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--YRR1/BY4741--YRR1.fa
  
  Database contains 867 sequences, 433862 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCATACAT
       
        AGTGGTWA
        8
        AGTGGTTA
       
        CAACTKGG
        8
        CAACTTGG
       
        ARAAAAR
        7
        AAAAAAA
       
        GCKCTACC
        8
        GCGCTACC
       
        CGCSTTA
        7
        CGCCTTA
       
        CGTWGCC
        7
        CGTTGCC
       
        CRCCCA
        6
        CACCCA
       
        ACCACTYG
        8
        ACCACTTG
       
        CCGATGAW
        8
        CCGATGAA
       
        GMTTAACA
        8
        GCTTAACA
       
        GGTCTCY
        7
        GGTCTCT
       
        AGACCACR
        8
        AGACCACG
       
        AGTCAKAC
        8
        AGTCATAC
       
        CGGTGAAA
        8
        CGGTGAAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background):

A 0.318 C 0.182 G 0.182 T 0.318

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
CCRTACAY	8	CCATACAT
AGTGGTWA	8	AGTGGTTA
CAACTKGG	8	CAACTTGG
ARAAAAR	7	AAAAAAA
GCKCTACC	8	GCGCTACC
CGCSTTA	7	CGCCTTA
CGTWGCC	7	CGTTGCC
CRCCCA	6	CACCCA
ACCACTYG	8	ACCACTTG
CCGATGAW	8	CCGATGAA
GMTTAACA	8	GCTTAACA
GGTCTCY	7	GGTCTCT
AGACCACR	8	AGACCACG
AGTCAKAC	8	AGTCATAC
CGGTGAAA	8	CGGTGAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 39 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
CGGTGAAA	DREME-16	chrX	+	115970	115977	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIII	+	137948	137955	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXI	+	141049	141056	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXVI	+	210223	210230	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXI	+	308392	308399	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVII	+	401558	401565	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	+	452606	452613	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	+	452606	452613	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	+	452606	452613	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	+	452606	452613	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	+	452606	452613	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrV	+	487362	487369	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	+	491230	491237	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	+	556246	556253	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	+	579298	579305	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	+	579298	579305	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVII	+	649102	649109	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	+	1028471	1028478	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVIII	-	5382	5389	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXVI	-	75802	75809	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrV	-	177130	177137	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXIII	-	290832	290839	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVII	-	312023	312030	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVII	-	328614	328621	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrV	-	354965	354972	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIX	-	370448	370455	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrVII	-	541881	541888	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	-	556084	556091	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrIV	-	556240	556247	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXVI	-	622758	622765	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXIII	-	632818	632825	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrII	-	645198	645205	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXVI	-	732038	732045	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	-	838475	838482	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	-	838475	838482	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	-	838475	838482	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	-	838475	838482	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXII	-	903593	903600	1.12e-05	0.247	CGGTGAAA
CGGTGAAA	DREME-16	chrXV	-	979034	979041	1.12e-05	0.247	CGGTGAAA

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--YRR1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/background --motif CGGTGAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--YRR1/BY4741--YRR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--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