues

  MOTIFS aa_memeout/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRNTCGAA
        8
        GAATCGAA
       
        CCRTRCA
        7
        CCATACA
       
        AARAAAWA
        8
        AAAAAAAA
       
        CCYTAACC
        8
        CCTTAACC
       
        ACTBGGCC
        8
        ACTCGGCC
       
        ACCAYTA
        7
        ACCACTA
       
        BGCGC
        5
        TGCGC
       
        AGAYCGGG
        8
        AGATCGGG
       
        GTGATAGY
        8
        GTGATAGT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GAWTTGAA
        8
        GAATTGAA
       
        ACCGTGS
        7
        ACCGTGG
       
        GATYAGAA
        8
        GATTAGAA
       
        ACTSACG
        7
        ACTCACG
       
        CASACGC
        7
        CACACGC
       
        KTAGCTCA
        8
        TTAGCTCA
       
        ACACSCA
        7
        ACACCCA
       
        TCKCCCA
        7
        TCTCCCA
       
        ATCYCCGC
        8
        ATCCCCGC
       
Random model letter frequencies (aa_memeout/background):

A 0.311 C 0.189 G 0.189 T 0.311

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRNTCGAA	8	GAATCGAA
CCRTRCA	7	CCATACA
AARAAAWA	8	AAAAAAAA
CCYTAACC	8	CCTTAACC
ACTBGGCC	8	ACTCGGCC
ACCAYTA	7	ACCACTA
BGCGC	5	TGCGC
AGAYCGGG	8	AGATCGGG
GTGATAGY	8	GTGATAGT
ATGGCAWC	8	ATGGCAAC
GAWTTGAA	8	GAATTGAA
ACCGTGS	7	ACCGTGG
GATYAGAA	8	GATTAGAA
ACTSACG	7	ACTCACG
CASACGC	7	CACACGC
KTAGCTCA	8	TTAGCTCA
ACACSCA	7	ACACCCA
TCKCCCA	7	TCTCCCA
ATCYCCGC	8	ATCCCCGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 0 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the tab-delimited plain text output file fimo.txt, the GFF 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.

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

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc aa_memeout/fimo_out_6 --bgfile aa_memeout/background --motif BGCGC aa_memeout/dreme_out/dreme.xml aa_memeout/aa_peaks.fa

Settings:


  
    output_directory = aa_memeout/fimo_out_6
    MEME file name = aa_memeout/dreme_out/dreme.xml
    sequence file name = aa_memeout/aa_peaks.fa
  
  
    background file name = aa_memeout/background
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = true
  
  
    text only = false
    scan both strands = true
    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.

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output_directory = aa_memeout/fimo_out_6	MEME file name = aa_memeout/dreme_out/dreme.xml	sequence file name = aa_memeout/aa_peaks.fa
background file name = aa_memeout/background	alphabet = DNA	max stored scores = 100000
allow clobber = true	compute q-values = true	parse genomic coord. = true
text only = false	scan both strands = true	max strand = false
threshold type = p-value	output theshold = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1