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--MGA2/BY4741--MGA2.fa
  
  Database contains 755 sequences, 321844 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        CCRTRCA
        7
        CCATACA
       
        ACCACTV
        7
        ACCACTA
       
        DCGCCTTA
        8
        GCGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        CCAACTKG
        8
        CCAACTTG
       
        CCAAVAGA
        8
        CCAAGAGA
       
        RAARAAA
        7
        AAAAAAA
       
        TGGCGYA
        7
        TGGCGCA
       
        GATTWGAA
        8
        GATTAGAA
       
        ACCCABAC
        8
        ACCCACAC
       
        CACGGTGM
        8
        CACGGTGA
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CACTATAK
        8
        CACTATAT
       
        ACTCASG
        7
        ACTCACG
       
        ACTWGACC
        8
        ACTAGACC
       
        GCAYGCGA
        8
        GCATGCGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/background):

A 0.319 C 0.181 G 0.181 T 0.319

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
CCRTRCA	7	CCATACA
ACCACTV	7	ACCACTA
DCGCCTTA	8	GCGCCTTA
ATGGCAWC	8	ATGGCAAC
GCKCTACC	8	GCGCTACC
CCAACTKG	8	CCAACTTG
CCAAVAGA	8	CCAAGAGA
RAARAAA	7	AAAAAAA
TGGCGYA	7	TGGCGCA
GATTWGAA	8	GATTAGAA
ACCCABAC	8	ACCCACAC
CACGGTGM	8	CACGGTGA
AAGCGWGA	8	AAGCGTGA
CACTATAK	8	CACTATAT
ACTCASG	7	ACTCACG
ACTWGACC	8	ACTAGACC
GCAYGCGA	8	GCATGCGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 38 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
GCAYGCGA	DREME-18	chrX	-	204768	204775	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrIX	+	324332	324339	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrX	-	355489	355496	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrVII	+	371377	371384	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrX	+	374453	374460	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrII	-	405993	406000	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXII	-	427165	427172	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXIII	-	463587	463594	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXI	+	513361	513368	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrX	-	541541	541548	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrVII	+	544606	544613	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrIV	-	568997	569004	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXV	-	571991	571998	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXII	-	793951	793958	3.62e-06	0.164	GCACGCGA
GCAYGCGA	DREME-18	chrXII	+	92611	92618	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrVI	+	101439	101446	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrI	+	139215	139222	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXIII	-	196098	196105	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrVII	+	277167	277174	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXV	+	301159	301166	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrVIII	-	388923	388930	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXV	+	464512	464519	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXIV	+	547157	547164	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXIV	+	568178	568185	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrXV	+	980748	980755	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrIV	-	1300927	1300934	9.97e-06	0.243	GCATGCGA
GCAYGCGA	DREME-18	chrVIII	+	126938	126945	1.99e-05	0.407	GCAGGCGA
GCAYGCGA	DREME-18	chrXII	+	150490	150497	1.99e-05	0.407	GCAAGCGA
GCAYGCGA	DREME-18	chrV	-	311970	311977	1.99e-05	0.407	GCAAGCGA
GCAYGCGA	DREME-18	chrII	-	592960	592967	1.99e-05	0.407	GCAGGCGA
GCAYGCGA	DREME-18	chrIV	+	1257242	1257249	1.99e-05	0.407	GCAGGCGA
GCAYGCGA	DREME-18	chrX	+	74215	74222	3.54e-05	0.59	GCTCGCGA
GCAYGCGA	DREME-18	chrXVI	+	76450	76457	3.54e-05	0.59	GCACGCGG
GCAYGCGA	DREME-18	chrII	+	165159	165166	3.54e-05	0.59	GCACGCGG
GCAYGCGA	DREME-18	chrXII	+	687707	687714	3.54e-05	0.59	GCTCGCGA
GCAYGCGA	DREME-18	chrVII	+	726666	726673	3.54e-05	0.59	GCACGCGG
GCAYGCGA	DREME-18	chrIV	+	946600	946607	3.54e-05	0.59	GCGCGCGA
GCAYGCGA	DREME-18	chrXII	-	370650	370657	3.54e-05	0.59	GCACGCGC

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--MGA2/fimo_out_14 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/background --motif GCAYGCGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/fimo_out_14
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/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--MGA2/fimo_out_14	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/BY4741--MGA2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--MGA2/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