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--SWI1/BY4742--SWI1.fa
  
  Database contains 895 sequences, 313894 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        AGTGGTW
        7
        AGTGGTT
       
        AGAAAH
        6
        AGAAAA
       
        CABACGC
        7
        CACACGC
       
        CGCSTTA
        7
        CGCCTTA
       
        CTBGGCCA
        8
        CTTGGCCA
       
        GCTACCGA
        8
        GCTACCGA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCATGGGW
        8
        GCATGGGT
       
        ACCCAMAC
        8
        ACCCACAC
       
        GGAGACCK
        8
        GGAGACCG
       
        CTATCACR
        8
        CTATCACA
       
        AAAGCGWG
        8
        AAAGCGTG
       
        ACTGAGCT
        8
        ACTGAGCT
       
        CAGAWCG
        7
        CAGAACG
       
        SATCGTGA
        8
        CATCGTGA
       
        ATCTKCTG
        8
        ATCTTCTG
       
        ACACTATA
        8
        ACACTATA
       
        ATCCKTGC
        8
        ATCCGTGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
AGTGGTW	7	AGTGGTT
AGAAAH	6	AGAAAA
CABACGC	7	CACACGC
CGCSTTA	7	CGCCTTA
CTBGGCCA	8	CTTGGCCA
GCTACCGA	8	GCTACCGA
ATGGCAWC	8	ATGGCAAC
GCATGGGW	8	GCATGGGT
ACCCAMAC	8	ACCCACAC
GGAGACCK	8	GGAGACCG
CTATCACR	8	CTATCACA
AAAGCGWG	8	AAAGCGTG
ACTGAGCT	8	ACTGAGCT
CAGAWCG	7	CAGAACG
SATCGTGA	8	CATCGTGA
ATCTKCTG	8	ATCTTCTG
ACACTATA	8	ACACTATA
ATCCKTGC	8	ATCCGTGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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-19	chrIII	+	82520	82527	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrX	+	115997	116004	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrV	+	131140	131147	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrVIII	-	134325	134332	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXI	+	141076	141083	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXIII	+	146121	146128	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIII	+	168359	168366	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrV	-	177103	177110	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXVI	+	210250	210257	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrV	-	250290	250297	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXIII	-	290805	290812	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIX	+	316384	316391	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrVII	-	328587	328594	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrII	-	350831	350838	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrV	-	354938	354945	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIX	-	370421	370428	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrVII	+	401585	401592	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXV	-	408229	408236	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXII	+	448708	448715	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrV	+	487389	487396	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXIV	-	495391	495398	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIV	-	520976	520983	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrVII	-	541854	541861	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrII	-	645171	645178	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIV	+	645211	645218	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXVI	+	769131	769138	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXII	-	797182	797189	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrIV	+	802789	802796	3.14e-05	0.667	ACACTATA
ACACTATA	DREME-19	chrXIII	+	808304	808311	3.14e-05	0.667	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--SWI1/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/background --motif ACACTATA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/BY4742--SWI1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/BY4742--SWI1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/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--SWI1/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/BY4742--SWI1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--SWI1/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