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/BY4741--ACE2/BY4741--ACE2.fa
  
  Database contains 712 sequences, 205934 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CCRTACA
        7
        CCATACA
       
        AGTGGTWA
        8
        AGTGGTTA
       
        CAACTKGG
        8
        CAACTTGG
       
        GCKCTACC
        8
        GCGCTACC
       
        AAGGCRCC
        8
        AAGGCGCC
       
        GGYTCGA
        7
        GGTTCGA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TGGCGYA
        7
        TGGCGCA
       
        AAGARA
        6
        AAGAAA
       
        ACCCAVAC
        8
        ACCCACAC
       
        ACACTATA
        8
        ACACTATA
       
        GATTWGAA
        8
        GATTTGAA
       
        GTGGTCTA
        8
        GTGGTCTA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/background):

A 0.320 C 0.180 G 0.180 T 0.320

MOTIF	WIDTH	BEST POSSIBLE MATCH
CCRTACA	7	CCATACA
AGTGGTWA	8	AGTGGTTA
CAACTKGG	8	CAACTTGG
GCKCTACC	8	GCGCTACC
AAGGCRCC	8	AAGGCGCC
GGYTCGA	7	GGTTCGA
ATGGCAWC	8	ATGGCAAC
TGGCGYA	7	TGGCGCA
AAGARA	6	AAGAAA
ACCCAVAC	8	ACCCACAC
ACACTATA	8	ACACTATA
GATTWGAA	8	GATTTGAA
GTGGTCTA	8	GTGGTCTA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 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
ACACTATA	DREME-11	chrVIII	-	134325	134332	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrV	-	177103	177110	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrV	-	250290	250297	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXIII	-	290805	290812	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrVII	-	328587	328594	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrII	-	350831	350838	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrV	-	354938	354945	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIX	-	370421	370428	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXIV	-	495391	495398	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIV	-	520976	520983	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrVII	-	541854	541861	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrII	-	645171	645178	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXII	-	797182	797189	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIII	+	82520	82527	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrX	+	115997	116004	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrV	+	131140	131147	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXI	+	141076	141083	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXIII	+	146121	146128	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIII	+	168359	168366	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXVI	+	210250	210257	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIX	+	316384	316391	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrVII	+	401585	401592	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXV	+	447383	447390	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXII	+	448708	448715	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrV	+	487389	487396	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIV	+	645211	645218	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXVI	+	769131	769138	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrVII	+	785050	785057	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrIV	+	802789	802796	3.49e-05	0.467	ACACTATA
ACACTATA	DREME-11	chrXIII	+	808304	808311	3.49e-05	0.467	ACACTATA

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/BY4741--ACE2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/background --motif ACACTATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/BY4741--ACE2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/BY4741--ACE2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/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/BY4741--ACE2/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/BY4741--ACE2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--ACE2/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