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 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
AGTCAKAC	DREME-16	chrXIII	+	131864	131871	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrV	-	138689	138696	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXIII	-	162436	162443	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXI	+	162526	162533	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrII	-	181446	181453	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrX	-	355397	355404	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrX	+	374545	374552	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrVII	-	405493	405500	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrII	-	405901	405908	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrIV	-	568905	568912	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXV	-	710316	710323	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrVII	-	736363	736370	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXIII	+	747931	747938	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXIII	-	808464	808471	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrVII	+	828762	828769	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrIV	-	836018	836025	1.25e-05	0.264	AGTCAGAC
AGTCAKAC	DREME-16	chrXVI	+	56393	56400	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrI	-	82223	82230	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrVII	-	122293	122300	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrV	+	135464	135471	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrVII	+	185753	185760	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrXI	-	203023	203030	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrVI	+	226727	226734	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrIX	+	300267	300274	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrVII	+	311314	311321	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrX	-	414990	414997	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrX	+	424552	424559	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrV	+	435791	435798	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrXIII	+	480660	480667	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrVII	-	876418	876425	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrIV	-	1201774	1201781	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrIV	+	1352505	1352512	3.21e-05	0.337	AGTCATAC
AGTCAKAC	DREME-16	chrV	-	68393	68400	6.42e-05	0.568	AGTCACAC
AGTCAKAC	DREME-16	chrVII	+	423066	423073	6.42e-05	0.568	AGTCACAC
AGTCAKAC	DREME-16	chrXIII	-	463409	463416	6.42e-05	0.568	AGTCACAC
AGTCAKAC	DREME-16	chrXIII	+	504869	504876	6.42e-05	0.568	AGTCACAC
AGTCAKAC	DREME-16	chrIV	-	580126	580133	6.42e-05	0.568	AGTCAAAC
AGTCAKAC	DREME-16	chrXV	+	594549	594556	6.42e-05	0.568	AGTCACAC

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_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif AGTCAKAC /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_15
    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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_15	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