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--MAC1/BY4742--MAC1.fa
  
  Database contains 759 sequences, 310680 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRVTCGAA
        8
        GAATCGAA
       
        AGTGGTW
        7
        AGTGGTT
       
        TGTAYGGR
        8
        TGTATGGA
       
        AACTKGGC
        8
        AACTTGGC
       
        AARAAAWA
        8
        AAAAAAAA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ACCCAVAC
        8
        ACCCACAC
       
        GYGGTCTA
        8
        GTGGTCTA
       
        AGAYCGGG
        8
        AGATCGGG
       
        CCTTAAMC
        8
        CCTTAACC
       
        ACACTATA
        8
        ACACTATA
       
        GCGCCA
        6
        GCGCCA
       
        CTATCACR
        8
        CTATCACA
       
        CASACGC
        7
        CACACGC
       
        CRTGCTAA
        8
        CGTGCTAA
       
        CGCGGGSA
        8
        CGCGGGGA
       
        AAAGCRTG
        8
        AAAGCGTG
       
        TAKCTCA
        7
        TATCTCA
       
        GGCCMAAC
        8
        GGCCCAAC
       
        CTKCGGTC
        8
        CTTCGGTC
       
        GAYCTCCA
        8
        GATCTCCA
       
        TCCGTGSA
        8
        TCCGTGGA
       
        CCAAMAGA
        8
        CCAACAGA
       
        TCTAATCW
        8
        TCTAATCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background):

A 0.313 C 0.187 G 0.187 T 0.313

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRVTCGAA	8	GAATCGAA
AGTGGTW	7	AGTGGTT
TGTAYGGR	8	TGTATGGA
AACTKGGC	8	AACTTGGC
AARAAAWA	8	AAAAAAAA
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
ACCCAVAC	8	ACCCACAC
GYGGTCTA	8	GTGGTCTA
AGAYCGGG	8	AGATCGGG
CCTTAAMC	8	CCTTAACC
ACACTATA	8	ACACTATA
GCGCCA	6	GCGCCA
CTATCACR	8	CTATCACA
CASACGC	7	CACACGC
CRTGCTAA	8	CGTGCTAA
CGCGGGSA	8	CGCGGGGA
AAAGCRTG	8	AAAGCGTG
TAKCTCA	7	TATCTCA
GGCCMAAC	8	GGCCCAAC
CTKCGGTC	8	CTTCGGTC
GAYCTCCA	8	GATCTCCA
TCCGTGSA	8	TCCGTGGA
CCAAMAGA	8	CCAACAGA
TCTAATCW	8	TCTAATCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 58 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
GGCCMAAC	DREME-20	chrV	+	61914	61921	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrIII	+	142725	142732	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXIII	+	183922	183929	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrII	+	197653	197660	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrII	+	197653	197660	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXV	+	226635	226642	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrX	+	396750	396757	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrVII	+	930977	930984	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrIV	-	83585	83592	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrVI	-	162265	162272	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXV	-	282201	282208	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrX	-	531865	531872	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrX	-	531865	531872	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXVI	-	572306	572313	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXVI	-	795396	795403	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrVII	-	845686	845693	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrXVI	-	860416	860423	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrIV	-	992869	992876	4.19e-06	0.142	GGCCCAAC
GGCCMAAC	DREME-20	chrV	-	53536	53543	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrI	-	181144	181151	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrVII	-	205524	205531	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrVII	+	254279	254286	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrV	-	322221	322228	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrVII	-	423095	423102	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXIV	-	443009	443016	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXI	-	458560	458567	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXIV	+	494495	494502	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXIII	-	504898	504905	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXIII	-	504898	504905	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXII	+	592607	592614	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrX	-	617922	617929	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXII	-	628386	628393	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXII	-	732093	732100	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrVII	+	788335	788342	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrVII	+	857479	857486	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXIII	-	889066	889073	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrIV	+	1461817	1461824	1.12e-05	0.185	GGCCAAAC
GGCCMAAC	DREME-20	chrXV	+	92991	92998	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrV	+	117808	117815	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXIII	-	253435	253442	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrVII	+	278305	278312	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXVI	+	281219	281226	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXVI	+	281219	281226	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXI	+	431616	431623	2.24e-05	0.291	GGCCTAAC
GGCCMAAC	DREME-20	chrXV	-	780423	780430	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXV	-	780423	780430	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXV	-	780423	780430	2.24e-05	0.291	GGCCGAAC
GGCCMAAC	DREME-20	chrXI	+	74522	74529	4.08e-05	0.429	GGCCCAGC
GGCCMAAC	DREME-20	chrII	+	89646	89653	4.08e-05	0.429	GGCCCAGC
GGCCMAAC	DREME-20	chrIX	+	99774	99781	4.08e-05	0.429	GGCCCGAC
GGCCMAAC	DREME-20	chrXVI	+	215105	215112	4.08e-05	0.429	GGCCCGAC
GGCCMAAC	DREME-20	chrVIII	-	297128	297135	4.08e-05	0.429	GGCCCATC
GGCCMAAC	DREME-20	chrXI	-	322591	322598	4.08e-05	0.429	GGCCCCAC
GGCCMAAC	DREME-20	chrII	-	593000	593007	4.08e-05	0.429	GGCCCATC
GGCCMAAC	DREME-20	chrII	+	606053	606060	4.08e-05	0.429	GGCCCACC
GGCCMAAC	DREME-20	chrII	+	681974	681981	4.08e-05	0.429	GGCCCATC
GGCCMAAC	DREME-20	chrXVI	+	794702	794709	4.08e-05	0.429	GGCCCACC
GGCCMAAC	DREME-20	chrVII	-	857322	857329	4.08e-05	0.429	GGCCCACC

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--MAC1/fimo_out_19 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background --motif GGCCMAAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/fimo_out_19
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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--MAC1/fimo_out_19	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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