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--MAC1/BY4742--MAC1.fa
  
  Database contains 759 sequences, 310680 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRVTCGAA
        8
        GAATCGAA
       
        AGTGGTW
        7
        AGTGGTT
       
        TGTAYGGR
        8
        TGTATGGA
       
        AACTKGGC
        8
        AACTTGGC
       
        AARAAAWA
        8
        AAAAAAAA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ACCCAVAC
        8
        ACCCACAC
       
        GYGGTCTA
        8
        GTGGTCTA
       
        AGAYCGGG
        8
        AGATCGGG
       
        CCTTAAMC
        8
        CCTTAACC
       
        ACACTATA
        8
        ACACTATA
       
        GCGCCA
        6
        GCGCCA
       
        CTATCACR
        8
        CTATCACA
       
        CASACGC
        7
        CACACGC
       
        CRTGCTAA
        8
        CGTGCTAA
       
        CGCGGGSA
        8
        CGCGGGGA
       
        AAAGCRTG
        8
        AAAGCGTG
       
        TAKCTCA
        7
        TATCTCA
       
        GGCCMAAC
        8
        GGCCCAAC
       
        CTKCGGTC
        8
        CTTCGGTC
       
        GAYCTCCA
        8
        GATCTCCA
       
        TCCGTGSA
        8
        TCCGTGGA
       
        CCAAMAGA
        8
        CCAACAGA
       
        TCTAATCW
        8
        TCTAATCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background):

A 0.313 C 0.187 G 0.187 T 0.313

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRVTCGAA	8	GAATCGAA
AGTGGTW	7	AGTGGTT
TGTAYGGR	8	TGTATGGA
AACTKGGC	8	AACTTGGC
AARAAAWA	8	AAAAAAAA
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
ACCCAVAC	8	ACCCACAC
GYGGTCTA	8	GTGGTCTA
AGAYCGGG	8	AGATCGGG
CCTTAAMC	8	CCTTAACC
ACACTATA	8	ACACTATA
GCGCCA	6	GCGCCA
CTATCACR	8	CTATCACA
CASACGC	7	CACACGC
CRTGCTAA	8	CGTGCTAA
CGCGGGSA	8	CGCGGGGA
AAAGCRTG	8	AAAGCGTG
TAKCTCA	7	TATCTCA
GGCCMAAC	8	GGCCCAAC
CTKCGGTC	8	CTTCGGTC
GAYCTCCA	8	GATCTCCA
TCCGTGSA	8	TCCGTGGA
CCAAMAGA	8	CCAACAGA
TCTAATCW	8	TCTAATCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 39 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
TCCGTGSA	DREME-23	chrV	-	42241	42248	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXVI	+	56215	56222	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXVI	+	76536	76543	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrI	-	82111	82118	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrXII	+	84260	84267	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXIII	+	225534	225541	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrVII	+	287396	287403	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXI	-	302968	302975	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXIII	+	379349	379356	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrX	+	415977	415984	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXII	+	498675	498682	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrVII	-	535005	535012	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrXII	-	781601	781608	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrXII	-	781657	781664	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrVII	-	788530	788537	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrVII	+	878756	878763	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrXII	-	932301	932308	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrXV	+	1025903	1025910	1.4e-05	0.408	TCCGTGGA
TCCGTGSA	DREME-23	chrIV	+	1116991	1116998	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrIV	-	1278781	1278788	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrIV	+	1301111	1301118	1.4e-05	0.408	TCCGTGCA
TCCGTGSA	DREME-23	chrVIII	-	85487	85494	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXI	+	108991	108998	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXI	+	110628	110635	3.75e-05	0.587	TCCGTGTA
TCCGTGSA	DREME-23	chrV	+	117816	117823	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrVIII	-	126063	126070	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrVIII	-	146430	146437	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrIX	+	210539	210546	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrVII	-	401487	401494	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrII	-	415650	415657	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrV	-	434730	434737	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrV	-	492538	492545	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXIV	+	546969	546976	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrIV	-	645339	645346	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrVII	+	736214	736221	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXII	+	796525	796532	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXVI	+	856777	856784	3.75e-05	0.587	TCCGTGAA
TCCGTGSA	DREME-23	chrXII	-	899198	899205	3.75e-05	0.587	TCCGTGTA
TCCGTGSA	DREME-23	chrXV	+	1028688	1028695	3.75e-05	0.587	TCCGTGAA

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--MAC1/fimo_out_22 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background --motif TCCGTGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/fimo_out_22
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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--MAC1/fimo_out_22	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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