FIMO Results

Database and Motifs

High-scoring Motif Occurences

Debugging Information

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 chipseq_overlap/chipseq.overlap.optimal_peak.fa
  
  Database contains 33355 sequences, 7002569 residues

  MOTIFS chipseq_overlap/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        ATGYANAT
        8
        ATGCAAAT
       
        MATRACAA
        8
        CATAACAA
       
        CTGKGD
        6
        CTGGGA
       
        RGAAA
        5
        AGAAA
       
        TATGYWAA
        8
        TATGCTAA
       
        TATTYW
        6
        TATTTT
       
        CDGSAG
        6
        CAGGAG
       
        ATGCGCAT
        8
        ATGCGCAT
       
        CBCCWCCC
        8
        CCCCTCCC
       
        RAATGY
        6
        AAATGT
       
        ACARAGV
        7
        ACAAAGA
       
        ACGTV
        5
        ACGTG
       
        ACACAYAC
        8
        ACACACAC
       
        AGRKGGCG
        8
        AGGGGGCG
       
        CYTCCY
        6
        CTTCCT
       
        TACAGGYR
        8
        TACAGGCA
       
        ATGNTAAT
        8
        ATGATAAT
       
        CAGWG
        5
        CAGAG
       
        CCRCCDCC
        8
        CCACCACC
       
        AAAAMAAA
        8
        AAAAAAAA
       
        CCCGCCBC
        8
        CCCGCCCC
       
        CAGCCTGG
        8
        CAGCCTGG
       
        CRGMCAC
        7
        CAGCCAC
       
        CDGGAA
        6
        CTGGAA
       
        TTTAHAAA
        8
        TTTAAAAA
       
        ATAATAA
        7
        ATAATAA
       
        CATTSTC
        7
        CATTGTC
       
        GCATYACA
        8
        GCATTACA
       
        CCACCABG
        8
        CCACCAGG
       
        CTGDCTTC
        8
        CTGGCTTC
       
        GAGAGAGA
        8
        GAGAGAGA
       
        AAATAY
        6
        AAATAT
       
        ATAAAWG
        7
        ATAAAAG
       
        ACASCTGG
        8
        ACACCTGG
       
        GTCTCYAC
        8
        GTCTCTAC
       
        AGCCACCG
        8
        AGCCACCG
       
        CAACATRG
        8
        CAACATGG
       
        CTGGSCTC
        8
        CTGGCCTC
       
        ACCWCGG
        7
        ACCTCGG
       
Random model letter frequencies (chipseq_overlap/background):

A 0.277 C 0.223 G 0.223 T 0.277

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 chipseq_overlap/fimo_out_15 --bgfile chipseq_overlap/background --motif CYTCCY chipseq_overlap/dreme_out/dreme.xml chipseq_overlap/chipseq.overlap.optimal_peak.fa

Settings:


  
    output_directory = chipseq_overlap/fimo_out_15
    MEME file name = chipseq_overlap/dreme_out/dreme.xml
    sequence file name = chipseq_overlap/chipseq.overlap.optimal_peak.fa
  
  
    background file name = chipseq_overlap/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.