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/RM11-1A--NRG1/RM11-1A--NRG1.fa
  
  Database contains 666 sequences, 220217 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCRA
        7
        GGTTCGA
       
        CTYGGCCA
        8
        CTCGGCCA
       
        SAAGAW
        6
        GAAGAA
       
        ACCCANAC
        8
        ACCCATAC
       
        CTTAAYCA
        8
        CTTAACCA
       
        TAGTGGTW
        8
        TAGTGGTA
       
        CATCCGTR
        8
        CATCCGTA
       
        GCGCYAC
        7
        GCGCTAC
       
        AKATCGG
        7
        AGATCGG
       
        CACCGTGS
        8
        CACCGTGG
       
        GGCAACGY
        8
        GGCAACGT
       
        ARAAAAW
        7
        AAAAAAA
       
        TGGCBCA
        7
        TGGCGCA
       
        CCAACWGA
        8
        CCAACTGA
       
        CTTGCGC
        7
        CTTGCGC
       
        CGCGTGSC
        8
        CGCGTGCC
       
        TGGTCTAR
        8
        TGGTCTAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCRA	7	GGTTCGA
CTYGGCCA	8	CTCGGCCA
SAAGAW	6	GAAGAA
ACCCANAC	8	ACCCATAC
CTTAAYCA	8	CTTAACCA
TAGTGGTW	8	TAGTGGTA
CATCCGTR	8	CATCCGTA
GCGCYAC	7	GCGCTAC
AKATCGG	7	AGATCGG
CACCGTGS	8	CACCGTGG
GGCAACGY	8	GGCAACGT
ARAAAAW	7	AAAAAAA
TGGCBCA	7	TGGCGCA
CCAACWGA	8	CCAACTGA
CTTGCGC	7	CTTGCGC
CGCGTGSC	8	CGCGTGCC
TGGTCTAR	8	TGGTCTAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 34 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
AKATCGG	DREME-9	chrVI	+	167495	167501	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIII	+	168853	168859	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	+	204777	204783	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIII	+	253422	253428	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXV	+	288250	288256	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIX	+	300120	300126	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXV	+	301091	301097	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	+	354302	354308	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	+	355498	355504	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	+	355498	355504	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrII	+	406002	406008	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXII	+	427174	427180	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIII	+	463596	463602	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXI	+	519076	519082	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	+	541550	541556	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIV	+	569006	569012	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIV	+	569006	569012	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXV	+	572000	572006	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrVII	+	700552	700558	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXII	+	793960	793966	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXII	+	793960	793966	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIII	+	837986	837992	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIV	+	946370	946376	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIV	+	1161853	1161859	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrVI	-	31377	31383	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXV	-	160337	160343	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrVI	-	210641	210647	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrIX	-	324324	324330	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	-	374445	374451	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXI	-	513353	513359	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIV	-	519120	519126	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrX	-	542978	542984	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrVII	-	544598	544604	4.07e-05	0.517	AGATCGG
AKATCGG	DREME-9	chrXIII	-	756775	756781	4.07e-05	0.517	AGATCGG

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/RM11-1A--NRG1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/background --motif AKATCGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/RM11-1A--NRG1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/RM11-1A--NRG1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/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/RM11-1A--NRG1/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/RM11-1A--NRG1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--NRG1/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