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--PDR3/RM11-1A--PDR3.fa
  
  Database contains 516 sequences, 222600 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRNTCGAA
        8
        GAATCGAA
       
        CCRTACAY
        8
        CCATACAT
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CKCTACC
        7
        CGCTACC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        ACCAYTA
        7
        ACCACTA
       
        AMACCCA
        7
        ACACCCA
       
        AAAAAAK
        7
        AAAAAAT
       
        CCGYGSA
        7
        CCGTGGA
       
        ATCKTGAG
        8
        ATCGTGAG
       
        GTGATAGY
        8
        GTGATAGC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GATTRGAA
        8
        GATTAGAA
       
        TGGCGYA
        7
        TGGCGCA
       
        RGCCCAA
        7
        GGCCCAA
       
        AACCCYG
        7
        AACCCCG
       
        GWGCTAA
        7
        GAGCTAA
       
        AAAGCGWG
        8
        AAAGCGTG
       
        AGAAGWT
        7
        AGAAGAT
       
        CTTARCA
        7
        CTTAACA
       
        CGTMTGAC
        8
        CGTATGAC
       
        CAGTCTKG
        8
        CAGTCTGG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRNTCGAA	8	GAATCGAA
CCRTACAY	8	CCATACAT
CTBGGCCA	8	CTCGGCCA
CKCTACC	7	CGCTACC
GCCTTAMC	8	GCCTTAAC
ACCAYTA	7	ACCACTA
AMACCCA	7	ACACCCA
AAAAAAK	7	AAAAAAT
CCGYGSA	7	CCGTGGA
ATCKTGAG	8	ATCGTGAG
GTGATAGY	8	GTGATAGC
ATGGCAWC	8	ATGGCAAC
GATTRGAA	8	GATTAGAA
TGGCGYA	7	TGGCGCA
RGCCCAA	7	GGCCCAA
AACCCYG	7	AACCCCG
GWGCTAA	7	GAGCTAA
AAAGCGWG	8	AAAGCGTG
AGAAGWT	7	AGAAGAT
CTTARCA	7	CTTAACA
CGTMTGAC	8	CGTATGAC
CAGTCTKG	8	CAGTCTGG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 35 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
AAAGCGWG	DREME-18	chrIII	+	82498	82505	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrX	+	115975	115982	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXI	+	141054	141061	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXVI	+	210228	210235	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrVII	+	401563	401570	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrV	+	487367	487374	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXV	+	968259	968266	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrV	-	177125	177132	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXIII	-	290827	290834	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrVII	-	328609	328616	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrV	-	354960	354967	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrV	-	354960	354967	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrIX	-	370443	370450	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrX	-	374623	374630	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrVII	-	541876	541883	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrII	-	645193	645200	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXII	-	797204	797211	1.2e-05	0.304	AAAGCGTG
AAAGCGWG	DREME-18	chrXIII	+	196137	196144	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrVIII	+	388962	388969	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrV	+	396466	396473	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrVII	+	857503	857510	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXII	-	92572	92579	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrVI	-	101400	101407	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrI	-	139176	139183	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXV	-	301121	301128	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXIV	-	375016	375023	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXIV	-	444566	444573	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXV	-	464474	464481	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXIV	-	547118	547125	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXIV	-	568139	568146	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXV	-	980707	980714	2.4e-05	0.334	AAAGCGAG
AAAGCGWG	DREME-18	chrXV	+	282158	282165	3.87e-05	0.476	AAAGCGCG
AAAGCGWG	DREME-18	chrII	-	332556	332563	3.87e-05	0.476	AAAGCGGG
AAAGCGWG	DREME-18	chrXII	-	460121	460128	3.87e-05	0.476	AAAGCGGG
AAAGCGWG	DREME-18	chrVII	+	856762	856769	3.87e-05	0.476	AAAGCGCG

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--PDR3/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/background --motif AAAGCGWG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/RM11-1A--PDR3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/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--PDR3/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/RM11-1A--PDR3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR3/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