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 memeout_e2/e2.fa
  
  Database contains 6008 sequences, 1300159 residues

  MOTIFS memeout_e2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGACCB
        6
        TGACCT
       
        ATGTCA
        6
        ATGTCA
       
        MGGGCR
        6
        AGGGCA
       
        HGATAA
        6
        AGATAA
       
        RTAAAYA
        7
        GTAAACA
       
        AGGTCG
        6
        AGGTCG
       
        AGGTTA
        6
        AGGTTA
       
        CCTGGS
        6
        CCTGGG
       
        TGACWCA
        7
        TGACACA
       
        AAAGMCCT
        8
        AAAGACCT
       
        RCAAAYA
        7
        GCAAACA
       
        ATCTMATC
        8
        ATCTCATC
       
        CBGTGAC
        7
        CTGTGAC
       
        ACAARATA
        8
        ACAAGATA
       
        AGGTTGCA
        8
        AGGTTGCA
       
        GTAAAGAA
        8
        GTAAAGAA
       
        GGAATGCA
        8
        GGAATGCA
       
        CHGGGGCA
        8
        CTGGGGCA
       
        AGGTGACM
        8
        AGGTGACA
       
        CGTGTCM
        7
        CGTGTCA
       
        CCTDAGGC
        8
        CCTGAGGC
       
        GGTYA
        5
        GGTCA
       
        ARATA
        5
        AGATA
       
        CCTGCCTY
        8
        CCTGCCTT
       
        CTGTAMTC
        8
        CTGTAATC
       
Random model letter frequencies (memeout_e2/background):

A 0.242 C 0.258 G 0.258 T 0.242

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGACCB	6	TGACCT
ATGTCA	6	ATGTCA
MGGGCR	6	AGGGCA
HGATAA	6	AGATAA
RTAAAYA	7	GTAAACA
AGGTCG	6	AGGTCG
AGGTTA	6	AGGTTA
CCTGGS	6	CCTGGG
TGACWCA	7	TGACACA
AAAGMCCT	8	AAAGACCT
RCAAAYA	7	GCAAACA
ATCTMATC	8	ATCTCATC
CBGTGAC	7	CTGTGAC
ACAARATA	8	ACAAGATA
AGGTTGCA	8	AGGTTGCA
GTAAAGAA	8	GTAAAGAA
GGAATGCA	8	GGAATGCA
CHGGGGCA	8	CTGGGGCA
AGGTGACM	8	AGGTGACA
CGTGTCM	7	CGTGTCA
CCTDAGGC	8	CCTGAGGC
GGTYA	5	GGTCA
ARATA	5	AGATA
CCTGCCTY	8	CCTGCCTT
CTGTAMTC	8	CTGTAATC

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 memeout_e2/fimo_out_5 --bgfile memeout_e2/background --motif CCTGGS memeout_e2/dreme_out/dreme.xml memeout_e2/e2.fa

Settings:


  
    output_directory = memeout_e2/fimo_out_5
    MEME file name = memeout_e2/dreme_out/dreme.xml
    sequence file name = memeout_e2/e2.fa
  
  
    background file name = memeout_e2/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 = memeout_e2/fimo_out_5	MEME file name = memeout_e2/dreme_out/dreme.xml	sequence file name = memeout_e2/e2.fa
background file name = memeout_e2/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