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--CAT8/RM11-1A--CAT8.fa
  
  Database contains 473 sequences, 156360 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        AYCCRTAC
        8
        ACCCATAC
       
        CGCSTTA
        7
        CGCCTTA
       
        CCAACTK
        7
        CCAACTT
       
        AARARA
        6
        AAAAAA
       
        CAASGATG
        8
        CAACGATG
       
        CATYACGC
        8
        CATCACGC
       
        CCGTGSA
        7
        CCGTGGA
       
        ATCTTSA
        7
        ATCTTGA
       
        CGSCCA
        6
        CGCCCA
       
        AGTCTKG
        7
        AGTCTTG
       
        GCTACCGA
        8
        GCTACCGA
       
        AGMAGAT
        7
        AGAAGAT
       
        GCGTMTGA
        8
        GCGTATGA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        GCTATMA
        7
        GCTATCA
       
        AACACSCA
        8
        AACACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
AYCCRTAC	8	ACCCATAC
CGCSTTA	7	CGCCTTA
CCAACTK	7	CCAACTT
AARARA	6	AAAAAA
CAASGATG	8	CAACGATG
CATYACGC	8	CATCACGC
CCGTGSA	7	CCGTGGA
ATCTTSA	7	ATCTTGA
CGSCCA	6	CGCCCA
AGTCTKG	7	AGTCTTG
GCTACCGA	8	GCTACCGA
AGMAGAT	7	AGAAGAT
GCGTMTGA	8	GCGTATGA
ATAGTKTA	8	ATAGTGTA
GCTATMA	7	GCTATCA
AACACSCA	8	AACACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 18 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
AGTCTKG	DREME-12	chrII	-	36423	36429	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrIII	+	123681	123687	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVI	+	157974	157980	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXII	-	199654	199660	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrIV	+	217380	217386	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVIII	+	237906	237912	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXIII	-	352305	352311	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVIII	+	358536	358542	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXIII	-	372337	372343	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXIV	-	374894	374900	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVIII	+	383028	383034	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVII	+	440774	440780	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrX	+	542917	542923	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXVI	+	560256	560262	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXVI	+	622598	622604	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrVII	-	848203	848209	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrXV	-	979015	979021	3.96e-05	0.676	AGTCTGG
AGTCTKG	DREME-12	chrIV	+	1095428	1095434	3.96e-05	0.676	AGTCTGG

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--CAT8/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/background --motif AGTCTKG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/RM11-1A--CAT8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/RM11-1A--CAT8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/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--CAT8/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/RM11-1A--CAT8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAT8/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