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 34 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
ATCKTGA	DREME-9	chrXI	+	74669	74675	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXIV	+	102761	102767	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrIII	+	127761	127767	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXIII	-	131827	131833	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVI	-	137506	137512	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrV	+	138727	138733	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXI	-	162489	162495	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXV	+	228376	228382	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXV	-	282310	282316	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	312455	312461	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	312455	312461	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	312455	312461	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	312455	312461	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrX	+	355435	355441	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrX	+	355435	355441	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXII	+	366367	366373	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrX	-	374508	374514	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	+	405531	405537	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrII	+	405939	405945	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrII	+	405939	405945	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXV	+	487484	487490	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrIV	-	491171	491177	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXVI	+	520454	520460	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrIV	+	568943	568949	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrIV	+	568943	568949	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXIV	+	632644	632650	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	731052	731058	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	+	731182	731188	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXIII	-	732245	732251	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	+	736401	736407	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXIII	-	747894	747900	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXVI	+	810721	810727	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrVII	-	828725	828731	6.35e-05	0.514	ATCGTGA
ATCKTGA	DREME-9	chrXII	-	976003	976009	6.35e-05	0.514	ATCGTGA

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_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--INO80/background --motif ATCKTGA /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_8
    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_8	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