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--NOT3/YJM789--NOT3.fa
  
  Database contains 504 sequences, 167254 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TBGGCCA
        7
        TCGGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        GGTTCRA
        7
        GGTTCGA
       
        ATGTAYGG
        8
        ATGTATGG
       
        TGGCGYA
        7
        TGGCGCA
       
        AGCGCV
        6
        AGCGCG
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTARACCA
        8
        CTAGACCA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CACGGA
        6
        CACGGA
       
        TAGCTCR
        7
        TAGCTCA
       
        TCTCCACR
        8
        TCTCCACA
       
        GTTGGK
        6
        GTTGGT
       
        ARAAARAA
        8
        AAAAAAAA
       
        ATTAASAG
        8
        ATTAAGAG
       
        TAATCWGA
        8
        TAATCAGA
       
        AGCGWGA
        7
        AGCGTGA
       
        RCACCCA
        7
        ACACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/background):

A 0.316 C 0.184 G 0.184 T 0.316

MOTIF	WIDTH	BEST POSSIBLE MATCH
TBGGCCA	7	TCGGCCA
CGCSTTA	7	CGCCTTA
GGTTCRA	7	GGTTCGA
ATGTAYGG	8	ATGTATGG
TGGCGYA	7	TGGCGCA
AGCGCV	6	AGCGCG
ATGGCAWC	8	ATGGCAAC
CTARACCA	8	CTAGACCA
ATAGTKTA	8	ATAGTGTA
CACGGA	6	CACGGA
TAGCTCR	7	TAGCTCA
TCTCCACR	8	TCTCCACA
GTTGGK	6	GTTGGT
ARAAARAA	8	AAAAAAAA
ATTAASAG	8	ATTAAGAG
TAATCWGA	8	TAATCAGA
AGCGWGA	7	AGCGTGA
RCACCCA	7	ACACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 27 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
TAATCWGA	DREME-16	chrXIII	-	131854	131861	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrV	+	138699	138706	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrXI	-	162516	162523	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrXIV	+	174396	174403	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrX	+	355407	355414	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrX	+	355407	355414	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrX	-	374535	374542	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrVII	+	405503	405510	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrII	+	405911	405918	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrIV	+	568915	568922	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrIV	+	568915	568922	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrXII	-	673964	673971	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrVII	+	736373	736380	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrXIII	-	747921	747928	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrVII	-	828752	828759	3.38e-05	0.738	TAATCAGA
TAATCWGA	DREME-16	chrX	-	139436	139443	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrI	+	166539	166546	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrXII	+	374239	374246	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrX	-	391072	391079	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrX	+	422971	422978	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrXIII	-	572912	572919	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrIV	+	668337	668344	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrXII	+	673961	673968	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrVII	+	736223	736230	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrXV	+	976455	976462	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrXII	+	1028360	1028367	6.76e-05	0.82	TAATCTGA
TAATCWGA	DREME-16	chrIV	+	1175863	1175870	6.76e-05	0.82	TAATCTGA

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--NOT3/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/background --motif TAATCWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/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