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--RIM101/BY4742--RIM101.fa
  
  Database contains 566 sequences, 206709 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCGTACAT
       
        CTYGGCC
        7
        CTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AGTGGTWA
        8
        AGTGGTTA
       
        ACACSC
        6
        ACACCC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACATYAC
        8
        CACATCAC
       
        AACCRACT
        8
        AACCAACT
       
        AGAAAWA
        7
        AGAAAAA
       
        GATTAASA
        8
        GATTAAGA
       
        ATCTKTTG
        8
        ATCTGTTG
       
        ATAGTKTA
        8
        ATAGTGTA
       
        ACTRCGCC
        8
        ACTGCGCC
       
        AGCGCMAG
        8
        AGCGCAAG
       
        ATGGGYGC
        8
        ATGGGCGC
       
        CCGTGSA
        7
        CCGTGGA
       
        TAKCTCA
        7
        TATCTCA
       
        CACGCGAS
        8
        CACGCGAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CCRTACAY	8	CCGTACAT
CTYGGCC	7	CTTGGCC
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
AGTGGTWA	8	AGTGGTTA
ACACSC	6	ACACCC
ATGGCAWC	8	ATGGCAAC
CACATYAC	8	CACATCAC
AACCRACT	8	AACCAACT
AGAAAWA	7	AGAAAAA
GATTAASA	8	GATTAAGA
ATCTKTTG	8	ATCTGTTG
ATAGTKTA	8	ATAGTGTA
ACTRCGCC	8	ACTGCGCC
AGCGCMAG	8	AGCGCAAG
ATGGGYGC	8	ATGGGCGC
CCGTGSA	7	CCGTGGA
TAKCTCA	7	TATCTCA
CACGCGAS	8	CACGCGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 41 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
AGCGCMAG	DREME-16	chrII	+	36419	36426	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrVI	-	157977	157984	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrVIII	-	237909	237916	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXIII	+	352301	352308	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrVIII	-	358539	358546	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXIV	+	374890	374897	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXII	+	424363	424370	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrVII	-	440777	440784	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrVIII	+	505826	505833	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXVI	-	560259	560266	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXVI	-	622601	622608	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXII	-	796537	796544	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrXV	-	882389	882396	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrIV	-	1095431	1095438	4.88e-06	0.141	AGCGCCAG
AGCGCMAG	DREME-16	chrV	-	61953	61960	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrIV	+	83546	83553	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrIII	-	142764	142771	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrVI	+	162226	162233	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrVI	-	181037	181044	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrII	-	197692	197699	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrXV	-	226674	226681	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrV	-	306033	306040	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrX	-	396789	396796	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrX	+	531826	531833	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrVII	+	845647	845654	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrXVI	+	860377	860384	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrVII	-	931016	931023	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrIV	+	992830	992837	1.26e-05	0.183	AGCGCAAG
AGCGCMAG	DREME-16	chrIX	-	98	105	2.53e-05	0.32	AGCGCGAG
AGCGCMAG	DREME-16	chrV	-	6202	6209	2.53e-05	0.32	AGCGCGAG
AGCGCMAG	DREME-16	chrV	+	269317	269324	2.53e-05	0.32	AGCGCTAG
AGCGCMAG	DREME-16	chrXIV	+	434604	434611	2.53e-05	0.32	AGCGCTAG
AGCGCMAG	DREME-16	chrV	-	86472	86479	4.73e-05	0.468	AGCGCCGG
AGCGCMAG	DREME-16	chrIII	+	123672	123679	4.73e-05	0.468	AGCGCCTG
AGCGCMAG	DREME-16	chrXIII	+	225697	225704	4.73e-05	0.468	AGCGCCTG
AGCGCMAG	DREME-16	chrIII	-	246851	246858	4.73e-05	0.468	AGCGCCCG
AGCGCMAG	DREME-16	chrVII	-	310764	310771	4.73e-05	0.468	CGCGCCAG
AGCGCMAG	DREME-16	chrVIII	+	455897	455904	4.73e-05	0.468	CGCGCCAG
AGCGCMAG	DREME-16	chrV	+	491218	491225	4.73e-05	0.468	AGCGCCCG
AGCGCMAG	DREME-16	chrXII	+	651161	651168	4.73e-05	0.468	AGCGCCTG
AGCGCMAG	DREME-16	chrXII	+	932078	932085	4.73e-05	0.468	GGCGCCAG

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--RIM101/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/background --motif AGCGCMAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/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--RIM101/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/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