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--SWR1/YJM789--SWR1.fa
  
  Database contains 405 sequences, 84034 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGA
       
        ACCRACT
        7
        ACCAACT
       
        AACCACTH
        8
        AACCACTT
       
        RGTTCGA
        7
        GGTTCGA
       
        CACGS
        5
        CACGG
       
        AMACCCA
        7
        ACACCCA
       
        TCAGWA
        6
        TCAGAA
       
        AGMGCG
        6
        AGAGCG
       
        ATAGTKTA
        8
        ATAGTGTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CAAGAAAW
        8
        CAAGAAAT
       
        CCTTGTTR
        8
        CCTTGTTG
       
        GCCWTAGA
        8
        GCCTTAGA
       
        ACCACTA
        7
        ACCACTA
       
        GGCTAYC
        7
        GGCTATC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGA
ACCRACT	7	ACCAACT
AACCACTH	8	AACCACTT
RGTTCGA	7	GGTTCGA
CACGS	5	CACGG
AMACCCA	7	ACACCCA
TCAGWA	6	TCAGAA
AGMGCG	6	AGAGCG
ATAGTKTA	8	ATAGTGTA
ATGGCAWC	8	ATGGCAAC
CAAGAAAW	8	CAAGAAAT
CCTTGTTR	8	CCTTGTTG
GCCWTAGA	8	GCCTTAGA
ACCACTA	7	ACCACTA
GGCTAYC	7	GGCTATC

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
GGCTAYC	DREME-15	chrV	+	177114	177120	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrIX	+	197607	197613	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrIII	+	227993	227999	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXIII	+	290816	290822	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrVII	+	328598	328604	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrV	+	354949	354955	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrIX	+	370432	370438	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrVII	+	541865	541871	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXI	+	619081	619087	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrII	+	645182	645188	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXII	+	797193	797199	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrX	-	115987	115993	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXI	-	141066	141072	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXVI	-	210240	210246	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrVIII	-	475755	475761	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrV	-	487379	487385	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrXI	-	578943	578949	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrIV	-	1017255	1017261	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrIV	-	1075521	1075527	4.05e-05	0.348	GGCTATC
GGCTAYC	DREME-15	chrVI	-	167441	167447	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrXIII	-	168799	168805	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrVI	+	210695	210701	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrXV	-	288196	288202	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrX	-	354248	354254	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrX	+	543032	543038	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrXII	+	637366	637372	6.61e-05	0.4	GGCTACC
GGCTAYC	DREME-15	chrXIII	-	837932	837938	6.61e-05	0.4	GGCTACC

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--SWR1/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/background --motif GGCTAYC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/YJM789--SWR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/YJM789--SWR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/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--SWR1/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/YJM789--SWR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SWR1/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