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/RM11-1A--INO80/RM11-1A--INO80.fa
  
  Database contains 425 sequences, 140299 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        ACCRACT
        7
        ACCAACT
       
        AGTGGTW
        7
        AGTGGTT
       
        CCRTACA
        7
        CCATACA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        AMACTAT
        7
        AAACTAT
       
        GSGCCA
        6
        GCGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATCKTGA
        7
        ATCGTGA
       
        AGTCAKAC
        8
        AGTCAGAC
       
        CCCATKC
        7
        CCCATGC
       
        ATCTTYTG
        8
        ATCTTCTG
       
        CCRTGGAG
        8
        CCGTGGAG
       
        AAAAAAAW
        8
        AAAAAAAA
       
        CGGCCAA
        7
        CGGCCAA
       
        CGTGYTAA
        8
        CGTGCTAA
       
        AATGGTCA
        8
        AATGGTCA
       
        ACAAGGMT
        8
        ACAAGGCT
       
        ACKGAAGA
        8
        ACTGAAGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
ACCRACT	7	ACCAACT
AGTGGTW	7	AGTGGTT
CCRTACA	7	CCATACA
ATGGCAWC	8	ATGGCAAC
AMACTAT	7	AAACTAT
GSGCCA	6	GCGCCA
CGCSTTA	7	CGCCTTA
ATCKTGA	7	ATCGTGA
AGTCAKAC	8	AGTCAGAC
CCCATKC	7	CCCATGC
ATCTTYTG	8	ATCTTCTG
CCRTGGAG	8	CCGTGGAG
AAAAAAAW	8	AAAAAAAA
CGGCCAA	7	CGGCCAA
CGTGYTAA	8	CGTGCTAA
AATGGTCA	8	AATGGTCA
ACAAGGMT	8	ACAAGGCT
ACKGAAGA	8	ACTGAAGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 22 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
AATGGTCA	DREME-17	chrXIV	-	102823	102830	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	+	204747	204754	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	+	233951	233958	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrVII	-	316836	316843	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXV	-	340350	340357	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	+	355468	355475	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	+	355468	355475	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXII	+	374367	374374	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	-	374474	374481	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrII	+	405972	405979	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrII	+	405972	405979	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXII	+	427144	427151	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXIII	+	463566	463573	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrV	-	492403	492410	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXI	-	513382	513389	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrX	+	541520	541527	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrVII	-	544627	544634	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrIV	+	568976	568983	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrIV	+	568976	568983	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXV	+	571970	571977	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrIV	-	620020	620027	1.96e-05	0.245	AATGGTCA
AATGGTCA	DREME-17	chrXII	+	793930	793937	1.96e-05	0.245	AATGGTCA

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/RM11-1A--INO80/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/background --motif AATGGTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/RM11-1A--INO80.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/RM11-1A--INO80.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/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/RM11-1A--INO80/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/RM11-1A--INO80.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/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