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--YAP1/AWRI1631--YAP1.fa
  
  Database contains 638 sequences, 192385 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        TAAGGCR
        7
        TAAGGCG
       
        ACTBGGCC
        8
        ACTTGGCC
       
        TAGTGGTW
        8
        TAGTGGTA
       
        CAASA
        5
        CAAGA
       
        GGAGABC
        7
        GGAGACC
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ACTGAGCT
        8
        ACTGAGCT
       
        RAARAAAA
        8
        AAAAAAAA
       
        TCTTCTGR
        8
        TCTTCTGA
       
        CACTATAK
        8
        CACTATAT
       
        AGTMATAC
        8
        AGTAATAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/background):

A 0.315 C 0.185 G 0.185 T 0.315

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
TAAGGCR	7	TAAGGCG
ACTBGGCC	8	ACTTGGCC
TAGTGGTW	8	TAGTGGTA
CAASA	5	CAAGA
GGAGABC	7	GGAGACC
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
ACTGAGCT	8	ACTGAGCT
RAARAAAA	8	AAAAAAAA
TCTTCTGR	8	TCTTCTGA
CACTATAK	8	CACTATAT
AGTMATAC	8	AGTAATAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
CACTATAK	DREME-12	chrVIII	-	134324	134331	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrIII	+	168360	168367	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrXI	-	308253	308260	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrXII	+	448709	448716	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrIV	-	520975	520982	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrVIII	-	554768	554775	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrIV	+	645212	645219	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrVII	-	727245	727252	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrVII	+	785051	785058	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrIV	+	802790	802797	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrXIII	+	808305	808312	1.96e-05	0.671	CACTATAG
CACTATAK	DREME-12	chrIII	+	82521	82528	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXV	-	96668	96675	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrX	+	115998	116005	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrIV	+	130241	130248	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrV	-	177102	177109	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXVI	+	210251	210258	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXIII	-	290804	290811	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrVII	-	328586	328593	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrV	-	354937	354944	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrIX	-	370420	370427	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrV	-	396953	396960	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXII	+	460154	460161	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrV	+	487390	487397	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrVII	-	541853	541860	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrII	-	645170	645177	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXII	-	797181	797188	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXV	+	827978	827985	5.3e-05	0.686	CACTATAT
CACTATAK	DREME-12	chrXV	+	902850	902857	5.3e-05	0.686	CACTATAT

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--YAP1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/background --motif CACTATAK /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/AWRI1631--YAP1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/AWRI1631--YAP1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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/AWRI1631--YAP1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP1/AWRI1631--YAP1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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