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--PDR8/YJM789--PDR8.fa
  
  Database contains 456 sequences, 139903 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CGCSTTA
        7
        CGCCTTA
       
        TGTAYGGR
        8
        TGTATGGG
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        AACTKGGC
        8
        AACTTGGC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTATCACR
        8
        CTATCACG
       
        ATGGGBG
        7
        ATGGGTG
       
        GCKCTACC
        8
        GCGCTACC
       
        TGGCGYA
        7
        TGGCGCA
       
        SAAGA
        5
        CAAGA
       
        CCCAVACA
        8
        CCCACACA
       
        CGTGYTAA
        8
        CGTGTTAA
       
        AGARTCAT
        8
        AGAGTCAT
       
        GRTCTCCA
        8
        GGTCTCCA
       
        ACTGAGC
        7
        ACTGAGC
       
        ACTTSTAA
        8
        ACTTCTAA
       
        CAGWCGC
        7
        CAGACGC
       
        ACCACTTR
        8
        ACCACTTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
CGCSTTA	7	CGCCTTA
TGTAYGGR	8	TGTATGGG
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
AACTKGGC	8	AACTTGGC
ATGGCAWC	8	ATGGCAAC
CTATCACR	8	CTATCACG
ATGGGBG	7	ATGGGTG
GCKCTACC	8	GCGCTACC
TGGCGYA	7	TGGCGCA
SAAGA	5	CAAGA
CCCAVACA	8	CCCACACA
CGTGYTAA	8	CGTGTTAA
AGARTCAT	8	AGAGTCAT
GRTCTCCA	8	GGTCTCCA
ACTGAGC	7	ACTGAGC
ACTTSTAA	8	ACTTCTAA
CAGWCGC	7	CAGACGC
ACCACTTR	8	ACCACTTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 31 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
CGTGYTAA	DREME-13	chrII	+	197521	197528	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXIV	+	602339	602346	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXII	+	734829	734836	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrVII	+	739149	739156	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXVI	+	819556	819563	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrIX	-	183477	183484	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrV	-	443239	443246	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrV	-	551322	551329	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXIV	-	569904	569911	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrIV	-	668044	668051	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXVI	-	880333	880340	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrXII	-	1052108	1052115	1.25e-05	0.284	CGTGCTAA
CGTGYTAA	DREME-13	chrVIII	+	148996	149003	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXI	+	308177	308184	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXIII	+	372478	372485	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrVII	+	412327	412334	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXIII	+	420621	420628	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXIII	+	586669	586676	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXV	+	663845	663852	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrX	-	378391	378398	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrXI	-	379711	379718	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrV	-	438731	438738	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrV	-	469488	469495	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrX	-	531804	531811	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrVII	-	823513	823520	3.2e-05	0.35	CGTGTTAA
CGTGYTAA	DREME-13	chrII	+	227200	227207	6.41e-05	0.565	CGTGGTAA
CGTGYTAA	DREME-13	chrIII	-	295560	295567	6.41e-05	0.565	CGTGATAA
CGTGYTAA	DREME-13	chrIII	-	295560	295567	6.41e-05	0.565	CGTGATAA
CGTGYTAA	DREME-13	chrV	+	438568	438575	6.41e-05	0.565	CGTGATAA
CGTGYTAA	DREME-13	chrIV	+	492051	492058	6.41e-05	0.565	CGTGGTAA
CGTGYTAA	DREME-13	chrXIV	-	494268	494275	6.41e-05	0.565	CGTGGTAA

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--PDR8/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/background --motif CGTGYTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/YJM789--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/YJM789--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/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--PDR8/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/YJM789--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/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