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 35 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
AGACCACR	DREME-16	chrXII	-	369968	369975	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrX	-	378364	378371	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrV	-	438704	438711	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrV	-	469461	469468	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrVII	-	823486	823493	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXI	+	308204	308211	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXIII	+	372505	372512	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrVII	+	412354	412361	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXIII	+	420648	420655	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXIII	+	586696	586703	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXV	+	663872	663879	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXII	+	687919	687926	7.61e-06	0.152	AGACCACG
AGACCACR	DREME-16	chrXII	-	92552	92559	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrVI	-	101380	101387	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrIII	+	123635	123642	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrI	-	139156	139163	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrXIII	+	196157	196164	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrXV	-	301101	301108	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrIX	+	316202	316209	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrXV	-	464454	464461	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrXIV	-	568119	568126	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrXIV	+	631904	631911	1.98e-05	0.216	AGACCACA
AGACCACR	DREME-16	chrII	-	9595	9602	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrXI	-	84220	84227	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrIX	-	183437	183444	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrII	-	347615	347622	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrIV	-	519755	519762	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrVII	-	700687	700694	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrIV	-	1095483	1095490	3.97e-05	0.28	AGACCACC
AGACCACR	DREME-16	chrX	+	424494	424501	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrXIV	+	569935	569942	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrXIV	+	726196	726203	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrVII	+	726650	726657	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrXII	+	963034	963041	3.97e-05	0.28	AGACCACT
AGACCACR	DREME-16	chrXV	+	80032	80039	9.09e-05	0.623	AGTCCACG

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_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--SWR1/background --motif AGACCACR /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_15
    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_15	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