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/BY4741--YRR1/BY4741--YRR1.fa
  
  Database contains 580 sequences, 434371 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GTTCGANY
        8
        GTTCGATT
       
        CGCSTTA
        7
        CGCCTTA
       
        ACCWCT
        6
        ACCACT
       
        AACTKGGC
        8
        AACTTGGC
       
        GCKCTACC
        8
        GCGCTACC
       
        AAAAADA
        7
        AAAAAAA
       
        CCHTAACC
        8
        CCATAACC
       
        ACTSTTAA
        8
        ACTCTTAA
       
        GCGTGTK
        7
        GCGTGTG
       
        CCGTGMTA
        8
        CCGTGATA
       
        AATGGTCW
        8
        AATGGTCA
       
        CRCCCA
        6
        CACCCA
       
        CCAACRA
        7
        CCAACAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/background):

A 0.312 C 0.188 G 0.188 T 0.312

MOTIF	WIDTH	BEST POSSIBLE MATCH
GTTCGANY	8	GTTCGATT
CGCSTTA	7	CGCCTTA
ACCWCT	6	ACCACT
AACTKGGC	8	AACTTGGC
GCKCTACC	8	GCGCTACC
AAAAADA	7	AAAAAAA
CCHTAACC	8	CCATAACC
ACTSTTAA	8	ACTCTTAA
GCGTGTK	7	GCGTGTG
CCGTGMTA	8	CCGTGATA
AATGGTCW	8	AATGGTCA
CRCCCA	6	CACCCA
CCAACRA	7	CCAACAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 67 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
CCAACRA	DREME-13	chrV	+	6315	6321	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrV	+	61917	61923	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrI	+	72071	72077	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrI	+	72437	72443	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	+	97363	97369	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVIII	+	104487	104493	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	+	118011	118017	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	+	122257	122263	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIII	+	124286	124292	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIII	+	142728	142734	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	+	159575	159581	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	+	161220	161226	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVI	+	181001	181007	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrII	+	181576	181582	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIII	+	183925	183931	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrII	+	197656	197662	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	+	216808	216814	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	+	226638	226644	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	+	232168	232174	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrX	+	233722	233728	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	+	254698	254704	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	+	263880	263886	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	+	283086	283092	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXI	+	327440	327446	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrX	+	396753	396759	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	+	441596	441602	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	+	481857	481863	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVIII	+	557117	557123	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrII	+	592473	592479	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	+	713571	713577	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	+	930980	930986	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	+	1525598	1525604	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVI	-	4545	4551	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIII	-	5398	5404	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	5522	5528	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIV	-	6478	6484	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	11057	11063	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrII	-	45361	45367	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	-	83583	83589	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	97396	97402	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIII	-	124173	124179	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrV	-	139683	139689	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXI	-	141484	141490	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	-	160496	160502	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVI	-	162263	162269	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	-	185542	185548	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	233929	233935	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIX	-	255694	255700	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrV	-	270329	270335	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	-	282199	282205	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIX	-	300304	300310	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXV	-	446718	446724	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	-	482082	482088	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	-	508495	508501	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrX	-	531863	531869	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXVI	-	572304	572310	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrII	-	642917	642923	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXIII	-	650851	650857	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	-	802662	802668	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	-	845684	845690	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXVI	-	860414	860420	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrVII	-	883694	883700	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	898945	898951	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	-	992867	992873	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	1052285	1052291	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrXII	-	1065345	1065351	3.81e-05	0.488	CCAACGA
CCAACRA	DREME-13	chrIV	-	1352542	1352548	3.81e-05	0.488	CCAACGA

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/BY4741--YRR1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/background --motif CCAACRA /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/BY4741--YRR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/BY4741--YRR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/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/BY4741--YRR1/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/BY4741--YRR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/gm_results/BY4741--YRR1/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