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 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/BY4742--RPB2.fa
  
  Database contains 1734 sequences, 2717368 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AAGWWG
        6
        AAGAAG
       
        AVCDTC
        6
        AACTTC
       
        GGTGVTA
        7
        GGTGGTA
       
        RDCCAA
        6
        AACCAA
       
        CGSTA
        5
        CGGTA
       
        ATGGMAA
        7
        ATGGCAA
       
        ACCASC
        6
        ACCACC
       
        ATTTCTTS
        8
        ATTTCTTC
       
        AGAAAGG
        7
        AGAAAGG
       
        AATTRGGT
        8
        AATTGGGT
       
        CTGCTRC
        7
        CTGCTGC
       
        GYTCCA
        6
        GTTCCA
       
        CCTTGDTA
        8
        CCTTGTTA
       
        CGAYGA
        6
        CGATGA
       
        CAGCTGGC
        8
        CAGCTGGC
       
        CWTACC
        6
        CTTACC
       
        CCAASAGA
        8
        CCAAGAGA
       
        CCAGAGGW
        8
        CCAGAGGT
       
        AATKGCGT
        8
        AATGGCGT
       
        CAAKACC
        7
        CAAGACC
       
        ACSGCTTC
        8
        ACGGCTTC
       
        AYATACA
        7
        ATATACA
       
        CCAAGTCK
        8
        CCAAGTCG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AAGWWG	6	AAGAAG
AVCDTC	6	AACTTC
GGTGVTA	7	GGTGGTA
RDCCAA	6	AACCAA
CGSTA	5	CGGTA
ATGGMAA	7	ATGGCAA
ACCASC	6	ACCACC
ATTTCTTS	8	ATTTCTTC
AGAAAGG	7	AGAAAGG
AATTRGGT	8	AATTGGGT
CTGCTRC	7	CTGCTGC
GYTCCA	6	GTTCCA
CCTTGDTA	8	CCTTGTTA
CGAYGA	6	CGATGA
CAGCTGGC	8	CAGCTGGC
CWTACC	6	CTTACC
CCAASAGA	8	CCAAGAGA
CCAGAGGW	8	CCAGAGGT
AATKGCGT	8	AATGGCGT
CAAKACC	7	CAAGACC
ACSGCTTC	8	ACGGCTTC
AYATACA	7	ATATACA
CCAAGTCK	8	CCAAGTCG

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 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/background --motif CWTACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/BY4742--RPB2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/BY4742--RPB2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/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 = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/BY4742--RPB2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RPB2/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