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--SMP1/YJM789--SMP1.fa
  
  Database contains 476 sequences, 152761 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        CGCSTTA
        7
        CGCCTTA
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        AAGAAAHA
        8
        AAGAAAAA
       
        AACTKGG
        7
        AACTTGG
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GACCAY
        6
        GACCAT
       
        GCKCTACC
        8
        GCGCTACC
       
        CCCATKC
        7
        CCCATGC
       
        CTATCACR
        8
        CTATCACG
       
        CCGTGSA
        7
        CCGTGGA
       
        ACTGMGC
        7
        ACTGAGC
       
        AGCGCMAG
        8
        AGCGCAAG
       
        ATTAGAAR
        8
        ATTAGAAG
       
        SCACGCGA
        8
        GCACGCGA
       
        AAAGCGWG
        8
        AAAGCGTG
       
        AAAARAAA
        8
        AAAAAAAA
       
        AKATCGG
        7
        AGATCGG
       
        ATCGTGA
        7
        ATCGTGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
CGCSTTA	7	CGCCTTA
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
AAGAAAHA	8	AAGAAAAA
AACTKGG	7	AACTTGG
ATGGCAWC	8	ATGGCAAC
GACCAY	6	GACCAT
GCKCTACC	8	GCGCTACC
CCCATKC	7	CCCATGC
CTATCACR	8	CTATCACG
CCGTGSA	7	CCGTGGA
ACTGMGC	7	ACTGAGC
AGCGCMAG	8	AGCGCAAG
ATTAGAAR	8	ATTAGAAG
SCACGCGA	8	GCACGCGA
AAAGCGWG	8	AAAGCGTG
AAAARAAA	8	AAAAAAAA
AKATCGG	7	AGATCGG
ATCGTGA	7	ATCGTGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 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
ATCGTGA	DREME-20	chrXI	+	74669	74675	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXIV	+	102761	102767	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	+	122221	122227	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrIII	+	127761	127767	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXIII	-	131827	131833	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVI	-	137506	137512	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrV	+	138727	138733	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXI	-	162489	162495	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXV	+	228376	228382	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXV	-	282310	282316	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrX	+	355435	355441	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrX	+	355435	355441	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXII	+	366367	366373	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrX	-	374508	374514	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	+	405531	405537	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrII	+	405939	405945	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXV	+	487484	487490	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrIV	-	491171	491177	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXVI	+	520454	520460	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrIV	+	568943	568949	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrIV	+	568943	568949	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXIV	+	632644	632650	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	-	731052	731058	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	+	731182	731188	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXIII	-	732245	732251	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	+	736401	736407	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXIII	-	747894	747900	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXVI	+	810721	810727	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrVII	-	828725	828731	6.38e-05	0.638	ATCGTGA
ATCGTGA	DREME-20	chrXII	-	976003	976009	6.38e-05	0.638	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/YJM789--SMP1/fimo_out_19 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/background --motif ATCGTGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/YJM789--SMP1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/fimo_out_19
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/YJM789--SMP1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/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--SMP1/fimo_out_19	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/YJM789--SMP1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/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