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 39 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
CRTGCTAA	DREME-16	chrII	+	197521	197528	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrII	+	197521	197528	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrIX	+	210692	210699	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXIV	+	602339	602346	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXII	+	734829	734836	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrVII	+	739149	739156	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXVI	+	819556	819563	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrIX	-	183477	183484	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrV	-	443239	443246	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrV	-	551322	551329	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXIV	-	569904	569911	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrIV	-	668044	668051	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXVI	-	880333	880340	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrXII	-	1052108	1052115	1.17e-05	0.512	CGTGCTAA
CRTGCTAA	DREME-16	chrV	+	61717	61724	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrVIII	+	146275	146282	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXIV	+	174642	174649	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrX	+	197346	197353	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrII	+	197421	197428	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrII	+	197421	197428	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrVI	+	204957	204964	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXI	-	219925	219932	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrIV	-	410409	410416	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrIV	+	434212	434219	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrIV	-	491685	491692	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXI	-	518018	518025	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXVI	-	645775	645782	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXVI	-	645775	645782	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXII	-	656851	656858	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXII	+	656967	656974	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrVII	-	774379	774386	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXVI	-	856932	856939	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrIV	-	992765	992772	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrIV	+	1403211	1403218	3.14e-05	0.564	CATGCTAA
CRTGCTAA	DREME-16	chrXI	+	46821	46828	6.28e-05	0.983	CCTGCTAA
CRTGCTAA	DREME-16	chrVII	-	439142	439149	6.28e-05	0.983	CTTGCTAA
CRTGCTAA	DREME-16	chrIV	-	491662	491669	6.28e-05	0.983	CCTGCTAA
CRTGCTAA	DREME-16	chrXI	+	520945	520952	6.28e-05	0.983	CCTGCTAA
CRTGCTAA	DREME-16	chrVII	-	857336	857343	6.28e-05	0.983	CCTGCTAA

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_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background --motif CRTGCTAA /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_15
    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.

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output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/fimo_out_15	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