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--SOK2/RM11-1A--SOK2.fa
  
  Database contains 965 sequences, 420806 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCGA
        7
        GGTTCGA
       
        AARAAAW
        7
        AAAAAAA
       
        BCACGG
        6
        GCACGG
       
        ATGTAYGG
        8
        ATGTATGG
       
        CCTTAAMC
        8
        CCTTAACC
       
        GCKCTACC
        8
        GCGCTACC
       
        CAGAARA
        7
        CAGAAGA
       
        CTYGGCCA
        8
        CTCGGCCA
       
        CAACGWTG
        8
        CAACGATG
       
        DCACCCA
        7
        ACACCCA
       
        AASAAGAA
        8
        AAGAAGAA
       
        CACTATW
        7
        CACTATA
       
        ACTGAGCT
        8
        ACTGAGCT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCGA	7	GGTTCGA
AARAAAW	7	AAAAAAA
BCACGG	6	GCACGG
ATGTAYGG	8	ATGTATGG
CCTTAAMC	8	CCTTAACC
GCKCTACC	8	GCGCTACC
CAGAARA	7	CAGAAGA
CTYGGCCA	8	CTCGGCCA
CAACGWTG	8	CAACGATG
DCACCCA	7	ACACCCA
AASAAGAA	8	AAGAAGAA
CACTATW	7	CACTATA
ACTGAGCT	8	ACTGAGCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 24 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
ACTGAGCT	DREME-13	chrII	-	36405	36412	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrVII	-	115495	115502	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrVI	+	157991	157998	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrVIII	+	237923	237930	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXIII	+	298402	298409	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXIII	+	298402	298409	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXIII	+	298402	298409	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXIII	-	352287	352294	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrIV	-	359584	359591	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXIV	-	374876	374883	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrX	+	391099	391106	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrX	-	422944	422951	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXV	-	438650	438657	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrVII	+	440791	440798	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXVI	+	560273	560280	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXI	-	578972	578979	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXII	+	605416	605423	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXVI	+	622615	622622	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrVII	+	701032	701039	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXII	-	875383	875390	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrIV	-	884368	884375	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrXV	-	976428	976435	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrIV	+	1095445	1095452	1.26e-05	0.435	ACTGAGCT
ACTGAGCT	DREME-13	chrIV	-	1175836	1175843	1.26e-05	0.435	ACTGAGCT

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--SOK2/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/background --motif ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/RM11-1A--SOK2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/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--SOK2/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/RM11-1A--SOK2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SOK2/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