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--PDR8/BY4742--PDR8.fa
  
  Database contains 777 sequences, 258262 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        AGTGGTWW
        8
        AGTGGTTA
       
        GGHTCGA
        7
        GGTTCGA
       
        GCKCTACC
        8
        GCGCTACC
       
        TTTCTTB
        7
        TTTCTTT
       
        CAACTKGG
        8
        CAACTTGG
       
        CGCSTTA
        7
        CGCCTTA
       
        TGGCGYA
        7
        TGGCGCA
       
        ACCCAVAC
        8
        ACCCACAC
       
        GTCAKAC
        7
        GTCATAC
       
        AATGGTCW
        8
        AATGGTCA
       
        GCCWTAAC
        8
        GCCATAAC
       
        GTGATAGY
        8
        GTGATAGC
       
        CCCWTGCA
        8
        CCCATGCA
       
        CGSTCTCC
        8
        CGGTCTCC
       
        CACGCCC
        7
        CACGCCC
       
        ACTGAGCT
        8
        ACTGAGCT
       
        AWAATA
        6
        AAAATA
       
        ACACTATA
        8
        ACACTATA
       
        SAAGA
        5
        CAAGA
       
        CGACWAG
        7
        CGACTAG
       
        TCCGTRCA
        8
        TCCGTGCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/background):

A 0.318 C 0.182 G 0.182 T 0.318

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
AGTGGTWW	8	AGTGGTTA
GGHTCGA	7	GGTTCGA
GCKCTACC	8	GCGCTACC
TTTCTTB	7	TTTCTTT
CAACTKGG	8	CAACTTGG
CGCSTTA	7	CGCCTTA
TGGCGYA	7	TGGCGCA
ACCCAVAC	8	ACCCACAC
GTCAKAC	7	GTCATAC
AATGGTCW	8	AATGGTCA
GCCWTAAC	8	GCCATAAC
GTGATAGY	8	GTGATAGC
CCCWTGCA	8	CCCATGCA
CGSTCTCC	8	CGGTCTCC
CACGCCC	7	CACGCCC
ACTGAGCT	8	ACTGAGCT
AWAATA	6	AAAATA
ACACTATA	8	ACACTATA
SAAGA	5	CAAGA
CGACWAG	7	CGACTAG
TCCGTRCA	8	TCCGTGCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 70 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
GCCWTAAC	DREME-12	chrV	-	86598	86605	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrX	-	378377	378384	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXI	-	379697	379704	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrV	-	397410	397417	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrV	-	438717	438724	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrV	-	469474	469481	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrVII	-	823499	823506	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrIV	-	1017431	1017438	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrVII	+	73876	73883	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrI	+	82010	82017	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrVIII	+	85345	85352	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXI	+	308191	308198	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXIII	+	372492	372499	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrVII	+	412341	412348	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXIII	+	420635	420642	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrII	+	477174	477181	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXIII	+	586683	586690	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXV	+	663859	663866	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXII	+	687906	687913	1.12e-05	0.172	GCCATAAC
GCCWTAAC	DREME-12	chrXI	-	74641	74648	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrV	-	86620	86627	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIV	-	102733	102740	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIII	-	127733	127740	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrII	-	197511	197518	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrII	-	197511	197518	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIX	-	210682	210689	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrII	-	227091	227098	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIII	-	227958	227965	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXV	-	228348	228355	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIX	-	248866	248873	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXV	-	274689	274696	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	-	437788	437795	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXV	-	487456	487463	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIV	-	602329	602336	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIV	-	632616	632623	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXVI	-	689581	689588	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVII	-	731154	731161	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXII	-	734819	734826	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVII	-	739139	739146	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXII	-	784370	784377	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXVI	-	810693	810700	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXVI	-	819546	819553	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	-	1305646	1305653	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	+	118768	118775	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVIII	+	133082	133089	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVI	+	137533	137540	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXII	+	168000	168007	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrI	+	182578	182585	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIX	+	183487	183494	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVI	+	191588	191595	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIII	+	259214	259221	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrV	+	288499	288506	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIV	+	404855	404862	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrV	+	443249	443256	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXVI	+	516353	516360	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrV	+	522920	522927	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrX	+	524068	524075	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrV	+	551332	551339	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrVII	+	561718	561725	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXIV	+	569914	569921	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	+	668054	668061	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXVI	+	880343	880350	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXII	+	976030	976037	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	+	981030	981037	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrXII	+	1052118	1052125	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrIV	+	1150916	1150923	2.25e-05	0.172	GCCTTAAC
GCCWTAAC	DREME-12	chrII	-	395142	395149	3.54e-05	0.256	GCCCTAAC
GCCWTAAC	DREME-12	chrVII	-	702586	702593	3.54e-05	0.256	GCCGTAAC
GCCWTAAC	DREME-12	chrXV	+	216344	216351	3.54e-05	0.256	GCCCTAAC
GCCWTAAC	DREME-12	chrXVI	+	771784	771791	3.54e-05	0.256	GCCCTAAC

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--PDR8/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/background --motif GCCWTAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/BY4742--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/BY4742--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/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--PDR8/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/BY4742--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR8/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