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--SWI1/BY4741--SWI1.fa
  
  Database contains 923 sequences, 390882 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CGCSTTA
        7
        CGCCTTA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GGTTCGA
        7
        GGTTCGA
       
        ACCACKA
        7
        ACCACTA
       
        ATGGGYG
        7
        ATGGGTG
       
        TCCGBACA
        8
        TCCGTACA
       
        GCKCTACC
        8
        GCGCTACC
       
        TTTCTTB
        7
        TTTCTTT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACGGYG
        7
        CACGGTG
       
        CCCAYACA
        8
        CCCACACA
       
        CTATCAC
        7
        CTATCAC
       
        GATTWGAA
        8
        GATTAGAA
       
        CCACACSC
        8
        CCACACCC
       
        ATCKTGAG
        8
        ATCGTGAG
       
        AYTCTCG
        7
        ATTCTCG
       
        CTGAGCTA
        8
        CTGAGCTA
       
        CAWATATA
        8
        CATATATA
       
        TCKCCCA
        7
        TCTCCCA
       
        ACCACTTK
        8
        ACCACTTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background):

A 0.320 C 0.180 G 0.180 T 0.320

MOTIF	WIDTH	BEST POSSIBLE MATCH
CGCSTTA	7	CGCCTTA
CTBGGCCA	8	CTCGGCCA
GGTTCGA	7	GGTTCGA
ACCACKA	7	ACCACTA
ATGGGYG	7	ATGGGTG
TCCGBACA	8	TCCGTACA
GCKCTACC	8	GCGCTACC
TTTCTTB	7	TTTCTTT
ATGGCAWC	8	ATGGCAAC
CACGGYG	7	CACGGTG
CCCAYACA	8	CCCACACA
CTATCAC	7	CTATCAC
GATTWGAA	8	GATTAGAA
CCACACSC	8	CCACACCC
ATCKTGAG	8	ATCGTGAG
AYTCTCG	7	ATTCTCG
CTGAGCTA	8	CTGAGCTA
CAWATATA	8	CATATATA
TCKCCCA	7	TCTCCCA
ACCACTTK	8	ACCACTTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 51 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
ATCKTGAG	DREME-15	chrXI	+	74669	74676	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXIV	+	102761	102768	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXIV	+	102761	102768	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	+	122221	122228	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrIII	+	127761	127768	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrV	+	138727	138734	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrV	+	138727	138734	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXV	+	228376	228383	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrX	+	355435	355442	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	+	405531	405538	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrII	+	405939	405946	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrII	+	405939	405946	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrIX	+	439271	439278	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrIV	+	568943	568950	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrIV	+	568943	568950	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXIV	+	632644	632651	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	+	731182	731189	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	+	731182	731189	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	+	736401	736408	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXVI	+	810721	810728	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXIII	-	131826	131833	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVI	-	137505	137512	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXI	-	162488	162495	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrX	-	374507	374514	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXIII	-	747893	747900	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVII	-	828724	828731	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrIV	-	916239	916246	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrXII	-	976002	976009	1.1e-05	0.301	ATCGTGAG
ATCKTGAG	DREME-15	chrVI	+	167489	167496	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIII	+	168847	168854	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIII	+	168847	168854	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIII	+	286773	286780	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXV	+	288244	288251	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXV	+	340374	340381	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrX	+	354296	354303	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrX	+	354296	354303	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrV	+	443392	443399	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIV	+	575816	575823	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXV	+	678816	678823	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIII	+	837980	837987	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXIII	+	837980	837987	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrIV	+	946364	946371	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrIV	+	946364	946371	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrVI	-	210646	210653	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrVII	-	316957	316964	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXV	-	432057	432064	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXV	-	445097	445104	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrX	-	542983	542990	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXII	-	646138	646145	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrVII	-	779683	779690	3.05e-05	0.46	ATCTTGAG
ATCKTGAG	DREME-15	chrXII	-	815696	815703	3.05e-05	0.46	ATCTTGAG

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--SWI1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background --motif ATCKTGAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/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--SWI1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/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