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/RM11-1A--ACE2/RM11-1A--ACE2.fa
  
  Database contains 484 sequences, 155576 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ACCCADAC
        8
        ACCCATAC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        ATCCGTRC
        8
        ATCCGTAC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GGTCTM
        6
        GGTCTC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        RGCSCAA
        7
        GGCGCAA
       
        AARAAA
        6
        AAAAAA
       
        GTGATARC
        8
        GTGATAGC
       
        ARTCATAC
        8
        AGTCATAC
       
        GCCASAC
        7
        GCCACAC
       
        CGCGGGS
        7
        CGCGGGG
       
        ACTGAGCT
        8
        ACTGAGCT
       
        ATCAKAAG
        8
        ATCAGAAG
       
        GAGTTCRA
        8
        GAGTTCAA
       
        TCTCCCA
        7
        TCTCCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CTBGGCCA	8	CTCGGCCA
ACCCADAC	8	ACCCATAC
GCCTTAMC	8	GCCTTAAC
GCKCTACC	8	GCGCTACC
ATCCGTRC	8	ATCCGTAC
ATGGCAWC	8	ATGGCAAC
GGTCTM	6	GGTCTC
ATAGTKTA	8	ATAGTGTA
RGCSCAA	7	GGCGCAA
AARAAA	6	AAAAAA
GTGATARC	8	GTGATAGC
ARTCATAC	8	AGTCATAC
GCCASAC	7	GCCACAC
CGCGGGS	7	CGCGGGG
ACTGAGCT	8	ACTGAGCT
ATCAKAAG	8	ATCAGAAG
GAGTTCRA	8	GAGTTCAA
TCTCCCA	7	TCTCCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 62 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
ATAGTKTA	DREME-9	chrIII	-	82519	82526	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	-	92466	92473	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrX	-	115996	116003	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrV	-	131139	131146	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXI	-	141075	141082	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	-	146120	146127	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIII	-	168358	168365	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXVI	-	210249	210256	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIX	-	316383	316390	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	-	401584	401591	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	-	448707	448714	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	-	460152	460159	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	-	475764	475771	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrV	-	487388	487395	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	-	506118	506125	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	645210	645217	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	802788	802795	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	-	808303	808310	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	1075530	1075537	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	1305583	1305590	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIV	+	96321	96328	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	+	134326	134333	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	177104	177111	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrI	+	182414	182421	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	250291	250298	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	+	290806	290813	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	+	328588	328595	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrII	+	350832	350839	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	354939	354946	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIX	+	370422	370429	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIV	+	495392	495399	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	+	520977	520984	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	+	541855	541862	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXVI	+	581979	581986	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrII	+	645172	645179	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	+	797183	797190	3.1e-05	0.262	ATAGTGTA
ATAGTKTA	DREME-9	chrXIV	-	104977	104984	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrVI	-	191639	191646	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrIX	-	324360	324367	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrIX	-	336406	336413	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	-	349535	349542	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	-	374481	374488	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	-	459666	459673	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXI	-	513389	513396	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	-	544634	544641	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	-	794308	794315	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrV	+	53671	53678	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	204740	204747	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355335	355342	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355461	355468	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrII	+	405965	405972	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	+	423264	423271	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	427137	427144	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	438537	438544	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXIII	+	463559	463566	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	+	531615	531622	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	541513	541520	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrIV	+	568969	568976	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	571963	571970	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	734748	734755	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXVI	+	744190	744197	7.99e-05	0.392	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	793923	793930	7.99e-05	0.392	ATAGTTTA

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/RM11-1A--ACE2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/background --motif ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/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/RM11-1A--ACE2/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/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