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--NOT3/BY4742--NOT3.fa
  
  Database contains 513 sequences, 171825 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTYGGTW
        8
        AGTTGGTT
       
        CCRTACAY
        8
        CCATACAT
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGGGNG
        7
        ATGGGTG
       
        GCGCTHCC
        8
        GCGCTACC
       
        AAGAAAWA
        8
        AAGAAAAA
       
        ATMCAAC
        7
        ATACAAC
       
        CCASAC
        6
        CCACAC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CYATGGCC
        8
        CTATGGCC
       
        AATCTTYT
        8
        AATCTTTT
       
        GCGCAAK
        7
        GCGCAAG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAGRTTAG
        8
        AAGGTTAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CCAASAG
        7
        CCAAGAG
       
        CCGTGMTA
        8
        CCGTGATA
       
        GGCTAYC
        7
        GGCTATC
       
        CGCGRGC
        7
        CGCGAGC
       
        GCGTGCSA
        8
        GCGTGCGA
       
        ACTSACG
        7
        ACTGACG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTYGGTW	8	AGTTGGTT
CCRTACAY	8	CCATACAT
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
CGCSTTA	7	CGCCTTA
ATGGCAWC	8	ATGGCAAC
ATGGGNG	7	ATGGGTG
GCGCTHCC	8	GCGCTACC
AAGAAAWA	8	AAGAAAAA
ATMCAAC	7	ATACAAC
CCASAC	6	CCACAC
GRTCTCCA	8	GGTCTCCA
CYATGGCC	8	CTATGGCC
AATCTTYT	8	AATCTTTT
GCGCAAK	7	GCGCAAG
AGTCAKAC	8	AGTCATAC
AAGRTTAG	8	AAGGTTAG
AAGCGWGA	8	AAGCGTGA
CCAASAG	7	CCAAGAG
CCGTGMTA	8	CCGTGATA
GGCTAYC	7	GGCTATC
CGCGRGC	7	CGCGAGC
GCGTGCSA	8	GCGTGCGA
ACTSACG	7	ACTGACG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 44 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
ATMCAAC	DREME-10	chrXI	+	86	92	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIII	+	551	557	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVI	+	4846	4852	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIII	+	5774	5780	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXII	+	11378	11384	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXII	+	11537	11543	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	+	83517	83523	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	+	83569	83575	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVI	+	95593	95599	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIII	+	131769	131775	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVI	+	162249	162255	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrI	+	166352	166358	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXV	+	282185	282191	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrII	+	326793	326799	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrX	+	391177	391183	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	+	488798	488804	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrX	+	531849	531855	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXVI	+	572290	572296	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVII	+	845670	845676	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXVI	+	860400	860406	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	+	992816	992822	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	+	992853	992859	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrV	-	61931	61937	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIV	-	96316	96322	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXI	-	141188	141194	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIII	-	142742	142748	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVI	-	181015	181021	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIII	-	183939	183945	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrII	-	197670	197676	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrII	-	197670	197676	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXV	-	226652	226658	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrV	-	312110	312116	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIX	-	316532	316538	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrX	-	396767	396773	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrX	-	414817	414823	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXI	-	513412	513418	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVIII	-	556667	556673	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXV	-	664010	664016	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXI	-	666453	666459	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXVI	-	732123	732129	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIV	-	783990	783996	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrXIII	-	924098	924104	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrVII	-	930994	931000	6.42e-05	0.491	ATCCAAC
ATMCAAC	DREME-10	chrIV	-	1525334	1525340	6.42e-05	0.491	ATCCAAC

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--NOT3/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif ATMCAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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--NOT3/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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