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 32 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
ACACTATA	DREME-12	chrIII	+	82520	82527	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrX	+	115997	116004	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	+	131140	131147	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrVIII	-	134325	134332	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXI	+	141076	141083	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXIII	+	146121	146128	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIII	+	168359	168366	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	-	177103	177110	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXVI	+	210250	210257	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrI	-	229409	229416	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	-	250290	250297	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXIII	-	290805	290812	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIX	+	316384	316391	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrVII	-	328587	328594	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrII	-	350831	350838	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	-	354938	354945	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	-	354938	354945	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXII	-	370104	370111	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIX	-	370421	370428	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrVII	+	401585	401592	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXII	+	448708	448715	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrV	+	487389	487396	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXIV	-	495391	495398	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIV	-	520976	520983	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrVII	-	541854	541861	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrII	-	645171	645178	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIV	+	645211	645218	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXVI	+	769131	769138	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXII	-	797182	797189	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrIV	+	802789	802796	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXIII	+	808304	808311	3.29e-05	0.628	ACACTATA
ACACTATA	DREME-12	chrXII	-	931451	931458	3.29e-05	0.628	ACACTATA

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_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background --motif ACACTATA /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_11
    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_11	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