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/AWRI1631--CAT8/AWRI1631--CAT8.fa
  
  Database contains 485 sequences, 160587 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        ACCWCT
        6
        ACCACT
       
        CCRTACAY
        8
        CCATACAT
       
        AACTKGGC
        8
        AACTTGGC
       
        CGCCTTA
        7
        CGCCTTA
       
        GTSATA
        6
        GTGATA
       
        ACCCANAC
        8
        ACCCACAC
       
        CGCKCTAC
        8
        CGCGCTAC
       
        AAAAAAMT
        8
        AAAAAAAT
       
        CASACGC
        7
        CAGACGC
       
        CCATCGTK
        8
        CCATCGTT
       
        CACGGTGM
        8
        CACGGTGA
       
        CAAGAK
        6
        CAAGAT
       
        CAACGWTG
        8
        CAACGTTG
       
        GCCRTTAC
        8
        GCCGTTAC
       
        TCAKAA
        6
        TCAGAA
       
        ACTTSTAA
        8
        ACTTCTAA
       
        AYTGCGCC
        8
        ATTGCGCC
       
        CGCGGGSA
        8
        CGCGGGGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
ACCWCT	6	ACCACT
CCRTACAY	8	CCATACAT
AACTKGGC	8	AACTTGGC
CGCCTTA	7	CGCCTTA
GTSATA	6	GTGATA
ACCCANAC	8	ACCCACAC
CGCKCTAC	8	CGCGCTAC
AAAAAAMT	8	AAAAAAAT
CASACGC	7	CAGACGC
CCATCGTK	8	CCATCGTT
CACGGTGM	8	CACGGTGA
CAAGAK	6	CAAGAT
CAACGWTG	8	CAACGTTG
GCCRTTAC	8	GCCGTTAC
TCAKAA	6	TCAGAA
ACTTSTAA	8	ACTTCTAA
AYTGCGCC	8	ATTGCGCC
CGCGGGSA	8	CGCGGGGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 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
CGCGGGSA	DREME-19	chrII	+	197532	197539	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrIX	+	210703	210710	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrXII	+	734840	734847	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrVII	+	739160	739167	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrXVI	+	819567	819574	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrIX	-	183466	183473	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrV	-	443228	443235	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrV	-	551311	551318	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrXIV	-	569893	569900	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrIV	-	668033	668040	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrXVI	-	880322	880329	3.29e-06	0.0861	CGCGGGGA
CGCGGGSA	DREME-19	chrVIII	+	133049	133056	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrXII	+	167967	167974	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrI	+	182545	182552	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrXIII	+	259181	259188	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrV	+	288466	288473	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrX	+	524035	524042	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrIV	+	980997	981004	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrV	-	86653	86660	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrII	-	227124	227131	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrIII	-	228010	228017	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrIX	-	248899	248906	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrIV	-	437821	437828	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrXVI	-	689614	689621	6.58e-06	0.0861	CGCGGGCA
CGCGGGSA	DREME-19	chrVII	+	700745	700752	1.69e-05	0.204	CGCGGGTA
CGCGGGSA	DREME-19	chrVII	-	205667	205674	1.69e-05	0.204	CGCGGGTA
CGCGGGSA	DREME-19	chrXI	-	382331	382338	2.44e-05	0.273	CGCGGGGT
CGCGGGSA	DREME-19	chrVII	-	700741	700748	2.44e-05	0.273	CGCGGGGT
CGCGGGSA	DREME-19	chrVII	+	726669	726676	3.19e-05	0.333	CGCGGGCT
CGCGGGSA	DREME-19	chrIV	-	1305680	1305687	3.19e-05	0.333	CGCGGGCC

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/AWRI1631--CAT8/fimo_out_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/background --motif CGCGGGSA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/fimo_out_17
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/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/AWRI1631--CAT8/fimo_out_17	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/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