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/RM11-1A--YAP1/RM11-1A--YAP1.fa
  
  Database contains 544 sequences, 174062 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTGGTWA
        8
        AGTGGTTA
       
        SGGTTCGA
        8
        GGGTTCGA
       
        CAACTKGG
        8
        CAACTTGG
       
        RCGCCTTA
        8
        GCGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        CGWTGCC
        7
        CGTTGCC
       
        CAASAA
        6
        CAACAA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        ACMATTG
        7
        ACCATTG
       
        AAARCCGA
        8
        AAAACCGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/background):

A 0.314 C 0.186 G 0.186 T 0.314

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTGGTWA	8	AGTGGTTA
SGGTTCGA	8	GGGTTCGA
CAACTKGG	8	CAACTTGG
RCGCCTTA	8	GCGCCTTA
GCKCTACC	8	GCGCTACC
CGWTGCC	7	CGTTGCC
CAASAA	6	CAACAA
ACTGAGCT	8	ACTGAGCT
ACMATTG	7	ACCATTG
AAARCCGA	8	AAAACCGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 26 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
ACTGAGCT	DREME-8	chrVI	+	157991	157998	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrVIII	+	237923	237930	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrVIII	+	358553	358560	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrX	+	391099	391106	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrVII	+	440791	440798	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrX	+	517948	517955	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXVI	+	560273	560280	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXIII	+	572939	572946	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXII	+	605416	605423	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXVI	+	622615	622622	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrVII	+	701032	701039	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXVI	+	769286	769293	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrIV	+	1095445	1095452	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrII	-	36405	36412	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrVII	-	115495	115502	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrIII	-	142323	142330	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXIII	-	352287	352294	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXIV	-	374876	374883	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrX	-	422944	422951	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXV	-	438650	438657	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXI	-	578972	578979	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrIV	-	720571	720578	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXII	-	875383	875390	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrIV	-	884368	884375	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrXV	-	976428	976435	1.17e-05	0.153	ACTGAGCT
ACTGAGCT	DREME-8	chrIV	-	1175836	1175843	1.17e-05	0.153	ACTGAGCT

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/RM11-1A--YAP1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/background --motif ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/RM11-1A--YAP1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/RM11-1A--YAP1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/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/RM11-1A--YAP1/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/RM11-1A--YAP1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--YAP1/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