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/YJM789--ARR1/YJM789--ARR1.fa
  
  Database contains 449 sequences, 136314 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGA
       
        CTYGGCC
        7
        CTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        ACCACKA
        7
        ACCACTA
       
        ACACSC
        6
        ACACCC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        SGGTTCGA
        8
        GGGTTCGA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        AGCTCAG
        7
        AGCTCAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        AGCGCMAG
        8
        AGCGCAAG
       
        CACCGTGS
        8
        CACCGTGG
       
        AGTCAKAC
        8
        AGTCATAC
       
        ATGGGBG
        7
        ATGGGTG
       
        AAGAAAWA
        8
        AAGAAAAA
       
        CGCGTGSC
        8
        CGCGTGGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGA
CTYGGCC	7	CTTGGCC
CGCSTTA	7	CGCCTTA
ACCACKA	7	ACCACTA
ACACSC	6	ACACCC
ATGGCAWC	8	ATGGCAAC
SGGTTCGA	8	GGGTTCGA
GCKCTACC	8	GCGCTACC
ATAGTKTA	8	ATAGTGTA
AGCTCAG	7	AGCTCAG
AAGCGWGA	8	AAGCGTGA
AGCGCMAG	8	AGCGCAAG
CACCGTGS	8	CACCGTGG
AGTCAKAC	8	AGTCATAC
ATGGGBG	7	ATGGGTG
AAGAAAWA	8	AAGAAAAA
CGCGTGSC	8	CGCGTGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 33 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
AGTCAKAC	DREME-14	chrV	-	138689	138696	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrII	-	181446	181453	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrX	-	355397	355404	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrX	-	355397	355404	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrVII	-	405493	405500	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrII	-	405901	405908	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrIV	-	568905	568912	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrVII	-	736363	736370	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrXIII	-	808464	808471	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrXIII	+	131864	131871	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrXI	+	162526	162533	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrX	+	374545	374552	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrXIII	+	747931	747938	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrVII	+	828762	828769	1.2e-05	0.229	AGTCAGAC
AGTCAKAC	DREME-14	chrVII	-	122293	122300	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrX	-	414990	414997	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrVII	-	876418	876425	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrIV	-	1201774	1201781	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrV	+	135464	135471	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrI	+	142237	142244	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrIII	+	151323	151330	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrIX	+	175119	175126	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrVII	+	185753	185760	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrVI	+	226727	226734	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrIX	+	300267	300274	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrX	+	424552	424559	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrV	+	435791	435798	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrXIII	+	480660	480667	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrIV	+	1352505	1352512	3.17e-05	0.291	AGTCATAC
AGTCAKAC	DREME-14	chrXII	+	202095	202102	6.33e-05	0.511	AGTCAAAC
AGTCAKAC	DREME-14	chrVII	+	423066	423073	6.33e-05	0.511	AGTCACAC
AGTCAKAC	DREME-14	chrXIII	+	504869	504876	6.33e-05	0.511	AGTCACAC
AGTCAKAC	DREME-14	chrXV	+	594549	594556	6.33e-05	0.511	AGTCACAC

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/YJM789--ARR1/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/background --motif AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/YJM789--ARR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/YJM789--ARR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/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/YJM789--ARR1/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/YJM789--ARR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/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