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--MIG1/BY4741--MIG1.fa
  
  Database contains 791 sequences, 437187 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        ACCWCT
        6
        ACCACT
       
        ARAAAAR
        7
        AAAAAAA
       
        TAAGGCR
        7
        TAAGGCG
       
        CCRTACA
        7
        CCATACA
       
        AAGATTTM
        8
        AAGATTTC
       
        CTTRGC
        6
        CTTGGC
       
        ACCTAAAS
        8
        ACCTAAAC
       
        GTCACTS
        7
        GTCACTG
       
        AGCKCGC
        7
        AGCGCGC
       
        ATAATACA
        8
        ATAATACA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CAMGGA
        6
        CAAGGA
       
        AGAAGYCA
        8
        AGAAGTCA
       
        ATCWGAAG
        8
        ATCAGAAG
       
        RCGGGGA
        7
        ACGGGGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/background):

A 0.318 C 0.182 G 0.182 T 0.318

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
ACCWCT	6	ACCACT
ARAAAAR	7	AAAAAAA
TAAGGCR	7	TAAGGCG
CCRTACA	7	CCATACA
AAGATTTM	8	AAGATTTC
CTTRGC	6	CTTGGC
ACCTAAAS	8	ACCTAAAC
GTCACTS	7	GTCACTG
AGCKCGC	7	AGCGCGC
ATAATACA	8	ATAATACA
ATGGCAWC	8	ATGGCAAC
CAMGGA	6	CAAGGA
AGAAGYCA	8	AGAAGTCA
ATCWGAAG	8	ATCAGAAG
RCGGGGA	7	ACGGGGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 44 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
ACCTAAAS	DREME-8	chrI	+	749	756	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrI	+	749	756	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXV	+	795	802	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIV	+	852	859	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIII	+	1046	1053	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVIII	+	5453	5460	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrV	+	6421	6428	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrII	+	6556	6563	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrV	+	148116	148123	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVI	-	157746	157753	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXVI	-	188917	188924	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVIII	+	292085	292092	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIII	-	315826	315833	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIX	-	439111	439118	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIV	+	519695	519702	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVIII	-	556148	556155	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrV	-	569642	569649	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXI	-	665947	665954	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIV	-	916126	916133	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXIII	-	923583	923590	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXVI	-	942439	942446	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrXV	-	980186	980193	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVII	+	1057730	1057737	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrVII	-	1083678	1083685	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIV	-	1355968	1355975	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrIV	-	1524668	1524675	1.96e-05	0.647	ACCTAAAC
ACCTAAAS	DREME-8	chrX	-	228413	228420	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrX	-	228413	228420	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrII	+	326757	326764	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrX	-	390952	390959	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrIV	-	465429	465436	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	+	481124	481131	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrXVI	-	577352	577359	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrIV	+	599854	599861	3.92e-05	0.765	ACCTAAAG
ACCTAAAS	DREME-8	chrVII	-	876545	876552	3.92e-05	0.765	ACCTAAAG

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--MIG1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/background --motif ACCTAAAS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/BY4741--MIG1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/BY4741--MIG1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/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/BY4741--MIG1/fimo_out_8	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/BY4741--MIG1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MIG1/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