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 intersect_memechip_out/intersect.fa
  
  Database contains 33732 sequences, 6575273 residues

  MOTIFS intersect_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGRKGGCR
        8
        AGGGGGCA
       
        CCASYAGR
        8
        CCACCAGG
       
        DTTTCY
        6
        TTTTCT
       
        AGRKGGAG
        8
        AGGGGGAG
       
        BGTGGY
        6
        TGTGGC
       
        ATTHY
        5
        ATTCT
       
        GCGCCBCC
        8
        GCGCCCCC
       
        CKBCCTCC
        8
        CTGCCTCC
       
        RGRAA
        5
        AGGAA
       
        CCKCYAGG
        8
        CCTCCAGG
       
        CTGYAGK
        7
        CTGCAGG
       
        GTCRCTGY
        8
        GTCACTGT
       
        ATTTAH
        6
        ATTTAA
       
        GTGGHCA
        7
        GTGGACA
       
        GAKGGYGC
        8
        GAGGGTGC
       
        AAAAMAAA
        8
        AAAAAAAA
       
        RGWGACA
        7
        AGAGACA
       
        RAACWGCA
        8
        GAACTGCA
       
        CBGCCGCC
        8
        CGGCCGCC
       
        CCCCGCCC
        8
        CCCCGCCC
       
        AAATAH
        6
        AAATAC
       
        GSTGCTGY
        8
        GCTGCTGC
       
        CAGCRTC
        7
        CAGCATC
       
        CCGCTAGA
        8
        CCGCTAGA
       
        ACTGACA
        7
        ACTGACA
       
        CGBCTCC
        7
        CGGCTCC
       
        GCRGCCRC
        8
        GCAGCCGC
       
        TTTTAWA
        7
        TTTTAAA
       
        AGAGGCCA
        8
        AGAGGCCA
       
        GWAAACA
        7
        GTAAACA
       
        GGACRC
        6
        GGACAC
       
        GCAGTWCC
        8
        GCAGTACC
       
        CGTBTTC
        7
        CGTCTTC
       
        ACASACAC
        8
        ACACACAC
       
        GTAACA
        6
        GTAACA
       
        CCACTGGR
        8
        CCACTGGG
       
        CTCTGCWG
        8
        CTCTGCTG
       
        CDCTTCC
        7
        CTCTTCC
       
        GCWCCTCC
        8
        GCTCCTCC
       
        CACGTK
        6
        CACGTT
       
        ATCACMGC
        8
        ATCACAGC
       
Random model letter frequencies (intersect_memechip_out/background):

A 0.247 C 0.253 G 0.253 T 0.247

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 intersect_memechip_out/fimo_out_34 --bgfile intersect_memechip_out/background --motif CACGTK intersect_memechip_out/dreme_out/dreme.xml intersect_memechip_out/intersect.fa

Settings:


  
    output_directory = intersect_memechip_out/fimo_out_34
    MEME file name = intersect_memechip_out/dreme_out/dreme.xml
    sequence file name = intersect_memechip_out/intersect.fa
  
  
    background file name = intersect_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.