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/AWRI1631--SWR1/AWRI1631--SWR1.fa
  
  Database contains 446 sequences, 123197 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CCRTACA
        7
        CCATACA
       
        AGTGGTW
        7
        AGTGGTT
       
        GGHTCGA
        7
        GGTTCGA
       
        AGTYGGTW
        8
        AGTTGGTT
       
        CACGGW
        6
        CACGGA
       
        CRCCCA
        6
        CACCCA
       
        AASGCG
        6
        AAGGCG
       
        CCAAVAGA
        8
        CCAAGAGA
       
        GCGCTHCC
        8
        GCGCTACC
       
        CGGCCAM
        7
        CGGCCAA
       
        CGCCASAC
        8
        CGCCACAC
       
        GACTSTTA
        8
        GACTCTTA
       
        GCTAWCA
        7
        GCTATCA
       
        ATCKTGA
        7
        ATCTTGA
       
        ARAAAAA
        7
        AAAAAAA
       
        AGACCACR
        8
        AGACCACG
       
        GCCATRGA
        8
        GCCATAGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
CCRTACA	7	CCATACA
AGTGGTW	7	AGTGGTT
GGHTCGA	7	GGTTCGA
AGTYGGTW	8	AGTTGGTT
CACGGW	6	CACGGA
CRCCCA	6	CACCCA
AASGCG	6	AAGGCG
CCAAVAGA	8	CCAAGAGA
GCGCTHCC	8	GCGCTACC
CGGCCAM	7	CGGCCAA
CGCCASAC	8	CGCCACAC
GACTSTTA	8	GACTCTTA
GCTAWCA	7	GCTATCA
ATCKTGA	7	ATCTTGA
ARAAAAA	7	AAAAAAA
AGACCACR	8	AGACCACG
GCCATRGA	8	GCCATAGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 26 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
GCTAWCA	DREME-13	chrVII	+	122228	122234	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrV	+	177115	177121	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrIX	+	197608	197614	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrVII	+	254288	254294	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXIII	+	290817	290823	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrVII	+	328599	328605	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrV	+	354950	354956	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrIX	+	370433	370439	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrVII	+	541866	541872	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXIV	+	632720	632726	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrII	+	645183	645189	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXII	+	797194	797200	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrIV	+	992702	992708	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXIV	-	48057	48063	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXVI	-	56119	56125	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrX	-	115986	115992	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXI	-	141065	141071	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXVI	-	210239	210245	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrVIII	-	475754	475760	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrV	-	487378	487384	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXII	-	838781	838787	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXII	-	838847	838853	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXII	-	976100	976106	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrXV	-	976300	976306	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrIV	-	1017254	1017260	6.37e-05	0.59	GCTATCA
GCTAWCA	DREME-13	chrIV	-	1075520	1075526	6.37e-05	0.59	GCTATCA

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/AWRI1631--SWR1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/background --motif GCTAWCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/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/AWRI1631--SWR1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/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