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 28 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
AGARTCAT	DREME-14	chrVII	-	122295	122302	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrV	+	135462	135469	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrIII	+	151321	151328	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrVII	+	185751	185758	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrVI	+	226725	226732	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrIX	+	300265	300272	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrX	-	414992	414999	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrV	+	435789	435796	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrXIII	+	480658	480665	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrVII	-	876420	876427	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrIV	-	1201776	1201783	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrIV	+	1352503	1352510	1.96e-05	0.446	AGAGTCAT
AGARTCAT	DREME-14	chrXII	-	92566	92573	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrVI	-	101394	101401	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrIII	+	123621	123628	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrI	-	139170	139177	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXIII	+	196143	196150	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXV	-	301115	301122	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrVII	-	366130	366137	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrVIII	+	388968	388975	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXV	-	464468	464475	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXIV	-	547112	547119	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXIV	-	568133	568140	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXIV	+	631890	631897	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrX	+	652233	652240	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXV	-	779821	779828	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrVII	+	828896	828903	5.04e-05	0.492	AGAATCAT
AGARTCAT	DREME-14	chrXV	-	980701	980708	5.04e-05	0.492	AGAATCAT

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_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--PDR8/background --motif AGARTCAT /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_11
    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_11	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