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/AWRI1631--SWI1/AWRI1631--SWI1.fa
  
  Database contains 851 sequences, 333102 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        AARAAAW
        7
        AAAAAAA
       
        CCRTGSA
        7
        CCGTGGA
       
        CAAMTTGG
        8
        CAACTTGG
       
        TAAGGCR
        7
        TAAGGCG
       
        CRCCCA
        6
        CACCCA
       
        GCKCTACC
        8
        GCGCTACC
       
        GTGATAGY
        8
        GTGATAGC
       
        TACCACYA
        8
        TACCACTA
       
        ATCKTGAG
        8
        ATCGTGAG
       
        AKATGTA
        7
        AGATGTA
       
        CTSGGCCA
        8
        CTCGGCCA
       
        AWCACGC
        7
        AACACGC
       
        GCARATGC
        8
        GCAGATGC
       
        GGATCRAA
        8
        GGATCGAA
       
        ATAGTGTA
        8
        ATAGTGTA
       
        GGAAGAR
        7
        GGAAGAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
AARAAAW	7	AAAAAAA
CCRTGSA	7	CCGTGGA
CAAMTTGG	8	CAACTTGG
TAAGGCR	7	TAAGGCG
CRCCCA	6	CACCCA
GCKCTACC	8	GCGCTACC
GTGATAGY	8	GTGATAGC
TACCACYA	8	TACCACTA
ATCKTGAG	8	ATCGTGAG
AKATGTA	7	AGATGTA
CTSGGCCA	8	CTCGGCCA
AWCACGC	7	AACACGC
GCARATGC	8	GCAGATGC
GGATCRAA	8	GGATCGAA
ATAGTGTA	8	ATAGTGTA
GGAAGAR	7	GGAAGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 41 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
ATAGTGTA	DREME-17	chrIII	-	82519	82526	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrX	-	115996	116003	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	-	131139	131146	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXI	-	141075	141082	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIII	-	146120	146127	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIII	-	168358	168365	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXVI	-	210249	210256	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIX	-	316383	316390	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVII	-	401584	401591	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXII	-	448707	448714	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVIII	-	475764	475771	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	-	487388	487395	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVIII	-	506118	506125	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIV	-	645210	645217	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIV	-	802788	802795	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIII	-	808303	808310	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIV	-	1075530	1075537	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIV	-	1305583	1305590	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIV	+	96321	96328	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVIII	+	134326	134333	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIII	+	139379	139386	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIII	+	139379	139386	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	+	177104	177111	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	+	177104	177111	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVI	+	224179	224186	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	+	250291	250298	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIII	+	290806	290813	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVII	+	328588	328595	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrII	+	350832	350839	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	+	354939	354946	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrV	+	354939	354946	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIX	+	370422	370429	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIV	+	495392	495399	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrIV	+	520977	520984	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIII	+	540636	540643	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrVII	+	541855	541862	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXIII	+	552068	552075	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXVI	+	576203	576210	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXVI	+	581979	581986	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrII	+	645172	645179	3.2e-05	0.51	ATAGTGTA
ATAGTGTA	DREME-17	chrXII	+	797183	797190	3.2e-05	0.51	ATAGTGTA

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/AWRI1631--SWI1/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/background --motif ATAGTGTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/AWRI1631--SWI1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/AWRI1631--SWI1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/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/AWRI1631--SWI1/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/AWRI1631--SWI1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWI1/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