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/gm_results/AWRI1631--PDR8/AWRI1631--PDR8.fa
  
  Database contains 508 sequences, 395712 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AAARAAAW
        8
        AAAAAAAA
       
        ACCWCT
        6
        ACCACT
       
        ACCAACTK
        8
        ACCAACTT
       
        CGGATGY
        7
        CGGATGT
       
        GTAKGAC
        7
        GTAGGAC
       
        CACCCA
        6
        CACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AAARAAAW	8	AAAAAAAA
ACCWCT	6	ACCACT
ACCAACTK	8	ACCAACTT
CGGATGY	7	CGGATGT
GTAKGAC	7	GTAGGAC
CACCCA	6	CACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 23 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
GTAKGAC	DREME-6	chrIII	-	588	594	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrII	+	89618	89624	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrV	-	117711	117717	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIX	-	128938	128944	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrVIII	+	134383	134389	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIII	-	168302	168308	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	+	199180	199186	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	-	199307	199313	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrV	+	250348	250354	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIII	+	316283	316289	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXIV	-	330929	330935	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrVII	+	412194	412200	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrX	+	423127	423133	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	-	448651	448657	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	-	499254	499260	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIV	+	521034	521040	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	+	522676	522682	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrVIII	+	556620	556626	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIV	-	645154	645160	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrX	+	745406	745412	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrIV	-	802732	802738	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXVI	-	860589	860595	4.07e-05	1	GTAGGAC
GTAKGAC	DREME-6	chrXII	-	1028327	1028333	4.07e-05	1	GTAGGAC

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/gm_results/AWRI1631--PDR8/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/background --motif GTAKGAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/AWRI1631--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/fimo_out_5
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/AWRI1631--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/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/gm_results/AWRI1631--PDR8/fimo_out_5	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/AWRI1631--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/AWRI1631--PDR8/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