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/BY4742--NOT3/BY4742--NOT3.fa
  
  Database contains 513 sequences, 171825 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTYGGTW
        8
        AGTTGGTT
       
        CCRTACAY
        8
        CCATACAT
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGGGNG
        7
        ATGGGTG
       
        GCGCTHCC
        8
        GCGCTACC
       
        AAGAAAWA
        8
        AAGAAAAA
       
        ATMCAAC
        7
        ATACAAC
       
        CCASAC
        6
        CCACAC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CYATGGCC
        8
        CTATGGCC
       
        AATCTTYT
        8
        AATCTTTT
       
        GCGCAAK
        7
        GCGCAAG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAGRTTAG
        8
        AAGGTTAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CCAASAG
        7
        CCAAGAG
       
        CCGTGMTA
        8
        CCGTGATA
       
        GGCTAYC
        7
        GGCTATC
       
        CGCGRGC
        7
        CGCGAGC
       
        GCGTGCSA
        8
        GCGTGCGA
       
        ACTSACG
        7
        ACTGACG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTYGGTW	8	AGTTGGTT
CCRTACAY	8	CCATACAT
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
CGCSTTA	7	CGCCTTA
ATGGCAWC	8	ATGGCAAC
ATGGGNG	7	ATGGGTG
GCGCTHCC	8	GCGCTACC
AAGAAAWA	8	AAGAAAAA
ATMCAAC	7	ATACAAC
CCASAC	6	CCACAC
GRTCTCCA	8	GGTCTCCA
CYATGGCC	8	CTATGGCC
AATCTTYT	8	AATCTTTT
GCGCAAK	7	GCGCAAG
AGTCAKAC	8	AGTCATAC
AAGRTTAG	8	AAGGTTAG
AAGCGWGA	8	AAGCGTGA
CCAASAG	7	CCAAGAG
CCGTGMTA	8	CCGTGATA
GGCTAYC	7	GGCTATC
CGCGRGC	7	CGCGAGC
GCGTGCSA	8	GCGTGCGA
ACTSACG	7	ACTGACG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 44 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
GCGTGCSA	DREME-23	chrXI	+	74647	74654	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXIV	+	102739	102746	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrIII	+	127739	127746	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrVI	-	137527	137534	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXV	+	228354	228361	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXV	+	487462	487469	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXIV	+	632622	632629	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrVII	+	731160	731167	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXVI	+	810699	810706	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrVII	-	856751	856758	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXII	-	976024	976031	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrXV	-	1004191	1004198	5.14e-06	0.128	GCGTGCGA
GCGTGCSA	DREME-23	chrX	+	204770	204777	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrIX	-	324330	324337	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrX	+	355491	355498	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrX	-	374451	374458	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrX	-	391278	391285	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrII	+	405995	406002	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXII	+	427167	427174	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXIII	+	463589	463596	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXI	-	513359	513366	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrVII	+	531645	531652	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrX	+	541543	541550	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrVII	-	544604	544611	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrIV	+	568999	569006	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXV	+	571993	572000	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXII	+	793953	793960	1.03e-05	0.128	GCGTGCCA
GCGTGCSA	DREME-23	chrXV	+	160445	160452	2.63e-05	0.286	GCGTGCAA
GCGTGCSA	DREME-23	chrVII	-	277365	277372	2.63e-05	0.286	GCGTGCAA
GCGTGCSA	DREME-23	chrV	-	442069	442076	2.63e-05	0.286	GCGTGCAA
GCGTGCSA	DREME-23	chrV	-	442069	442076	2.63e-05	0.286	GCGTGCAA
GCGTGCSA	DREME-23	chrXV	+	968277	968284	4.98e-05	0.465	GCGTGCGC
GCGTGCSA	DREME-23	chrXV	+	978860	978867	4.98e-05	0.465	GCGTGCGT
GCGTGCSA	DREME-23	chrXVI	-	76448	76455	4.98e-05	0.465	GCGTGCGC
GCGTGCSA	DREME-23	chrII	-	165157	165164	4.98e-05	0.465	GCGTGCGC
GCGTGCSA	DREME-23	chrVII	-	371375	371382	4.98e-05	0.465	GCGTGCGG
GCGTGCSA	DREME-23	chrV	+	69266	69273	7.32e-05	0.56	GCGGGCCA
GCGTGCSA	DREME-23	chrXIII	+	91767	91774	7.32e-05	0.56	GCGCGCCA
GCGTGCSA	DREME-23	chrX	+	157514	157521	7.32e-05	0.56	GCGTGCCC
GCGTGCSA	DREME-23	chrXV	+	505206	505213	7.32e-05	0.56	GCGTGCCT
GCGTGCSA	DREME-23	chrVII	+	774572	774579	7.32e-05	0.56	GCGTGCCC
GCGTGCSA	DREME-23	chrVII	+	920141	920148	7.32e-05	0.56	GCGCGCCA
GCGTGCSA	DREME-23	chrVIII	-	175160	175167	7.32e-05	0.56	GCGTGCCG
GCGTGCSA	DREME-23	chrIV	-	1305679	1305686	7.32e-05	0.56	GCGGGCCA

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/BY4742--NOT3/fimo_out_21 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif GCGTGCSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_21
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_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/aa_results/BY4742--NOT3/fimo_out_21	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_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