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/BY4741--PDR1/BY4741--PDR1.fa
  
  Database contains 812 sequences, 261617 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        ATGYAYGG
        8
        ATGTATGG
       
        TAAGGCR
        7
        TAAGGCG
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TTTCTTB
        7
        TTTCTTT
       
        GCGCTHCC
        8
        GCGCTACC
       
        AACCACTW
        8
        AACCACTT
       
        TGGCGYA
        7
        TGGCGCA
       
        CCCANACA
        8
        CCCACACA
       
        CTWGACC
        7
        CTAGACC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        TCTCCACR
        8
        TCTCCACA
       
        RCGGGGA
        7
        GCGGGGA
       
        CTCTMCCA
        8
        CTCTACCA
       
        TAKCTCA
        7
        TATCTCA
       
        CKTTGGGC
        8
        CGTTGGGC
       
        ATATATR
        7
        ATATATA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/background):

A 0.320 C 0.180 G 0.180 T 0.320

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
ATGYAYGG	8	ATGTATGG
TAAGGCR	7	TAAGGCG
CTBGGCCA	8	CTCGGCCA
ATGGCAWC	8	ATGGCAAC
TTTCTTB	7	TTTCTTT
GCGCTHCC	8	GCGCTACC
AACCACTW	8	AACCACTT
TGGCGYA	7	TGGCGCA
CCCANACA	8	CCCACACA
CTWGACC	7	CTAGACC
ATAGTKTA	8	ATAGTGTA
TCTCCACR	8	TCTCCACA
RCGGGGA	7	GCGGGGA
CTCTMCCA	8	CTCTACCA
TAKCTCA	7	TATCTCA
CKTTGGGC	8	CGTTGGGC
ATATATR	7	ATATATA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 70 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
ATGGCAWC	DREME-5	chrV	+	61923	61930	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrIV	-	83576	83583	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrV	+	86601	86608	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXIII	-	131874	131881	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrV	+	138679	138686	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrV	+	138679	138686	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrIII	+	142734	142741	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVI	-	162256	162263	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXI	-	162536	162543	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXII	-	168019	168026	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVI	+	181007	181014	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXIII	+	183931	183938	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrII	+	197662	197669	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrII	+	197662	197669	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXV	+	226644	226651	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXIII	-	259233	259240	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXV	-	282192	282199	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXI	+	327132	327139	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	-	346454	346461	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	+	355387	355394	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	-	374555	374562	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	+	391968	391975	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	+	396759	396766	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	+	405483	405490	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrII	+	405891	405898	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrII	+	405891	405898	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	-	531856	531863	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrX	-	531856	531863	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrIV	+	568895	568902	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXVI	-	572297	572304	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	+	736353	736360	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXIII	-	747941	747948	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	-	828772	828779	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrIV	+	835935	835942	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	-	845677	845684	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXVI	-	860407	860414	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrVII	+	930986	930993	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrIV	-	992860	992867	1.1e-05	0.147	ATGGCAAC
ATGGCAWC	DREME-5	chrXI	-	874	881	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXI	+	1007	1014	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrIII	-	1166	1173	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrVII	-	73873	73880	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrVIII	-	85342	85349	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrVI	-	233665	233672	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXI	-	308188	308195	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXIV	-	352198	352205	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXIII	-	372489	372496	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrX	+	378380	378387	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXI	+	379700	379707	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrVII	-	412338	412345	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXIII	-	420632	420639	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrV	+	423381	423388	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrV	+	438720	438727	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrV	+	469477	469484	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXV	-	663856	663863	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXII	-	687903	687910	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrVII	+	823502	823509	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrIV	-	974449	974456	2.2e-05	0.193	ATGGCATC
ATGGCAWC	DREME-5	chrXIII	+	25207	25214	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrXI	-	46910	46917	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrIV	+	117457	117464	3.44e-05	0.25	ATGGCAGC
ATGGCAWC	DREME-5	chrXII	-	241701	241708	3.44e-05	0.25	ATGGCAGC
ATGGCAWC	DREME-5	chrXV	+	254024	254031	3.44e-05	0.25	ATGGCAGC
ATGGCAWC	DREME-5	chrII	-	256660	256667	3.44e-05	0.25	ATGGCAGC
ATGGCAWC	DREME-5	chrV	-	442436	442443	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrV	-	442436	442443	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrV	-	442436	442443	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrXIV	-	721015	721022	3.44e-05	0.25	ATGGCAGC
ATGGCAWC	DREME-5	chrXII	+	932129	932136	3.44e-05	0.25	ATGGCACC
ATGGCAWC	DREME-5	chrXII	-	953072	953079	3.44e-05	0.25	ATGGCAGC

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/BY4741--PDR1/fimo_out_5 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/background --motif ATGGCAWC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/BY4741--PDR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/fimo_out_5
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/BY4741--PDR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/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/BY4741--PDR1/fimo_out_5	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/BY4741--PDR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR1/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