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--CIN5/RM11-1A--CIN5.fa
  
  Database contains 637 sequences, 201818 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        BTAAGGCG
        8
        TTAAGGCG
       
        ACTARACC
        8
        ACTAGACC
       
        CGCKCTAC
        8
        CGCGCTAC
       
        AAGAMAAA
        8
        AAGAAAAA
       
        GTGATAGY
        8
        GTGATAGC
       
        GAASTCA
        7
        GAAGTCA
       
        GTWGCCA
        7
        GTTGCCA
       
        CCGTGSA
        7
        CCGTGGA
       
        AYCAGAAG
        8
        ATCAGAAG
       
        ACTGMGC
        7
        ACTGAGC
       
        SCGCTTA
        7
        GCGCTTA
       
        GARTCATA
        8
        GAGTCATA
       
        ACACTATA
        8
        ACACTATA
       
        ACGCGRG
        7
        ACGCGAG
       
        AAAGCGTG
        8
        AAAGCGTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
CTBGGCCA	8	CTCGGCCA
BTAAGGCG	8	TTAAGGCG
ACTARACC	8	ACTAGACC
CGCKCTAC	8	CGCGCTAC
AAGAMAAA	8	AAGAAAAA
GTGATAGY	8	GTGATAGC
GAASTCA	7	GAAGTCA
GTWGCCA	7	GTTGCCA
CCGTGSA	7	CCGTGGA
AYCAGAAG	8	ATCAGAAG
ACTGMGC	7	ACTGAGC
SCGCTTA	7	GCGCTTA
GARTCATA	8	GAGTCATA
ACACTATA	8	ACACTATA
ACGCGRG	7	ACGCGAG
AAAGCGTG	8	AAAGCGTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 20 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
AAAGCGTG	DREME-18	chrIII	+	82498	82505	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXV	+	87686	87693	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrX	+	115975	115982	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXI	+	141054	141061	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXVI	+	210228	210235	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrVII	+	401563	401570	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrV	+	487367	487374	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXV	+	968259	968266	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrV	-	177125	177132	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXIII	-	290827	290834	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrVII	-	328609	328616	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrV	-	354960	354967	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrIX	-	370443	370450	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrX	-	374623	374630	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXV	-	408063	408070	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrVII	-	541876	541883	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXIV	-	577353	577360	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrII	-	645193	645200	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXIV	-	764000	764007	1.2e-05	0.237	AAAGCGTG
AAAGCGTG	DREME-18	chrXII	-	797204	797211	1.2e-05	0.237	AAAGCGTG

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--CIN5/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/background --motif AAAGCGTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/RM11-1A--CIN5.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/RM11-1A--CIN5.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CIN5/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