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--AFT2/YJM789--AFT2.fa
  
  Database contains 485 sequences, 150880 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGG
       
        BGGTTCGA
        8
        GGGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CTWRACC
        7
        CTTAACC
       
        GCKCTACC
        8
        GCGCTACC
       
        CRCCCA
        6
        CACCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        GGYTATCA
        8
        GGCTATCA
       
        GTCTGRC
        7
        GTCTGAC
       
        CACCGTGS
        8
        CACCGTGG
       
        AAGGCGCM
        8
        AAGGCGCC
       
        TTTCTTB
        7
        TTTCTTT
       
        GGATTTKA
        8
        GGATTTTA
       
        TGGCGYA
        7
        TGGCGCA
       
        TAATCAKA
        8
        TAATCATA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        CYTGCGC
        7
        CTTGCGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGG
BGGTTCGA	8	GGGTTCGA
CTBGGCCA	8	CTCGGCCA
CTWRACC	7	CTTAACC
GCKCTACC	8	GCGCTACC
CRCCCA	6	CACCCA
ATGGCAWC	8	ATGGCAAC
ATAGTKTA	8	ATAGTGTA
GGYTATCA	8	GGCTATCA
GTCTGRC	7	GTCTGAC
CACCGTGS	8	CACCGTGG
AAGGCGCM	8	AAGGCGCC
TTTCTTB	7	TTTCTTT
GGATTTKA	8	GGATTTTA
TGGCGYA	7	TGGCGCA
TAATCAKA	8	TAATCATA
ACTGAGCT	8	ACTGAGCT
CYTGCGC	7	CTTGCGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 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
CTWRACC	DREME-4	chrIII	+	58828	58834	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrIII	+	90902	90908	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVI	+	157953	157959	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVII	+	205564	205570	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVIII	+	237885	237891	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXV	+	288168	288174	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVIII	+	358515	358521	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVII	+	423135	423141	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVII	+	440753	440759	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXIV	+	443049	443055	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXI	+	458600	458606	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXIII	+	504938	504944	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXIII	+	504938	504944	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXVI	+	560235	560241	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrII	+	604223	604229	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrII	+	605852	605858	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXVI	+	622577	622583	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXII	+	838976	838982	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXII	+	897970	897976	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrIV	+	1095407	1095413	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrII	-	36443	36449	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrIII	-	78503	78509	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXI	-	334660	334666	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXIII	-	352325	352331	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXIV	-	374914	374920	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVII	-	541997	542003	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrXV	-	623016	623022	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrII	-	680534	680540	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrVII	-	857440	857446	3.99e-05	0.394	CTTGACC
CTWRACC	DREME-4	chrIV	-	1461777	1461783	3.99e-05	0.394	CTTGACC

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--AFT2/fimo_out_4 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/background --motif CTWRACC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/fimo_out_4
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/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--AFT2/fimo_out_4	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/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