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 memechip_out/chipseq.idr.optimal_peak.fa
  
  Database contains 4843 sequences, 1015049 residues

  MOTIFS memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CATRABAA
        8
        CATAACAA
       
        ATGYWAAT
        8
        ATGCAAAT
       
        AWATGCR
        7
        ATATGCA
       
        AATRASAA
        8
        AATAACAA
       
        CCWCCY
        6
        CCTCCC
       
        AAAGRVA
        7
        AAAGAAA
       
        CAGCRGG
        7
        CAGCAGG
       
        CATYACAA
        8
        CATCACAA
       
        TATGYARA
        8
        TATGCAAA
       
        CMCAGS
        6
        CCCAGG
       
        ATGCGCAT
        8
        ATGCGCAT
       
        ACAAWGG
        7
        ACAATGG
       
        RGAGA
        5
        AGAGA
       
        ATGAATAW
        8
        ATGAATAT
       
        GTAWTTM
        7
        GTATTTA
       
        RCATTCCW
        8
        GCATTCCT
       
        CACSTGS
        7
        CACCTGG
       
        GGTTCGA
        7
        GGTTCGA
       
        GAGTCAC
        7
        GAGTCAC
       
        CCACWGWG
        8
        CCACTGTG
       
        CATTAKAA
        8
        CATTAGAA
       
        KCCAGGTA
        8
        GCCAGGTA
       
        ATATGWAT
        8
        ATATGAAT
       
        CTAAYGAG
        8
        CTAATGAG
       
        GCTCTGSA
        8
        GCTCTGGA
       
Random model letter frequencies (memechip_out/background):

A 0.268 C 0.232 G 0.232 T 0.268

MOTIF	WIDTH	BEST POSSIBLE MATCH
CATRABAA	8	CATAACAA
ATGYWAAT	8	ATGCAAAT
AWATGCR	7	ATATGCA
AATRASAA	8	AATAACAA
CCWCCY	6	CCTCCC
AAAGRVA	7	AAAGAAA
CAGCRGG	7	CAGCAGG
CATYACAA	8	CATCACAA
TATGYARA	8	TATGCAAA
CMCAGS	6	CCCAGG
ATGCGCAT	8	ATGCGCAT
ACAAWGG	7	ACAATGG
RGAGA	5	AGAGA
ATGAATAW	8	ATGAATAT
GTAWTTM	7	GTATTTA
RCATTCCW	8	GCATTCCT
CACSTGS	7	CACCTGG
GGTTCGA	7	GGTTCGA
GAGTCAC	7	GAGTCAC
CCACWGWG	8	CCACTGTG
CATTAKAA	8	CATTAGAA
KCCAGGTA	8	GCCAGGTA
ATATGWAT	8	ATATGAAT
CTAAYGAG	8	CTAATGAG
GCTCTGSA	8	GCTCTGGA

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 memechip_out/fimo_out_9 --bgfile memechip_out/background --motif CMCAGS memechip_out/dreme_out/dreme.xml memechip_out/chipseq.idr.optimal_peak.fa

Settings:


  
    output_directory = memechip_out/fimo_out_9
    MEME file name = memechip_out/dreme_out/dreme.xml
    sequence file name = memechip_out/chipseq.idr.optimal_peak.fa
  
  
    background file name = memechip_out/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 = memechip_out/fimo_out_9	MEME file name = memechip_out/dreme_out/dreme.xml	sequence file name = memechip_out/chipseq.idr.optimal_peak.fa
background file name = memechip_out/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