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--INO80/BY4742--INO80.fa
  
  Database contains 529 sequences, 202507 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        CTWRACC
        7
        CTTAACC
       
        CCVTACA
        7
        CCATACA
       
        GCKCTMCC
        8
        GCGCTACC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TAGTGTAR
        8
        TAGTGTAG
       
        CYTGCGC
        7
        CTTGCGC
       
        AAGAAAW
        7
        AAGAAAA
       
        CCGTGSA
        7
        CCGTGGA
       
        ACACSC
        6
        ACACCC
       
        ATCGTRAG
        8
        ATCGTGAG
       
        GTGATAGY
        8
        GTGATAGC
       
        ACTRCGCC
        8
        ACTGCGCC
       
        CSCATGC
        7
        CCCATGC
       
        CGCCTTAS
        8
        CGCCTTAG
       
        GCGCCMA
        7
        GCGCCAA
       
        TAKCTCA
        7
        TAGCTCA
       
        AATCAKAA
        8
        AATCATAA
       
        ATCTGYTG
        8
        ATCTGTTG
       
        AGTTCGAW
        8
        AGTTCGAT
       
        RCGGGGA
        7
        ACGGGGA
       
        AAGATTTC
        8
        AAGATTTC
       
        ATSTGGAG
        8
        ATGTGGAG
       
        CKAGAATC
        8
        CGAGAATC
       
        AGTCGCMC
        8
        AGTCGCAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
CTWRACC	7	CTTAACC
CCVTACA	7	CCATACA
GCKCTMCC	8	GCGCTACC
CTBGGCCA	8	CTCGGCCA
ATGGCAWC	8	ATGGCAAC
TAGTGTAR	8	TAGTGTAG
CYTGCGC	7	CTTGCGC
AAGAAAW	7	AAGAAAA
CCGTGSA	7	CCGTGGA
ACACSC	6	ACACCC
ATCGTRAG	8	ATCGTGAG
GTGATAGY	8	GTGATAGC
ACTRCGCC	8	ACTGCGCC
CSCATGC	7	CCCATGC
CGCCTTAS	8	CGCCTTAG
GCGCCMA	7	GCGCCAA
TAKCTCA	7	TAGCTCA
AATCAKAA	8	AATCATAA
ATCTGYTG	8	ATCTGTTG
AGTTCGAW	8	AGTTCGAT
RCGGGGA	7	ACGGGGA
AAGATTTC	8	AAGATTTC
ATSTGGAG	8	ATGTGGAG
CKAGAATC	8	CGAGAATC
AGTCGCMC	8	AGTCGCAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 36 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
CTWRACC	DREME-2	chrIII	+	58828	58834	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVI	+	157953	157959	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrI	+	181184	181190	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVII	+	205564	205570	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	233454	233460	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	233454	233460	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	233454	233460	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	233454	233460	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	233454	233460	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVIII	+	237885	237891	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXV	+	288168	288174	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVIII	+	358515	358521	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVII	+	423135	423141	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVII	+	440753	440759	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXIV	+	443049	443055	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXI	+	458600	458606	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXIII	+	504938	504944	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXVI	+	560235	560241	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrII	+	592319	592325	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrII	+	604223	604229	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrII	+	605852	605858	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXVI	+	622577	622583	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXV	+	780521	780527	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXV	+	780521	780527	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	838976	838982	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXII	+	897970	897976	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrIV	+	1095407	1095413	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrII	-	36443	36449	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXVI	-	281123	281129	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXIII	-	298837	298843	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXIII	-	352325	352331	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVIII	-	358356	358362	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrXIV	-	374914	374920	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVII	-	541997	542003	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrVII	-	857440	857446	3.98e-05	0.441	CTTGACC
CTWRACC	DREME-2	chrIV	-	1461777	1461783	3.98e-05	0.441	CTTGACC

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--INO80/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background --motif CTWRACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/fimo_out_4
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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--INO80/fimo_out_4	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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