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--MIG1/YJM789--MIG1.fa
  
  Database contains 825 sequences, 303234 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCGA
        8
        GGGTTCGA
       
        ACTBGGCC
        8
        ACTTGGCC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        ATGGCAW
        7
        ATGGCAA
       
        GGWAGA
        6
        GGAAGA
       
        AAGARA
        6
        AAGAAA
       
        GACTSTTA
        8
        GACTCTTA
       
        CCVTACA
        7
        CCGTACA
       
        ACYGGGG
        7
        ACTGGGG
       
        AKACGCG
        7
        AGACGCG
       
        TGGTCWA
        7
        TGGTCAA
       
        AGCGCSC
        7
        AGCGCCC
       
        GGYTATCA
        8
        GGCTATCA
       
        ACTTCWAA
        8
        ACTTCTAA
       
        GCTTTGK
        7
        GCTTTGT
       
        ACTGAGCT
        8
        ACTGAGCT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCGA	8	GGGTTCGA
ACTBGGCC	8	ACTTGGCC
GCCTTAMC	8	GCCTTAAC
ATAGTKTA	8	ATAGTGTA
ATGGCAW	7	ATGGCAA
GGWAGA	6	GGAAGA
AAGARA	6	AAGAAA
GACTSTTA	8	GACTCTTA
CCVTACA	7	CCGTACA
ACYGGGG	7	ACTGGGG
AKACGCG	7	AGACGCG
TGGTCWA	7	TGGTCAA
AGCGCSC	7	AGCGCCC
GGYTATCA	8	GGCTATCA
ACTTCWAA	8	ACTTCTAA
GCTTTGK	7	GCTTTGT
ACTGAGCT	8	ACTGAGCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 39 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-8	chrVIII	+	34660	34667	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVIII	+	34660	34667	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVII	+	122297	122304	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVII	+	122297	122304	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrX	+	414994	415001	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrIV	+	525931	525938	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrIV	+	525931	525938	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVII	+	544667	544674	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrXVI	+	582090	582097	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVII	+	876422	876429	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrIV	+	1201778	1201785	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrV	-	135460	135467	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrXV	-	159464	159471	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVII	-	185749	185756	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrVI	-	226723	226730	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrV	-	435787	435794	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrXII	-	448849	448856	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrXIII	-	480656	480663	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrIV	-	1352501	1352508	1.96e-05	0.599	GACTCTTA
GACTSTTA	DREME-8	chrXI	+	74653	74660	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXIV	+	102745	102752	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXIV	+	102745	102752	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrIII	+	127745	127752	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXV	+	228360	228367	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	+	254657	254664	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	+	254657	254664	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXVI	+	282487	282494	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXVI	+	282487	282494	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXV	+	487468	487475	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrIV	+	492251	492258	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrVII	+	731166	731173	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXVI	+	810705	810712	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	-	87068	87075	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrX	-	122265	122272	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrVI	-	137521	137528	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	-	522933	522940	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	-	605212	605219	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXV	-	620593	620600	3.92e-05	0.599	GACTGTTA
GACTSTTA	DREME-8	chrXII	-	976018	976025	3.92e-05	0.599	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--MIG1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/background --motif GACTSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/YJM789--MIG1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/YJM789--MIG1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/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--MIG1/fimo_out_8	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/YJM789--MIG1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--MIG1/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