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--PDR1/BY4742--PDR1.fa
  
  Database contains 871 sequences, 349157 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        TGTAYGGR
        8
        TGTATGGG
       
        BTAAGGCG
        8
        TTAAGGCG
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCKCTACC
        8
        GCGCTACC
       
        CCGTGSA
        7
        CCGTGGA
       
        ARARAAA
        7
        AAAAAAA
       
        ATAGTDTA
        8
        ATAGTGTA
       
        CRCCCA
        6
        CACCCA
       
        CTARACCA
        8
        CTAGACCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTCTCSCA
        8
        CTCTCCCA
       
        ATCTTGAS
        8
        ATCTTGAC
       
        AGTCAKAC
        8
        AGTCATAC
       
        AATCTTYT
        8
        AATCTTTT
       
        CCAGWTCG
        8
        CCAGTTCG
       
        ACTSACGA
        8
        ACTCACGA
       
        GGYTATCA
        8
        GGTTATCA
       
        TGGCGYA
        7
        TGGCGCA
       
        ACCGARAG
        8
        ACCGAAAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/background):

A 0.311 C 0.189 G 0.189 T 0.311

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
TGTAYGGR	8	TGTATGGG
BTAAGGCG	8	TTAAGGCG
CTBGGCCA	8	CTCGGCCA
GCKCTACC	8	GCGCTACC
CCGTGSA	7	CCGTGGA
ARARAAA	7	AAAAAAA
ATAGTDTA	8	ATAGTGTA
CRCCCA	6	CACCCA
CTARACCA	8	CTAGACCA
ATGGCAWC	8	ATGGCAAC
CTCTCSCA	8	CTCTCCCA
ATCTTGAS	8	ATCTTGAC
AGTCAKAC	8	AGTCATAC
AATCTTYT	8	AATCTTTT
CCAGWTCG	8	CCAGTTCG
ACTSACGA	8	ACTCACGA
GGYTATCA	8	GGTTATCA
TGGCGYA	7	TGGCGCA
ACCGARAG	8	ACCGAAAG

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
ACTSACGA	DREME-17	chrXI	-	74670	74677	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXIV	-	102762	102769	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrIII	-	127762	127769	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXIII	+	131825	131832	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVI	+	137504	137511	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrV	-	138728	138735	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXI	+	162487	162494	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXV	-	228377	228384	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrX	-	355436	355443	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrX	-	355436	355443	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrX	+	374506	374513	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVII	-	405532	405539	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrII	-	405940	405947	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXV	-	487485	487492	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrIV	-	568944	568951	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrIV	-	568944	568951	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXIV	-	632645	632652	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVII	-	731183	731190	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVII	-	736402	736409	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXIII	+	747892	747899	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXVI	-	810722	810729	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVII	+	828723	828730	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXII	-	897806	897813	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrXII	+	976001	976008	1.2e-05	0.342	ACTCACGA
ACTSACGA	DREME-17	chrVIII	+	34709	34716	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrVII	-	287528	287535	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrVII	+	364222	364229	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXI	-	379778	379785	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXI	-	382345	382352	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrIX	+	384438	384445	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrIX	+	384438	384445	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXVI	-	405307	405314	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXVI	-	405307	405314	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXIV	-	716378	716385	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXVI	-	732095	732102	2.39e-05	0.456	ACTGACGA
ACTSACGA	DREME-17	chrXV	+	977932	977939	2.39e-05	0.456	ACTGACGA

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--PDR1/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/background --motif ACTSACGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/BY4742--PDR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/BY4742--PDR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--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/BY4742--PDR1/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--PDR1/BY4742--PDR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--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