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/BY4741--AFT2/BY4741--AFT2.fa
  
  Database contains 622 sequences, 262440 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SRGTTCGA
        8
        GGGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        CAYCCRTA
        8
        CATCCATA
       
        ACTBGGCC
        8
        ACTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        CCCAHACA
        8
        CCCACACA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACCGTG
        7
        CACCGTG
       
        ACTCWCG
        7
        ACTCACG
       
        AGACCACR
        8
        AGACCACA
       
        AYTGCGCC
        8
        ATTGCGCC
       
        ARAAAW
        6
        AAAAAA
       
        CACATYAC
        8
        CACATCAC
       
        CKAGAATC
        8
        CGAGAATC
       
        CKTTGGGC
        8
        CTTTGGGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/background):

A 0.319 C 0.181 G 0.181 T 0.319

MOTIF	WIDTH	BEST POSSIBLE MATCH
SRGTTCGA	8	GGGTTCGA
AGTGGTW	7	AGTGGTT
CAYCCRTA	8	CATCCATA
ACTBGGCC	8	ACTTGGCC
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
CCCAHACA	8	CCCACACA
ATGGCAWC	8	ATGGCAAC
CACCGTG	7	CACCGTG
ACTCWCG	7	ACTCACG
AGACCACR	8	AGACCACA
AYTGCGCC	8	ATTGCGCC
ARAAAW	6	AAAAAA
CACATYAC	8	CACATCAC
CKAGAATC	8	CGAGAATC
CKTTGGGC	8	CTTTGGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 42 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
CACCGTG	DREME-9	chrX	-	115968	115974	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIV	+	117186	117192	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIV	+	130274	130280	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	-	141047	141053	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	+	141236	141242	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXV	+	160434	160440	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	+	177133	177139	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIX	-	183481	183487	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrII	+	197518	197524	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrII	+	197518	197524	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIX	+	197626	197632	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	-	203269	203275	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXVI	-	210221	210227	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIX	+	210689	210695	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXIII	+	290835	290841	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	+	326688	326694	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	+	327081	327087	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXI	+	327081	327087	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrVII	+	328617	328623	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	+	354968	354974	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	+	354968	354974	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrX	-	374284	374290	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrVII	-	401556	401562	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	+	442107	442113	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	+	442107	442113	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	-	443243	443249	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	-	487360	487366	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXIV	-	495538	495544	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrVII	+	541884	541890	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrV	-	551326	551332	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXIV	-	569908	569914	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXV	-	594575	594581	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXIV	+	602336	602342	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrII	+	645201	645207	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIV	-	668048	668054	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXII	+	734826	734832	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrVII	+	739146	739152	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXII	+	797212	797218	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXVI	+	819553	819559	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXVI	-	880337	880343	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrIV	-	1017236	1017242	1.99e-05	0.245	CACCGTG
CACCGTG	DREME-9	chrXII	-	1052112	1052118	1.99e-05	0.245	CACCGTG

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/BY4741--AFT2/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/background --motif CACCGTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/BY4741--AFT2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/BY4741--AFT2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/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/BY4741--AFT2/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/BY4741--AFT2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--AFT2/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