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--CUP9/BY4742--CUP9.fa
  
  Database contains 821 sequences, 427317 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        CCTTAVC
        7
        CCTTAAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        AAGAAAD
        7
        AAGAAAA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        GTGATAGY
        8
        GTGATAGT
       
        KAATCATA
        8
        TAATCATA
       
        ATAYAACA
        8
        ATACAACA
       
        ATCTTYTG
        8
        ATCTTTTG
       
        CCGTGSA
        7
        CCGTGGA
       
        GTGGTYTA
        8
        GTGGTCTA
       
        AGTCAKAC
        8
        AGTCATAC
       
        TAGTGTAR
        8
        TAGTGTAG
       
        CTGAGCTA
        8
        CTGAGCTA
       
        MACACCCA
        8
        CACACCCA
       
        ACTSACG
        7
        ACTCACG
       
        CAGWTAAC
        8
        CAGTTAAC
       
        ATGGTCAS
        8
        ATGGTCAG
       
        CCAGWTCG
        8
        CCAGTTCG
       
        CCTTARAC
        8
        CCTTAAAC
       
        CKTTGGGC
        8
        CGTTGGGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
CCTTAVC	7	CCTTAAC
CTBGGCCA	8	CTCGGCCA
AAGAAAD	7	AAGAAAA
ATGGCAWC	8	ATGGCAAC
GCKCTACC	8	GCGCTACC
GTGATAGY	8	GTGATAGT
KAATCATA	8	TAATCATA
ATAYAACA	8	ATACAACA
ATCTTYTG	8	ATCTTTTG
CCGTGSA	7	CCGTGGA
GTGGTYTA	8	GTGGTCTA
AGTCAKAC	8	AGTCATAC
TAGTGTAR	8	TAGTGTAG
CTGAGCTA	8	CTGAGCTA
MACACCCA	8	CACACCCA
ACTSACG	7	ACTCACG
CAGWTAAC	8	CAGTTAAC
ATGGTCAS	8	ATGGTCAG
CCAGWTCG	8	CCAGTTCG
CCTTARAC	8	CCTTAAAC
CKTTGGGC	8	CGTTGGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 40 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
ATGGTCAS	DREME-20	chrII	+	136240	136247	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrX	+	204748	204755	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXII	+	282786	282793	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXI	+	284266	284273	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrX	+	355469	355476	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrII	+	405973	405980	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrII	+	405973	405980	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXII	+	427145	427152	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXIII	+	463567	463574	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXIII	+	463567	463574	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrX	+	541521	541528	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrIV	+	568977	568984	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrIV	+	568977	568984	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXV	+	571971	571978	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXII	+	793931	793938	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrV	-	85143	85150	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrIX	-	324352	324359	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrX	-	374473	374480	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXI	-	432319	432326	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXI	-	513381	513388	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrVII	-	544626	544633	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXIV	-	586169	586176	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXIV	-	586169	586176	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrIV	-	1095299	1095306	1.26e-05	0.442	ATGGTCAG
ATGGTCAS	DREME-20	chrXIII	+	24462	24469	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXIII	+	24462	24469	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXIII	+	24462	24469	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXIII	+	24462	24469	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXIII	+	24462	24469	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrVII	+	57012	57019	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrX	+	233952	233959	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXII	+	374368	374375	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrV	+	434435	434442	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXI	+	490981	490988	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXV	-	340349	340356	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrIV	-	465161	465168	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrXII	-	489436	489443	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrV	-	492402	492409	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrIV	-	620019	620026	2.52e-05	0.53	ATGGTCAC
ATGGTCAS	DREME-20	chrVII	-	878934	878941	2.52e-05	0.53	ATGGTCAC

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--CUP9/fimo_out_19 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/background --motif ATGGTCAS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/fimo_out_19
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/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--CUP9/fimo_out_19	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/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