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/BY4742--THP2/BY4742--THP2.fa
  
  Database contains 1112 sequences, 1329723 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TCTTCW
        6
        TCTTCT
       
        CCATBG
        6
        CCATTG
       
        CGGTR
        5
        CGGTA
       
        BTTGG
        5
        TTTGG
       
        AYCCRTAC
        8
        ATCCATAC
       
        TMAACAA
        7
        TCAACAA
       
        GATTCYA
        7
        GATTCTA
       
        AAGGYTGC
        8
        AAGGCTGC
       
        GGSTTCGA
        8
        GGGTTCGA
       
        ATTDGCTG
        8
        ATTTGCTG
       
        CGCCTTA
        7
        CGCCTTA
       
        GMAGTTGA
        8
        GAAGTTGA
       
        CTARACCA
        8
        CTAAACCA
       
        TGGTATGR
        8
        TGGTATGA
       
        TAAKAGCA
        8
        TAAGAGCA
       
        GAACCAS
        7
        GAACCAC
       
        CATCTRC
        7
        CATCTAC
       
        CGCTAGW
        7
        CGCTAGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
TCTTCW	6	TCTTCT
CCATBG	6	CCATTG
CGGTR	5	CGGTA
BTTGG	5	TTTGG
AYCCRTAC	8	ATCCATAC
TMAACAA	7	TCAACAA
GATTCYA	7	GATTCTA
AAGGYTGC	8	AAGGCTGC
GGSTTCGA	8	GGGTTCGA
ATTDGCTG	8	ATTTGCTG
CGCCTTA	7	CGCCTTA
GMAGTTGA	8	GAAGTTGA
CTARACCA	8	CTAAACCA
TGGTATGR	8	TGGTATGA
TAAKAGCA	8	TAAGAGCA
GAACCAS	7	GAACCAC
CATCTRC	7	CATCTAC
CGCTAGW	7	CGCTAGA

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/BY4742--THP2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/background --motif BTTGG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/BY4742--THP2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/BY4742--THP2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/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/BY4742--THP2/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/BY4742--THP2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--THP2/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