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 32 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
AAAGCGWG	DREME-17	chrX	+	115975	115982	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXI	+	141054	141061	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrV	-	177125	177132	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXVI	+	210228	210235	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXIII	-	290827	290834	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrVII	-	328609	328616	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrV	-	354960	354967	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrV	-	354960	354967	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrIX	-	370443	370450	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrV	+	487367	487374	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrVII	-	541876	541883	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrII	-	645193	645200	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXII	-	797204	797211	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXV	+	968259	968266	1.23e-05	0.263	AAAGCGTG
AAAGCGWG	DREME-17	chrXII	-	92572	92579	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrVI	-	101400	101407	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrI	-	139176	139183	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXIII	+	196137	196144	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXV	-	301121	301128	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrVIII	+	388962	388969	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrV	+	396466	396473	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXIV	-	444566	444573	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXV	-	464474	464481	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXIV	-	547118	547125	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXIV	-	568139	568146	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrVII	+	857503	857510	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXV	-	980707	980714	2.46e-05	0.273	AAAGCGAG
AAAGCGWG	DREME-17	chrXV	+	282158	282165	4.01e-05	0.375	AAAGCGCG
AAAGCGWG	DREME-17	chrII	-	332556	332563	4.01e-05	0.375	AAAGCGGG
AAAGCGWG	DREME-17	chrXII	-	460121	460128	4.01e-05	0.375	AAAGCGGG
AAAGCGWG	DREME-17	chrXIV	-	575627	575634	4.01e-05	0.375	AAAGCGGG
AAAGCGWG	DREME-17	chrVII	+	856762	856769	4.01e-05	0.375	AAAGCGCG

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_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--SMP1/background --motif AAAGCGWG /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_17
    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_17	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