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--ACE2/AWRI1631--ACE2.fa
  
  Database contains 484 sequences, 161033 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        CAYCCRTA
        8
        CACCCATA
       
        CAACTKGG
        8
        CAACTTGG
       
        CGCSTTA
        7
        CGCCTTA
       
        CCABAC
        6
        CCACAC
       
        CGCKCTAC
        8
        CGCGCTAC
       
        AARAAA
        6
        AAAAAA
       
        CCAAVAGA
        8
        CCAAGAGA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CAASGATG
        8
        CAACGATG
       
        GTGGAGA
        7
        GTGGAGA
       
        ATTAASAG
        8
        ATTAAGAG
       
        TGCGCCA
        7
        TGCGCCA
       
        AGMATGGG
        8
        AGAATGGG
       
        CCGTGCW
        7
        CCGTGCT
       
        AAGCGWGA
        8
        AAGCGTGA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        GCAACGY
        7
        GCAACGT
       
        AMACCCA
        7
        AAACCCA
       
        ACCGAWG
        7
        ACCGATG
       
        GCAYGCGA
        8
        GCACGCGA
       
        GRGTTCAA
        8
        GGGTTCAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
CAYCCRTA	8	CACCCATA
CAACTKGG	8	CAACTTGG
CGCSTTA	7	CGCCTTA
CCABAC	6	CCACAC
CGCKCTAC	8	CGCGCTAC
AARAAA	6	AAAAAA
CCAAVAGA	8	CCAAGAGA
ATAGTKTA	8	ATAGTGTA
CAASGATG	8	CAACGATG
GTGGAGA	7	GTGGAGA
ATTAASAG	8	ATTAAGAG
TGCGCCA	7	TGCGCCA
AGMATGGG	8	AGAATGGG
CCGTGCW	7	CCGTGCT
AAGCGWGA	8	AAGCGTGA
ACTGAGCT	8	ACTGAGCT
GCAACGY	7	GCAACGT
AMACCCA	7	AAACCCA
ACCGAWG	7	ACCGATG
GCAYGCGA	8	GCACGCGA
GRGTTCAA	8	GGGTTCAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 34 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
GTGGAGA	DREME-12	chrII	+	89850	89856	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXIV	+	104843	104849	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXV	+	113840	113846	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIX	+	175069	175075	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrV	+	177137	177143	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIX	+	197630	197636	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXII	+	232714	232720	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrII	+	266416	266422	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXIII	+	290839	290845	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIII	+	295522	295528	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIII	+	295522	295528	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIX	+	316576	316582	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrVII	+	328621	328627	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrV	+	354972	354978	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIX	+	370455	370461	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrVII	+	541888	541894	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrII	+	645205	645211	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXII	+	797216	797222	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrX	-	59126	59132	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIII	-	82487	82493	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrX	-	115964	115970	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrVIII	-	116133	116139	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXI	-	141043	141049	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXII	-	199565	199571	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXII	-	199565	199571	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXVI	-	210217	210223	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXV	-	354067	354073	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrVII	-	401552	401558	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIV	-	434290	434296	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrV	-	438623	438629	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrV	-	487356	487362	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIV	-	492079	492085	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrXIV	-	560719	560725	4.03e-05	0.373	GTGGAGA
GTGGAGA	DREME-12	chrIV	-	1017232	1017238	4.03e-05	0.373	GTGGAGA

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--ACE2/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/background --motif GTGGAGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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/AWRI1631--ACE2/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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