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/AWRI1631--PDR1/AWRI1631--PDR1.fa
  
  Database contains 584 sequences, 205455 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRNTCGAA
        8
        GAATCGAA
       
        TGTAYGGR
        8
        TGTATGGG
       
        AGTGGTW
        7
        AGTGGTT
       
        CGCSTTA
        7
        CGCCTTA
       
        CTTGGCY
        7
        CTTGGCC
       
        AGCGCGY
        7
        AGCGCGC
       
        TGGCGYA
        7
        TGGCGCA
       
        GTGGAGAY
        8
        GTGGAGAC
       
        GATTWGAA
        8
        GATTAGAA
       
        ACACSCA
        7
        ACACCCA
       
        AAAAAAMT
        8
        AAAAAAAT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CCAACWG
        7
        CCAACTG
       
        ACACTATA
        8
        ACACTATA
       
        GACTGTWA
        8
        GACTGTTA
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CTATCACR
        8
        CTATCACA
       
        ATCTKG
        6
        ATCTTG
       
        CCTTATKA
        8
        CCTTATGA
       
        GACCATTR
        8
        GACCATTA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/background):

A 0.313 C 0.187 G 0.187 T 0.313

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRNTCGAA	8	GAATCGAA
TGTAYGGR	8	TGTATGGG
AGTGGTW	7	AGTGGTT
CGCSTTA	7	CGCCTTA
CTTGGCY	7	CTTGGCC
AGCGCGY	7	AGCGCGC
TGGCGYA	7	TGGCGCA
GTGGAGAY	8	GTGGAGAC
GATTWGAA	8	GATTAGAA
ACACSCA	7	ACACCCA
AAAAAAMT	8	AAAAAAAT
ATGGCAWC	8	ATGGCAAC
CCAACWG	7	CCAACTG
ACACTATA	8	ACACTATA
GACTGTWA	8	GACTGTTA
AAGCGWGA	8	AAGCGTGA
CTATCACR	8	CTATCACA
ATCTKG	6	ATCTTG
CCTTATKA	8	CCTTATGA
GACCATTR	8	GACCATTA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 37 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
GACTGTWA	DREME-15	chrXI	+	74653	74660	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrII	+	89936	89943	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXIV	+	102745	102752	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXIV	+	102745	102752	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrIII	+	127745	127752	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXVI	-	135765	135772	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrVI	-	137521	137528	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrVI	+	167467	167474	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXIII	+	168825	168832	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXIII	+	168825	168832	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrVI	-	210668	210675	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXV	+	228360	228367	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrVII	+	254180	254187	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrII	-	255437	255444	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXVI	+	282487	282494	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXV	+	288222	288229	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXI	+	313563	313570	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrVII	-	328444	328451	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrVII	-	328444	328451	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrX	+	354274	354281	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrVII	-	405696	405703	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXIII	-	480706	480713	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrX	-	543005	543012	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrVII	+	545311	545318	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXII	-	605212	605219	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXV	-	620593	620600	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXIV	+	632628	632635	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrVII	+	731166	731173	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXVI	+	810705	810712	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrXIII	+	837958	837965	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrIV	+	946342	946349	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrIV	+	946342	946349	3.93e-05	0.479	GACTGTAA
GACTGTWA	DREME-15	chrXII	-	976018	976025	3.93e-05	0.479	GACTGTTA
GACTGTWA	DREME-15	chrIII	+	138635	138642	6.28e-05	0.684	GACTGTCA
GACTGTWA	DREME-15	chrIII	+	138635	138642	6.28e-05	0.684	GACTGTCA
GACTGTWA	DREME-15	chrI	+	166381	166388	6.28e-05	0.684	GACTGTCA
GACTGTWA	DREME-15	chrIX	-	316298	316305	6.28e-05	0.684	GACTGTCA

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/AWRI1631--PDR1/fimo_out_14 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/background --motif GACTGTWA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/AWRI1631--PDR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/fimo_out_14
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/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/AWRI1631--PDR1/fimo_out_14	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/AWRI1631--PDR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR1/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