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/BY4741--RIM101/BY4741--RIM101.fa
  
  Database contains 667 sequences, 288298 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CCWTAACC
        8
        CCTTAACC
       
        CCVTACA
        7
        CCATACA
       
        GCKCTACC
        8
        GCGCTACC
       
        CCACTAHA
        8
        CCACTAAA
       
        GTTRCCA
        7
        GTTGCCA
       
        AKAAAAAA
        8
        AGAAAAAA
       
        AGACCAY
        7
        AGACCAC
       
        CRCCCA
        6
        CACCCA
       
        GGAGASC
        7
        GGAGACC
       
        CGTGYTAA
        8
        CGTGTTAA
       
        TGGCGYA
        7
        TGGCGCA
       
        AMTCCGAT
        8
        AATCCGAT
       
        CTATCACR
        8
        CTATCACA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/background):

A 0.321 C 0.179 G 0.179 T 0.321

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
CTBGGCCA	8	CTCGGCCA
CCWTAACC	8	CCTTAACC
CCVTACA	7	CCATACA
GCKCTACC	8	GCGCTACC
CCACTAHA	8	CCACTAAA
GTTRCCA	7	GTTGCCA
AKAAAAAA	8	AGAAAAAA
AGACCAY	7	AGACCAC
CRCCCA	6	CACCCA
GGAGASC	7	GGAGACC
CGTGYTAA	8	CGTGTTAA
TGGCGYA	7	TGGCGCA
AMTCCGAT	8	AATCCGAT
CTATCACR	8	CTATCACA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 37 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
CGTGYTAA	DREME-12	chrIX	-	183477	183484	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrII	+	197521	197528	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrII	+	197521	197528	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrIX	+	210692	210699	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrV	-	443239	443246	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrV	-	551322	551329	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrXIV	+	602339	602346	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrIV	-	668044	668051	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrXII	+	734829	734836	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrVII	+	739149	739156	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrXVI	+	819556	819563	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrXVI	-	880333	880340	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrXII	-	1052108	1052115	1.09e-05	0.475	CGTGCTAA
CGTGYTAA	DREME-12	chrX	-	378391	378398	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXI	-	379711	379718	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrV	-	438731	438738	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVII	-	823513	823520	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVII	+	73862	73869	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVIII	+	85331	85338	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVIII	+	148996	149003	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVIII	+	300086	300093	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXI	+	308177	308184	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXIII	+	372478	372485	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrVII	+	412327	412334	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXIII	+	420621	420628	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXV	+	663845	663852	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrXII	+	687892	687899	3.04e-05	0.639	CGTGTTAA
CGTGYTAA	DREME-12	chrIII	-	295560	295567	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrVII	-	311428	311435	6.08e-05	0.933	CGTGGTAA
CGTGYTAA	DREME-12	chrII	-	414909	414916	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrXVI	-	435764	435771	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrVII	-	553990	553997	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrX	-	703283	703290	6.08e-05	0.933	CGTGGTAA
CGTGYTAA	DREME-12	chrXIII	+	169009	169016	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrII	+	227200	227207	6.08e-05	0.933	CGTGGTAA
CGTGYTAA	DREME-12	chrV	+	305733	305740	6.08e-05	0.933	CGTGATAA
CGTGYTAA	DREME-12	chrV	+	438568	438575	6.08e-05	0.933	CGTGATAA

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/BY4741--RIM101/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/background --motif CGTGYTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/BY4741--RIM101.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/BY4741--RIM101.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/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/BY4741--RIM101/fimo_out_11	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/BY4741--RIM101.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RIM101/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