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--STE12/RM11-1A--STE12.fa
  
  Database contains 721 sequences, 225021 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CCRTRCA
        7
        CCATACA
       
        SGGTTCGA
        8
        GGGTTCGA
       
        ACTYGGCC
        8
        ACTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        TAGTGGTW
        8
        TAGTGGTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACGGYG
        7
        CACGGTG
       
        AARARA
        6
        AAAAAA
       
        AGTCAKAC
        8
        AGTCATAC
       
        GCKCTACC
        8
        GCGCTACC
       
        AAATCCR
        7
        AAATCCA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        ACCCAVAC
        8
        ACCCACAC
       
        ATGGGBG
        7
        ATGGGCG
       
        ACGYCAC
        7
        ACGCCAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
CCRTRCA	7	CCATACA
SGGTTCGA	8	GGGTTCGA
ACTYGGCC	8	ACTTGGCC
CGCSTTA	7	CGCCTTA
TAGTGGTW	8	TAGTGGTA
ATGGCAWC	8	ATGGCAAC
CACGGYG	7	CACGGTG
AARARA	6	AAAAAA
AGTCAKAC	8	AGTCATAC
GCKCTACC	8	GCGCTACC
AAATCCR	7	AAATCCA
ATAGTKTA	8	ATAGTGTA
ACCCAVAC	8	ACCCACAC
ATGGGBG	7	ATGGGCG
ACGYCAC	7	ACGCCAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 43 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-9	chrXIII	+	131864	131871	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrXI	+	162526	162533	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrX	+	374545	374552	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrXIII	+	747931	747938	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrVII	+	828762	828769	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrV	-	138689	138696	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrII	-	181446	181453	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrX	-	355397	355404	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrX	-	355397	355404	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrVII	-	405493	405500	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrII	-	405901	405908	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrII	-	405901	405908	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrIV	-	568905	568912	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrIV	-	568905	568912	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrVII	-	736363	736370	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrXIII	-	808464	808471	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrIV	-	836018	836025	1.24e-05	0.32	AGTCAGAC
AGTCAKAC	DREME-9	chrVI	+	31133	31140	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrXVI	+	56393	56400	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVII	-	122293	122300	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrV	+	135464	135471	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrIX	+	175119	175126	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVII	+	185753	185760	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVI	+	226727	226734	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVII	-	255349	255356	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrIX	+	300267	300274	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVII	+	311314	311321	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrX	+	424552	424559	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrV	+	435791	435798	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrIV	-	465290	465297	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrXIII	+	480660	480667	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrXVI	-	582086	582093	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrXV	-	780725	780732	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrVII	-	876418	876425	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrXIII	-	889109	889116	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrIV	-	1201774	1201781	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrIV	+	1352505	1352512	3.2e-05	0.38	AGTCATAC
AGTCAKAC	DREME-9	chrII	+	410370	410377	6.39e-05	0.654	AGTCACAC
AGTCAKAC	DREME-9	chrVII	+	423066	423073	6.39e-05	0.654	AGTCACAC
AGTCAKAC	DREME-9	chrXV	+	594549	594556	6.39e-05	0.654	AGTCACAC
AGTCAKAC	DREME-9	chrXII	+	1052165	1052172	6.39e-05	0.654	AGTCACAC
AGTCAKAC	DREME-9	chrV	-	68393	68400	6.39e-05	0.654	AGTCACAC
AGTCAKAC	DREME-9	chrII	-	165068	165075	6.39e-05	0.654	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/RM11-1A--STE12/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/background --motif AGTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/RM11-1A--STE12.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/RM11-1A--STE12.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/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--STE12/fimo_out_8	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/RM11-1A--STE12.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--STE12/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