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--MGA2/BY4741--MGA2.fa
  
  Database contains 755 sequences, 321844 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        CCRTRCA
        7
        CCATACA
       
        ACCACTV
        7
        ACCACTA
       
        DCGCCTTA
        8
        GCGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        CCAACTKG
        8
        CCAACTTG
       
        CCAAVAGA
        8
        CCAAGAGA
       
        RAARAAA
        7
        AAAAAAA
       
        TGGCGYA
        7
        TGGCGCA
       
        GATTWGAA
        8
        GATTAGAA
       
        ACCCABAC
        8
        ACCCACAC
       
        CACGGTGM
        8
        CACGGTGA
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CACTATAK
        8
        CACTATAT
       
        ACTCASG
        7
        ACTCACG
       
        ACTWGACC
        8
        ACTAGACC
       
        GCAYGCGA
        8
        GCATGCGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/background):

A 0.319 C 0.181 G 0.181 T 0.319

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
CCRTRCA	7	CCATACA
ACCACTV	7	ACCACTA
DCGCCTTA	8	GCGCCTTA
ATGGCAWC	8	ATGGCAAC
GCKCTACC	8	GCGCTACC
CCAACTKG	8	CCAACTTG
CCAAVAGA	8	CCAAGAGA
RAARAAA	7	AAAAAAA
TGGCGYA	7	TGGCGCA
GATTWGAA	8	GATTAGAA
ACCCABAC	8	ACCCACAC
CACGGTGM	8	CACGGTGA
AAGCGWGA	8	AAGCGTGA
CACTATAK	8	CACTATAT
ACTCASG	7	ACTCACG
ACTWGACC	8	ACTAGACC
GCAYGCGA	8	GCATGCGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 40 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
CACTATAK	DREME-15	chrVII	-	122078	122085	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrVIII	-	134324	134331	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrV	-	250289	250296	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXI	-	308253	308260	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXI	-	432229	432236	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrIV	-	520975	520982	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXIII	-	737139	737146	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrIII	+	168360	168367	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXII	+	448709	448716	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrIV	+	645212	645219	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrVII	+	785051	785058	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrIV	+	802790	802797	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXIII	+	808305	808312	1.96e-05	0.855	CACTATAG
CACTATAK	DREME-15	chrXII	-	92324	92331	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXII	-	167858	167865	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrV	-	177102	177109	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrIV	-	222251	222258	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrI	-	229408	229415	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXIII	-	290804	290811	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrVII	-	328586	328593	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrV	-	354937	354944	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrIX	-	370420	370427	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXIII	-	379567	379574	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrVII	-	541853	541860	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrX	-	545652	545659	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrII	-	645170	645177	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXII	-	797181	797188	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXV	+	8170	8177	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrX	+	115998	116005	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrIV	+	130241	130248	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXI	+	141077	141084	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrI	+	143338	143345	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXIII	+	146122	146129	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXVI	+	210251	210258	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrVII	+	401586	401593	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrV	+	487390	487397	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXII	+	489252	489259	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXII	+	710851	710858	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrXII	+	710851	710858	5.4e-05	0.855	CACTATAT
CACTATAK	DREME-15	chrIV	+	964607	964614	5.4e-05	0.855	CACTATAT

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--MGA2/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/background --motif CACTATAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/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--MGA2/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/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