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--CAT8/BY4742--CAT8.fa
  
  Database contains 560 sequences, 171142 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCCWTAAC
        8
        GCCTTAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        CGARCCC
        7
        CGAACCC
       
        CCASAC
        6
        CCACAC
       
        CACTAWA
        7
        CACTATA
       
        ATCSTTG
        7
        ATCCTTG
       
        CTTARACC
        8
        CTTAGACC
       
        GGYTATCA
        8
        GGCTATCA
       
        GCGCAR
        6
        GCGCAA
       
        SAAGAAA
        7
        GAAGAAA
       
        AATCSAAC
        8
        AATCCAAC
       
        CATYACGC
        8
        CATTACGC
       
        ACCCRTGC
        8
        ACCCATGC
       
        AMACCCAA
        8
        ACACCCAA
       
        GTAKCTCA
        8
        GTATCTCA
       
        TCTCCACR
        8
        TCTCCACG
       
        ACGGAKG
        7
        ACGGATG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAAAARAA
        8
        AAAAAAAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
CTBGGCCA	8	CTCGGCCA
GCCWTAAC	8	GCCTTAAC
GCKCTACC	8	GCGCTACC
CGARCCC	7	CGAACCC
CCASAC	6	CCACAC
CACTAWA	7	CACTATA
ATCSTTG	7	ATCCTTG
CTTARACC	8	CTTAGACC
GGYTATCA	8	GGCTATCA
GCGCAR	6	GCGCAA
SAAGAAA	7	GAAGAAA
AATCSAAC	8	AATCCAAC
CATYACGC	8	CATTACGC
ACCCRTGC	8	ACCCATGC
AMACCCAA	8	ACACCCAA
GTAKCTCA	8	GTATCTCA
TCTCCACR	8	TCTCCACG
ACGGAKG	7	ACGGATG
AGTCAKAC	8	AGTCATAC
AAAAARAA	8	AAAAAAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 38 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
CTTARACC	DREME-9	chrII	-	9598	9605	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXI	-	84223	84230	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrI	-	181156	181163	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVII	-	205536	205543	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVI	-	224046	224053	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrII	-	347618	347625	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVII	-	423107	423114	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXIV	-	443021	443028	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXI	-	458572	458579	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXIII	-	504910	504917	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXIII	-	504910	504917	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrIV	-	519758	519765	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXII	-	628398	628405	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVII	-	700690	700697	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrX	+	424491	424498	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXIV	+	726193	726200	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVII	+	857467	857474	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrXII	+	963031	963038	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrIV	+	1461805	1461812	1.21e-05	0.213	CTTAGACC
CTTARACC	DREME-9	chrVI	-	167453	167460	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXIII	-	168811	168818	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXV	-	288208	288215	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrX	-	354260	354267	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrX	-	617934	617941	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXII	-	732105	732112	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXIII	-	837944	837951	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrIV	-	946328	946335	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXV	-	978961	978968	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrVI	+	210682	210689	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrX	+	543019	543026	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrXII	+	592595	592602	3.17e-05	0.342	CTTAAACC
CTTARACC	DREME-9	chrX	-	204858	204865	6.35e-05	0.559	CTTATACC
CTTARACC	DREME-9	chrXVI	-	436120	436127	6.35e-05	0.559	CTTACACC
CTTARACC	DREME-9	chrXIII	-	652606	652613	6.35e-05	0.559	CTTACACC
CTTARACC	DREME-9	chrXI	-	666554	666561	6.35e-05	0.559	CTTACACC
CTTARACC	DREME-9	chrXII	-	796829	796836	6.35e-05	0.559	CTTACACC
CTTARACC	DREME-9	chrVII	-	876550	876557	6.35e-05	0.559	CTTATACC
CTTARACC	DREME-9	chrVII	+	1000491	1000498	6.35e-05	0.559	CTTACACC

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--CAT8/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/background --motif CTTARACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/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--CAT8/fimo_out_8	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/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