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/YJM789--PDR3/YJM789--PDR3.fa
  
  Database contains 560 sequences, 160984 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        RGTTCGA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        ACCAACTK
        8
        ACCAACTT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCGCYAC
        7
        GCGCTAC
       
        CCGTGGAR
        8
        CCGTGGAA
       
        CCAAVAGA
        8
        CCAAGAGA
       
        CTATCACR
        8
        CTATCACG
       
        GYGGTCTA
        8
        GTGGTCTA
       
        SAAGAW
        6
        CAAGAA
       
        CGSCCA
        6
        CGCCCA
       
        ACAARGC
        7
        ACAAAGC
       
        GGCSCAA
        7
        GGCGCAA
       
        GCACGS
        6
        GCACGG
       
        GGRGATCA
        8
        GGGGATCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
RGTTCGA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
ACCAACTK	8	ACCAACTT
ATGGCAWC	8	ATGGCAAC
GCGCYAC	7	GCGCTAC
CCGTGGAR	8	CCGTGGAA
CCAAVAGA	8	CCAAGAGA
CTATCACR	8	CTATCACG
GYGGTCTA	8	GTGGTCTA
SAAGAW	6	CAAGAA
CGSCCA	6	CGCCCA
ACAARGC	7	ACAAAGC
GGCSCAA	7	GGCGCAA
GCACGS	6	GCACGG
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/YJM789--PDR3/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/background --motif SAAGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/YJM789--PDR3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/YJM789--PDR3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/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/YJM789--PDR3/fimo_out_11	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/YJM789--PDR3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR3/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