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 seqnotcut_memechip_out/idr.seqnotcut.fa
  
  Database contains 26985 sequences, 5867047 residues

  MOTIFS seqnotcut_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGRDGGCR
        8
        AGGGGGCA
       
        CCASYAGR
        8
        CCACCAGG
       
        GCKCCMYC
        8
        GCTCCCCC
       
        RKAAA
        5
        AGAAA
       
        CCTSYAG
        7
        CCTCCAG
       
        CYGCCNCC
        8
        CTGCCCCC
       
        ATTYY
        5
        ATTCT
       
        CRBCTCC
        7
        CAGCTCC
       
        RGGAA
        5
        GGGAA
       
        CCACAHGG
        8
        CCACAAGG
       
        ACAGCRVC
        8
        ACAGCAGC
       
        CTACTGVC
        8
        CTACTGGC
       
        GGWGACA
        7
        GGAGACA
       
        ACGT
        4
        ACGT
       
        AAAMAAAA
        8
        AAAAAAAA
       
        CRCCRCC
        7
        CACCACC
       
        AMACACAS
        8
        ACACACAC
       
        CTGYAG
        6
        CTGCAG
       
        AGRGGTCR
        8
        AGGGGTCA
       
        RTTAMA
        6
        GTTACA
       
        CWGTGGY
        7
        CTGTGGC
       
        GCAGCAKC
        8
        GCAGCAGC
       
        GARRACA
        7
        GAGGACA
       
        CCGCYAGG
        8
        CCGCCAGG
       
        AAATAY
        6
        AAATAC
       
        GTGASAAC
        8
        GTGACAAC
       
        CTGCCMTC
        8
        CTGCCCTC
       
        GAAGGTGR
        8
        GAAGGTGG
       
        CAGCBTCC
        8
        CAGCCTCC
       
        CGCCCCCA
        8
        CGCCCCCA
       
        AGACATTK
        8
        AGACATTG
       
        GGCSGGGA
        8
        GGCCGGGA
       
        CAGMAGAG
        8
        CAGCAGAG
       
        GGCCTCTA
        8
        GGCCTCTA
       
        GGAAGCCA
        8
        GGAAGCCA
       
        ATGTGGY
        7
        ATGTGGC
       
        AGCGCCYC
        8
        AGCGCCCC
       
        KTTTAAA
        7
        TTTTAAA
       
Random model letter frequencies (seqnotcut_memechip_out/background):

A 0.227 C 0.273 G 0.273 T 0.227

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 seqnotcut_memechip_out/fimo_out_8 --bgfile seqnotcut_memechip_out/background --motif RKAAA seqnotcut_memechip_out/dreme_out/dreme.xml seqnotcut_memechip_out/idr.seqnotcut.fa

Settings:


  
    output_directory = seqnotcut_memechip_out/fimo_out_8
    MEME file name = seqnotcut_memechip_out/dreme_out/dreme.xml
    sequence file name = seqnotcut_memechip_out/idr.seqnotcut.fa
  
  
    background file name = seqnotcut_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.