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 40 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
AGTCAKAC	DREME-20	chrV	-	138689	138696	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrII	-	181446	181453	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrX	-	355397	355404	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrVII	-	405493	405500	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrII	-	405901	405908	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrIV	-	568905	568912	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrVII	-	736363	736370	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrXIII	-	808464	808471	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrIV	-	836018	836025	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrXIII	+	131864	131871	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrXI	+	162526	162533	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrX	+	374545	374552	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrXIII	+	747931	747938	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrVII	+	828762	828769	1.21e-05	0.289	AGTCAGAC
AGTCAKAC	DREME-20	chrI	-	82223	82230	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVII	-	122293	122300	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXI	-	203023	203030	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrX	-	414990	414997	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXVI	-	582086	582093	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVII	-	876418	876425	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrIV	-	1201774	1201781	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXVI	+	56393	56400	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrV	+	135464	135471	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVII	+	185753	185760	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVI	+	226727	226734	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrIX	+	300267	300274	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVII	+	311314	311321	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrX	+	424552	424559	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrV	+	435791	435798	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXIII	+	480660	480667	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXVI	+	689772	689779	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrXV	+	976246	976253	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrIV	+	1352505	1352512	3.17e-05	0.322	AGTCATAC
AGTCAKAC	DREME-20	chrVIII	-	385966	385973	6.35e-05	0.531	AGTCAAAC
AGTCAKAC	DREME-20	chrXIII	-	463409	463416	6.35e-05	0.531	AGTCACAC
AGTCAKAC	DREME-20	chrXV	-	882411	882418	6.35e-05	0.531	AGTCAAAC
AGTCAKAC	DREME-20	chrVII	+	423066	423073	6.35e-05	0.531	AGTCACAC
AGTCAKAC	DREME-20	chrXIII	+	504869	504876	6.35e-05	0.531	AGTCACAC
AGTCAKAC	DREME-20	chrXIII	+	504869	504876	6.35e-05	0.531	AGTCACAC
AGTCAKAC	DREME-20	chrXV	+	594549	594556	6.35e-05	0.531	AGTCACAC

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_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/background --motif AGTCAKAC /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_16
    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_16	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