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--NOT3/BY4742--NOT3.fa
  
  Database contains 513 sequences, 171825 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTYGGTW
        8
        AGTTGGTT
       
        CCRTACAY
        8
        CCATACAT
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGGGNG
        7
        ATGGGTG
       
        GCGCTHCC
        8
        GCGCTACC
       
        AAGAAAWA
        8
        AAGAAAAA
       
        ATMCAAC
        7
        ATACAAC
       
        CCASAC
        6
        CCACAC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CYATGGCC
        8
        CTATGGCC
       
        AATCTTYT
        8
        AATCTTTT
       
        GCGCAAK
        7
        GCGCAAG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAGRTTAG
        8
        AAGGTTAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CCAASAG
        7
        CCAAGAG
       
        CCGTGMTA
        8
        CCGTGATA
       
        GGCTAYC
        7
        GGCTATC
       
        CGCGRGC
        7
        CGCGAGC
       
        GCGTGCSA
        8
        GCGTGCGA
       
        ACTSACG
        7
        ACTGACG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTYGGTW	8	AGTTGGTT
CCRTACAY	8	CCATACAT
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
CGCSTTA	7	CGCCTTA
ATGGCAWC	8	ATGGCAAC
ATGGGNG	7	ATGGGTG
GCGCTHCC	8	GCGCTACC
AAGAAAWA	8	AAGAAAAA
ATMCAAC	7	ATACAAC
CCASAC	6	CCACAC
GRTCTCCA	8	GGTCTCCA
CYATGGCC	8	CTATGGCC
AATCTTYT	8	AATCTTTT
GCGCAAK	7	GCGCAAG
AGTCAKAC	8	AGTCATAC
AAGRTTAG	8	AAGGTTAG
AAGCGWGA	8	AAGCGTGA
CCAASAG	7	CCAAGAG
CCGTGMTA	8	CCGTGATA
GGCTAYC	7	GGCTATC
CGCGRGC	7	CGCGAGC
GCGTGCSA	8	GCGTGCGA
ACTSACG	7	ACTGACG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 37 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
GGCTAYC	DREME-21	chrV	+	177114	177120	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIX	+	197607	197613	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIII	+	227993	227999	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrXIII	+	290816	290822	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVII	+	328598	328604	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrV	+	354949	354955	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIX	+	370432	370438	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVII	+	541865	541871	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrXI	+	619081	619087	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrII	+	645182	645188	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrXII	+	797193	797199	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIII	-	82510	82516	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrX	-	115987	115993	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	125590	125596	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	125590	125596	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrXI	-	141066	141072	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVII	-	185710	185716	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrXVI	-	210240	210246	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIX	-	300224	300230	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVII	-	401575	401581	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVIII	-	475755	475761	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrV	-	487379	487385	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	1017255	1017261	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	1075521	1075527	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	1175678	1175684	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrIV	-	1352462	1352468	4.11e-05	0.534	GGCTATC
GGCTAYC	DREME-21	chrVI	-	167441	167447	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrXIII	-	168799	168805	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrXIII	-	168951	168957	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrVI	+	210695	210701	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrXV	-	288196	288202	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrX	-	354248	354254	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrX	+	543032	543038	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrII	-	680411	680417	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrXIII	-	837932	837938	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrIV	-	946316	946322	6.74e-05	0.615	GGCTACC
GGCTAYC	DREME-21	chrIV	-	1236677	1236683	6.74e-05	0.615	GGCTACC

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--NOT3/fimo_out_19 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif GGCTAYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_19
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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--NOT3/fimo_out_19	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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