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 30 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
AGCTCAG	DREME-10	chrII	+	36405	36411	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVIII	+	75346	75352	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrII	+	89682	89688	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVII	+	115495	115501	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXIII	+	352287	352293	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXIV	+	374876	374882	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrX	+	422944	422950	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXV	+	438650	438656	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXI	+	513469	513475	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXI	+	578972	578978	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVII	+	856921	856927	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXII	+	875383	875389	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrIV	+	884368	884374	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXV	+	976428	976434	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrIV	+	1175836	1175842	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXIV	-	104800	104806	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVI	-	157992	157998	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVIII	-	237756	237762	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVIII	-	237924	237930	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVIII	-	358554	358560	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrX	-	391100	391106	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVII	-	440792	440798	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrX	-	517949	517955	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXVI	-	560274	560280	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXIII	-	572940	572946	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXII	-	605417	605423	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXVI	-	622616	622622	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrVII	-	701033	701039	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrXVI	-	769287	769293	3.88e-05	0.346	AGCTCAG
AGCTCAG	DREME-10	chrIV	-	1095446	1095452	3.88e-05	0.346	AGCTCAG

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_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--ARR1/background --motif AGCTCAG /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_11
    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_11	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