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/RM11-1A--YRR1/RM11-1A--YRR1.fa
  
  Database contains 490 sequences, 153713 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        TGTAYGGR
        8
        TGTATGGG
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AARAAAWA
        8
        AAAAAAAA
       
        CTARACCA
        8
        CTAGACCA
       
        CAASGATG
        8
        CAACGATG
       
        AMATCCG
        7
        AAATCCG
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CACCGTGS
        8
        CACCGTGG
       
        GTGATARC
        8
        GTGATAGC
       
        ATTAASAG
        8
        ATTAAGAG
       
        ACTGAGC
        7
        ACTGAGC
       
        GCCATWAC
        8
        GCCATTAC
       
        ACACSCA
        7
        ACACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
TGTAYGGR	8	TGTATGGG
CTBGGCCA	8	CTCGGCCA
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
AARAAAWA	8	AAAAAAAA
CTARACCA	8	CTAGACCA
CAASGATG	8	CAACGATG
AMATCCG	7	AAATCCG
ATAGTKTA	8	ATAGTGTA
CACCGTGS	8	CACCGTGG
GTGATARC	8	GTGATAGC
ATTAASAG	8	ATTAAGAG
ACTGAGC	7	ACTGAGC
GCCATWAC	8	GCCATTAC
ACACSCA	7	ACACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 32 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
ATTAASAG	DREME-13	chrXV	-	111087	111094	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrVII	-	122299	122306	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrV	-	131152	131159	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrV	+	135458	135465	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrVII	+	185747	185754	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrVI	+	226721	226728	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrIX	+	300261	300268	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrXVI	-	339032	339039	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrX	-	414996	415003	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrV	+	435785	435792	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrXIII	+	480654	480661	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrXI	-	490951	490958	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrXVI	+	744210	744217	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrVII	-	876424	876431	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrIV	-	1201780	1201787	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrIV	+	1352499	1352506	3.16e-05	0.593	ATTAAGAG
ATTAASAG	DREME-13	chrXI	-	74655	74662	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXIV	+	89579	89586	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXIV	-	102747	102754	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrIII	+	123741	123748	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrIII	-	127747	127754	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrVI	+	137519	137526	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrVIII	+	146196	146203	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXV	-	228362	228369	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXV	+	301142	301149	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrVII	+	405694	405701	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXV	-	487470	487477	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXIV	-	632630	632637	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrVII	-	731168	731175	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXVI	-	810707	810714	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXII	+	823001	823008	6.31e-05	0.593	ATTAACAG
ATTAASAG	DREME-13	chrXII	+	976016	976023	6.31e-05	0.593	ATTAACAG

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/RM11-1A--YRR1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/background --motif ATTAASAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/RM11-1A--YRR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/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/RM11-1A--YRR1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/RM11-1A--YRR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YRR1/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