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/BY4742--NOT3/BY4742--NOT3.fa
  
  Database contains 529 sequences, 323010 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AACCACTH
        8
        AACCACTT
       
        CAASTTGG
        8
        CAACTTGG
       
        GYGGTCTA
        8
        GTGGTCTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AAAAARAA
        8
        AAAAAAAA
       
        ATGGGYG
        7
        ATGGGTG
       
        ATCKTGA
        7
        ATCTTGA
       
        AGARGTC
        7
        AGAAGTC
       
        CCWTAACC
        8
        CCATAACC
       
        ATCCGTRC
        8
        ATCCGTAC
       
        CCRTGGAG
        8
        CCGTGGAG
       
        ATGGTCA
        7
        ATGGTCA
       
        AARGCGTG
        8
        AAGGCGTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AACCACTH	8	AACCACTT
CAASTTGG	8	CAACTTGG
GYGGTCTA	8	GTGGTCTA
GCKCTACC	8	GCGCTACC
AAAAARAA	8	AAAAAAAA
ATGGGYG	7	ATGGGTG
ATCKTGA	7	ATCTTGA
AGARGTC	7	AGAAGTC
CCWTAACC	8	CCATAACC
ATCCGTRC	8	ATCCGTAC
CCRTGGAG	8	CCGTGGAG
ATGGTCA	7	ATGGTCA
AARGCGTG	8	AAGGCGTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 38 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
AGARGTC	DREME-9	chrV	+	6754	6760	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrI	+	166307	166313	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXI	+	219935	219941	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIV	+	222235	222241	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXIII	+	298834	298840	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	310999	311005	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIX	+	316499	316505	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVIII	+	382977	382983	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIV	+	410419	410425	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXI	+	518028	518034	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	544495	544501	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXVI	+	689737	689743	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	774389	774395	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	794457	794463	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIV	+	802728	802734	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXVI	+	856942	856948	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	876366	876372	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVII	+	1000688	1000694	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXI	-	46071	46077	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXVI	-	76479	76485	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXV	-	93528	93534	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVIII	-	146266	146272	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXV	-	168371	168377	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrX	-	197337	197343	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVI	-	204948	204954	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVI	-	211005	211011	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXII	-	214907	214913	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrV	-	312047	312053	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXI	-	313299	313305	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXIII	-	321171	321177	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIX	-	438779	438785	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrVIII	-	451748	451754	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXI	-	520305	520311	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIV	-	645059	645065	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXII	-	656958	656964	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXIII	-	768393	768399	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrXV	-	854211	854217	4.07e-05	0.685	AGAGGTC
AGARGTC	DREME-9	chrIV	-	1355740	1355746	4.07e-05	0.685	AGAGGTC

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/BY4742--NOT3/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/background --motif AGARGTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/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/gm_results/BY4742--NOT3/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4742--NOT3/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