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--PDR8/RM11-1A--PDR8.fa
  
  Database contains 482 sequences, 155001 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        CCCATDC
        7
        CCCATAC
       
        CAACTKGG
        8
        CAACTTGG
       
        ATCCRTAC
        8
        ATCCGTAC
       
        BTAAGGCG
        8
        TTAAGGCG
       
        GCKCTACC
        8
        GCGCTACC
       
        GTGATAGY
        8
        GTGATAGC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACGGYG
        7
        CACGGTG
       
        ATCTTYTG
        8
        ATCTTTTG
       
        ACGCSAC
        7
        ACGCCAC
       
        RAAAAAA
        7
        AAAAAAA
       
        CCAASAGA
        8
        CCAAGAGA
       
        AACACSCA
        8
        AACACCCA
       
        ATCKTGAG
        8
        ATCGTGAG
       
        ACTGAGCT
        8
        ACTGAGCT
       
        AAGCGWGA
        8
        AAGCGTGA
       
        GGCSCAA
        7
        GGCCCAA
       
        ACACTATA
        8
        ACACTATA
       
        AGACCWC
        7
        AGACCAC
       
        GGRGATCA
        8
        GGGGATCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
CCCATDC	7	CCCATAC
CAACTKGG	8	CAACTTGG
ATCCRTAC	8	ATCCGTAC
BTAAGGCG	8	TTAAGGCG
GCKCTACC	8	GCGCTACC
GTGATAGY	8	GTGATAGC
ATGGCAWC	8	ATGGCAAC
CACGGYG	7	CACGGTG
ATCTTYTG	8	ATCTTTTG
ACGCSAC	7	ACGCCAC
RAAAAAA	7	AAAAAAA
CCAASAGA	8	CCAAGAGA
AACACSCA	8	AACACCCA
ATCKTGAG	8	ATCGTGAG
ACTGAGCT	8	ACTGAGCT
AAGCGWGA	8	AAGCGTGA
GGCSCAA	7	GGCCCAA
ACACTATA	8	ACACTATA
AGACCWC	7	AGACCAC
GGRGATCA	8	GGGGATCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 0 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

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--PDR8/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/background --motif RAAAAAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/RM11-1A--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/RM11-1A--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/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--PDR8/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/RM11-1A--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PDR8/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