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--RIM101/BY4742--RIM101.fa
  
  Database contains 566 sequences, 206709 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCGTACAT
       
        CTYGGCC
        7
        CTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AGTGGTWA
        8
        AGTGGTTA
       
        ACACSC
        6
        ACACCC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACATYAC
        8
        CACATCAC
       
        AACCRACT
        8
        AACCAACT
       
        AGAAAWA
        7
        AGAAAAA
       
        GATTAASA
        8
        GATTAAGA
       
        ATCTKTTG
        8
        ATCTGTTG
       
        ATAGTKTA
        8
        ATAGTGTA
       
        ACTRCGCC
        8
        ACTGCGCC
       
        AGCGCMAG
        8
        AGCGCAAG
       
        ATGGGYGC
        8
        ATGGGCGC
       
        CCGTGSA
        7
        CCGTGGA
       
        TAKCTCA
        7
        TATCTCA
       
        CACGCGAS
        8
        CACGCGAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CCRTACAY	8	CCGTACAT
CTYGGCC	7	CTTGGCC
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
AGTGGTWA	8	AGTGGTTA
ACACSC	6	ACACCC
ATGGCAWC	8	ATGGCAAC
CACATYAC	8	CACATCAC
AACCRACT	8	AACCAACT
AGAAAWA	7	AGAAAAA
GATTAASA	8	GATTAAGA
ATCTKTTG	8	ATCTGTTG
ATAGTKTA	8	ATAGTGTA
ACTRCGCC	8	ACTGCGCC
AGCGCMAG	8	AGCGCAAG
ATGGGYGC	8	ATGGGCGC
CCGTGSA	7	CCGTGGA
TAKCTCA	7	TATCTCA
CACGCGAS	8	CACGCGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 36 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
GATTAASA	DREME-12	chrX	+	75390	75397	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrV	+	135457	135464	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrVII	+	185746	185753	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrVI	+	226720	226727	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrVII	+	254492	254499	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrXV	+	282000	282007	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrIX	+	300260	300267	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrV	+	435784	435791	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrXIII	+	480653	480660	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrIV	+	1352498	1352505	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrV	-	118005	118012	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrVII	-	122300	122307	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrXI	-	203030	203037	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrX	-	414997	415004	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrXVI	-	582093	582100	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrVII	-	876425	876432	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrXII	-	1028357	1028364	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrIV	-	1201781	1201788	3.12e-05	0.702	GATTAAGA
GATTAASA	DREME-12	chrIII	+	123740	123747	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrVI	+	137518	137525	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXI	+	140874	140881	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXV	+	301141	301148	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXII	+	805771	805778	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXII	+	976015	976022	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXI	-	74656	74663	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXIV	-	102748	102755	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrVII	-	122170	122177	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrIII	-	127748	127755	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrI	-	166347	166354	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXV	-	228363	228370	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrVIII	-	358711	358718	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXV	-	487471	487478	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXIV	-	632631	632638	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrVII	-	731169	731176	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXVI	-	810708	810715	6.23e-05	0.702	GATTAACA
GATTAASA	DREME-12	chrXII	-	875539	875546	6.23e-05	0.702	GATTAACA

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--RIM101/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/background --motif GATTAASA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/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--RIM101/fimo_out_11	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/BY4742--RIM101.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--RIM101/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