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/YJM789--AFT1/YJM789--AFT1.fa
  
  Database contains 520 sequences, 161509 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGDTCGA
        7
        GGTTCGA
       
        TGTAYGGR
        8
        TGTATGGA
       
        CGCSTTA
        7
        CGCCTTA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        TGGGTGB
        7
        TGGGTGT
       
        GCKCTACC
        8
        GCGCTACC
       
        CTATCACR
        8
        CTATCACA
       
        GTWGCCA
        7
        GTTGCCA
       
        SAARAAA
        7
        GAAAAAA
       
        ACCACKA
        7
        ACCACTA
       
        TGGCGYA
        7
        TGGCGCA
       
        CACCGTGS
        8
        CACCGTGG
       
        CACTTKCG
        8
        CACTTGCG
       
        GGRAGA
        6
        GGAAGA
       
        GACTSTTA
        8
        GACTCTTA
       
        TCTAAYCA
        8
        TCTAATCA
       
        CTGAGCTA
        8
        CTGAGCTA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGDTCGA	7	GGTTCGA
TGTAYGGR	8	TGTATGGA
CGCSTTA	7	CGCCTTA
CTBGGCCA	8	CTCGGCCA
TGGGTGB	7	TGGGTGT
GCKCTACC	8	GCGCTACC
CTATCACR	8	CTATCACA
GTWGCCA	7	GTTGCCA
SAARAAA	7	GAAAAAA
ACCACKA	7	ACCACTA
TGGCGYA	7	TGGCGCA
CACCGTGS	8	CACCGTGG
CACTTKCG	8	CACTTGCG
GGRAGA	6	GGAAGA
GACTSTTA	8	GACTCTTA
TCTAAYCA	8	TCTAATCA
CTGAGCTA	8	CTGAGCTA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 25 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
GACTSTTA	DREME-15	chrVII	+	122297	122304	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrXVI	+	339030	339037	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrX	+	414994	415001	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrVII	+	544667	544674	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrVII	+	876422	876429	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrIV	+	1201778	1201785	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrV	-	135460	135467	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrVII	-	185749	185756	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrVI	-	226723	226730	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrIX	-	300263	300270	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrV	-	435787	435794	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrXII	-	448849	448856	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrXIII	-	480656	480663	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrIV	-	1352501	1352508	1.96e-05	0.442	GACTCTTA
GACTSTTA	DREME-15	chrXI	+	74653	74660	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXIV	+	102745	102752	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrIII	+	127745	127752	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXV	+	228360	228367	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXIV	+	632628	632635	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrVII	+	731166	731173	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXVI	+	810705	810712	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXII	-	87068	87075	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrVI	-	137521	137528	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXII	-	605212	605219	3.92e-05	0.495	GACTGTTA
GACTSTTA	DREME-15	chrXII	-	976018	976025	3.92e-05	0.495	GACTGTTA

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/YJM789--AFT1/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/background --motif GACTSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/YJM789--AFT1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/YJM789--AFT1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/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/YJM789--AFT1/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/YJM789--AFT1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT1/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