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 seqnotcut_memechip_out/seqnotcut.fa
  
  Database contains 22935 sequences, 4983528 residues

  MOTIFS seqnotcut_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGRDGGCR
        8
        AGGGGGCA
       
        CCASHAGR
        8
        CCACCAGG
       
        RKAAA
        5
        GGAAA
       
        GCKCCMYC
        8
        GCTCCCCC
       
        CCTSYAG
        7
        CCTCCAG
       
        CRCCDCC
        7
        CACCTCC
       
        ATTWY
        5
        ATTTT
       
        RGGAA
        5
        GGGAA
       
        CTGYCWCC
        8
        CTGCCTCC
       
        ACAGCRHC
        8
        ACAGCACC
       
        CTGCAG
        6
        CTGCAG
       
        ACGTG
        5
        ACGTG
       
        GYCACTGY
        8
        GCCACTGC
       
        CTACTGVC
        8
        CTACTGGC
       
        TGGGGGCR
        8
        TGGGGGCA
       
        GCAGCVKC
        8
        GCAGCAGC
       
        MCACAS
        6
        CCACAG
       
        KTTAAAW
        7
        TTTAAAT
       
        AAMAMAAA
        8
        AAAAAAAA
       
        AAATRY
        6
        AAATGC
       
        CTGCCMTC
        8
        CTGCCCTC
       
        TAGCGKTA
        8
        TAGCGGTA
       
        TGTGACAA
        8
        TGTGACAA
       
        GHGGCCRC
        8
        GAGGCCGC
       
        CAGYAGAG
        8
        CAGCAGAG
       
        GACDCCA
        7
        GACACCA
       
        GCBGGGA
        7
        GCTGGGA
       
        CAKCCTCC
        8
        CAGCCTCC
       
        TGSTGACA
        8
        TGCTGACA
       
        AYTCCAGC
        8
        ACTCCAGC
       
        AAACAKC
        7
        AAACAGC
       
        AGGGGTCR
        8
        AGGGGTCA
       
        KGGAGACA
        8
        GGGAGACA
       
Random model letter frequencies (seqnotcut_memechip_out/background):

A 0.226 C 0.274 G 0.274 T 0.226

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGRDGGCR	8	AGGGGGCA
CCASHAGR	8	CCACCAGG
RKAAA	5	GGAAA
GCKCCMYC	8	GCTCCCCC
CCTSYAG	7	CCTCCAG
CRCCDCC	7	CACCTCC
ATTWY	5	ATTTT
RGGAA	5	GGGAA
CTGYCWCC	8	CTGCCTCC
ACAGCRHC	8	ACAGCACC
CTGCAG	6	CTGCAG
ACGTG	5	ACGTG
GYCACTGY	8	GCCACTGC
CTACTGVC	8	CTACTGGC
TGGGGGCR	8	TGGGGGCA
GCAGCVKC	8	GCAGCAGC
MCACAS	6	CCACAG
KTTAAAW	7	TTTAAAT
AAMAMAAA	8	AAAAAAAA
AAATRY	6	AAATGC
CTGCCMTC	8	CTGCCCTC
TAGCGKTA	8	TAGCGGTA
TGTGACAA	8	TGTGACAA
GHGGCCRC	8	GAGGCCGC
CAGYAGAG	8	CAGCAGAG
GACDCCA	7	GACACCA
GCBGGGA	7	GCTGGGA
CAKCCTCC	8	CAGCCTCC
TGSTGACA	8	TGCTGACA
AYTCCAGC	8	ACTCCAGC
AAACAKC	7	AAACAGC
AGGGGTCR	8	AGGGGTCA
KGGAGACA	8	GGGAGACA

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_11 --bgfile seqnotcut_memechip_out/background --motif RGGAA seqnotcut_memechip_out/dreme_out/dreme.xml seqnotcut_memechip_out/seqnotcut.fa

Settings:


  
    output_directory = seqnotcut_memechip_out/fimo_out_11
    MEME file name = seqnotcut_memechip_out/dreme_out/dreme.xml
    sequence file name = seqnotcut_memechip_out/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.

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output_directory = seqnotcut_memechip_out/fimo_out_11	MEME file name = seqnotcut_memechip_out/dreme_out/dreme.xml	sequence file name = seqnotcut_memechip_out/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