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--SWR1/AWRI1631--SWR1.fa
  
  Database contains 446 sequences, 123197 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CCRTACA
        7
        CCATACA
       
        AGTGGTW
        7
        AGTGGTT
       
        GGHTCGA
        7
        GGTTCGA
       
        AGTYGGTW
        8
        AGTTGGTT
       
        CACGGW
        6
        CACGGA
       
        CRCCCA
        6
        CACCCA
       
        AASGCG
        6
        AAGGCG
       
        CCAAVAGA
        8
        CCAAGAGA
       
        GCGCTHCC
        8
        GCGCTACC
       
        CGGCCAM
        7
        CGGCCAA
       
        CGCCASAC
        8
        CGCCACAC
       
        GACTSTTA
        8
        GACTCTTA
       
        GCTAWCA
        7
        GCTATCA
       
        ATCKTGA
        7
        ATCTTGA
       
        ARAAAAA
        7
        AAAAAAA
       
        AGACCACR
        8
        AGACCACG
       
        GCCATRGA
        8
        GCCATAGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
CCRTACA	7	CCATACA
AGTGGTW	7	AGTGGTT
GGHTCGA	7	GGTTCGA
AGTYGGTW	8	AGTTGGTT
CACGGW	6	CACGGA
CRCCCA	6	CACCCA
AASGCG	6	AAGGCG
CCAAVAGA	8	CCAAGAGA
GCGCTHCC	8	GCGCTACC
CGGCCAM	7	CGGCCAA
CGCCASAC	8	CGCCACAC
GACTSTTA	8	GACTCTTA
GCTAWCA	7	GCTATCA
ATCKTGA	7	ATCTTGA
ARAAAAA	7	AAAAAAA
AGACCACR	8	AGACCACG
GCCATRGA	8	GCCATAGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 33 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
GCCATRGA	DREME-17	chrVI	+	137548	137555	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXII	+	976045	976052	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXI	-	74626	74633	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXIV	-	102718	102725	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrIII	-	127718	127725	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXV	-	228333	228340	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXV	-	487441	487448	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXIV	-	632601	632608	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrVII	-	731139	731146	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrXVI	-	810678	810685	7.61e-06	0.183	GCCATGGA
GCCATRGA	DREME-17	chrX	+	59161	59168	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrVIII	+	116168	116175	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrIII	+	163624	163631	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrVII	+	254415	254422	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrXV	+	354102	354109	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrIV	+	434325	434332	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrXIV	+	560754	560761	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrXII	+	781528	781535	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrXIV	-	104807	104814	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrXV	-	113804	113811	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrIX	-	175033	175040	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrII	-	266380	266387	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrIII	-	295486	295493	1.98e-05	0.207	GCCATAGA
GCCATRGA	DREME-17	chrV	+	85855	85862	3.97e-05	0.353	GCCATTGA
GCCATRGA	DREME-17	chrIII	+	163729	163736	3.97e-05	0.353	GCCATCGA
GCCATRGA	DREME-17	chrX	-	414874	414881	3.97e-05	0.353	GCCATCGA
GCCATRGA	DREME-17	chrXII	-	838897	838904	3.97e-05	0.353	GCCATCGA
GCCATRGA	DREME-17	chrV	+	140786	140793	9.09e-05	0.662	GCCGTGGA
GCCATRGA	DREME-17	chrX	+	147166	147173	9.09e-05	0.662	GCCATGGG
GCCATRGA	DREME-17	chrIV	-	87661	87668	9.09e-05	0.662	GCCTTGGA
GCCATRGA	DREME-17	chrXVI	-	281734	281741	9.09e-05	0.662	GCCGTGGA
GCCATRGA	DREME-17	chrXVI	-	860498	860505	9.09e-05	0.662	GCCTTGGA
GCCATRGA	DREME-17	chrVII	-	883554	883561	9.09e-05	0.662	GCCATGGG

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--SWR1/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/background --motif GCCATRGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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/AWRI1631--SWR1/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/AWRI1631--SWR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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