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/YJM789--MIG2/YJM789--MIG2.fa
  
  Database contains 760 sequences, 237446 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CTBGGCCA
        8
        CTCGGCCA
       
        CGCCTTA
        7
        CGCCTTA
       
        GGTTCGA
        7
        GGTTCGA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGTAYGG
        8
        ATGTATGG
       
        GCKCTACC
        8
        GCGCTACC
       
        SAAGAW
        6
        GAAGAA
       
        ATAGTGTA
        8
        ATAGTGTA
       
        CACRCCC
        7
        CACGCCC
       
        AAAGCGWG
        8
        AAAGCGTG
       
        GGAGASC
        7
        GGAGACC
       
        ACTAGACC
        8
        ACTAGACC
       
        GATTAGAA
        8
        GATTAGAA
       
        AWGTGATA
        8
        ATGTGATA
       
        TGGCKCAA
        8
        TGGCGCAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
CTBGGCCA	8	CTCGGCCA
CGCCTTA	7	CGCCTTA
GGTTCGA	7	GGTTCGA
ATGGCAWC	8	ATGGCAAC
ATGTAYGG	8	ATGTATGG
GCKCTACC	8	GCGCTACC
SAAGAW	6	GAAGAA
ATAGTGTA	8	ATAGTGTA
CACRCCC	7	CACGCCC
AAAGCGWG	8	AAAGCGTG
GGAGASC	7	GGAGACC
ACTAGACC	8	ACTAGACC
GATTAGAA	8	GATTAGAA
AWGTGATA	8	ATGTGATA
TGGCKCAA	8	TGGCGCAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 27 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
GATTAGAA	DREME-13	chrVIII	-	133070	133077	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrV	-	138696	138703	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrV	-	138696	138703	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXII	-	167988	167995	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXIII	-	259202	259209	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrX	-	355404	355411	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrX	-	355404	355411	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrVII	-	405500	405507	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrII	-	405908	405915	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrV	-	431154	431161	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrX	-	524056	524063	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrIV	-	568912	568919	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrIV	-	568912	568919	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrVII	-	736370	736377	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXV	-	904328	904335	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrV	+	62005	62012	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrV	+	86632	86639	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXI	+	162519	162526	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrII	+	227103	227110	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrX	+	374538	374545	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrIV	+	437800	437807	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrVIII	+	493434	493441	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXII	+	547327	547334	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXVI	+	642757	642764	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrXIII	+	747924	747931	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrVII	+	828755	828762	3.04e-05	0.523	GATTAGAA
GATTAGAA	DREME-13	chrIV	+	1305658	1305665	3.04e-05	0.523	GATTAGAA

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/YJM789--MIG2/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/background --motif GATTAGAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/YJM789--MIG2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/YJM789--MIG2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/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/YJM789--MIG2/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/YJM789--MIG2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG2/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