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/BY4742--NOT3/BY4742--NOT3.fa
  
  Database contains 513 sequences, 171825 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTYGGTW
        8
        AGTTGGTT
       
        CCRTACAY
        8
        CCATACAT
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGGGNG
        7
        ATGGGTG
       
        GCGCTHCC
        8
        GCGCTACC
       
        AAGAAAWA
        8
        AAGAAAAA
       
        ATMCAAC
        7
        ATACAAC
       
        CCASAC
        6
        CCACAC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CYATGGCC
        8
        CTATGGCC
       
        AATCTTYT
        8
        AATCTTTT
       
        GCGCAAK
        7
        GCGCAAG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAGRTTAG
        8
        AAGGTTAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CCAASAG
        7
        CCAAGAG
       
        CCGTGMTA
        8
        CCGTGATA
       
        GGCTAYC
        7
        GGCTATC
       
        CGCGRGC
        7
        CGCGAGC
       
        GCGTGCSA
        8
        GCGTGCGA
       
        ACTSACG
        7
        ACTGACG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTYGGTW	8	AGTTGGTT
CCRTACAY	8	CCATACAT
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
CGCSTTA	7	CGCCTTA
ATGGCAWC	8	ATGGCAAC
ATGGGNG	7	ATGGGTG
GCGCTHCC	8	GCGCTACC
AAGAAAWA	8	AAGAAAAA
ATMCAAC	7	ATACAAC
CCASAC	6	CCACAC
GRTCTCCA	8	GGTCTCCA
CYATGGCC	8	CTATGGCC
AATCTTYT	8	AATCTTTT
GCGCAAK	7	GCGCAAG
AGTCAKAC	8	AGTCATAC
AAGRTTAG	8	AAGGTTAG
AAGCGWGA	8	AAGCGTGA
CCAASAG	7	CCAAGAG
CCGTGMTA	8	CCGTGATA
GGCTAYC	7	GGCTATC
CGCGRGC	7	CGCGAGC
GCGTGCSA	8	GCGTGCGA
ACTSACG	7	ACTGACG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 44 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
CCGTGMTA	DREME-20	chrIX	-	183478	183485	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrII	+	197520	197527	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrII	+	197520	197527	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrIX	+	210691	210698	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrV	-	443240	443247	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrV	-	551323	551330	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXIV	-	569905	569912	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXIV	+	602338	602345	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrIV	-	668045	668052	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXII	+	734828	734835	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrVII	+	739148	739155	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXVI	+	819555	819562	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXVI	-	880334	880341	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrXII	-	1052109	1052116	8.02e-06	0.193	CCGTGCTA
CCGTGMTA	DREME-20	chrIX	-	324365	324372	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrX	-	374486	374493	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrXI	-	513394	513401	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrVII	-	544639	544646	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrX	+	204735	204742	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrX	+	355456	355463	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrII	+	405960	405967	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrXII	+	427132	427139	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrXIII	+	463554	463561	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrVII	+	531610	531617	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrX	+	541508	541515	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrIV	+	568964	568971	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrXV	+	571958	571965	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrXII	+	793918	793925	2.06e-05	0.247	CCGTGATA
CCGTGMTA	DREME-20	chrVIII	+	148995	149002	4.11e-05	0.419	CCGTGTTA
CCGTGMTA	DREME-20	chrIX	+	317289	317296	4.11e-05	0.419	CCGTGGTA
CCGTGMTA	DREME-20	chrXIII	+	321317	321324	4.11e-05	0.419	CCGTGTTA
CCGTGMTA	DREME-20	chrX	+	617764	617771	4.11e-05	0.419	CCGTGGTA
CCGTGMTA	DREME-20	chrXII	+	796802	796809	4.11e-05	0.419	CCGTGTTA
CCGTGMTA	DREME-20	chrXI	+	67892	67899	9.6e-05	0.734	CCGTGCTG
CCGTGMTA	DREME-20	chrXI	+	67904	67911	9.6e-05	0.734	CCGTGCTG
CCGTGMTA	DREME-20	chrXV	+	160436	160443	9.6e-05	0.734	CCGTGCCA
CCGTGMTA	DREME-20	chrXIII	+	224115	224122	9.6e-05	0.734	CCGAGCTA
CCGTGMTA	DREME-20	chrVI	+	225172	225179	9.6e-05	0.734	CCGTGCTT
CCGTGMTA	DREME-20	chrII	+	606072	606079	9.6e-05	0.734	CCGTGCTG
CCGTGMTA	DREME-20	chrIV	-	620153	620160	9.6e-05	0.734	CCGGGCTA
CCGTGMTA	DREME-20	chrXII	-	713350	713357	9.6e-05	0.734	CCGTGCTT
CCGTGMTA	DREME-20	chrXII	-	781600	781607	9.6e-05	0.734	CCGTGCAA
CCGTGMTA	DREME-20	chrXII	-	875313	875320	9.6e-05	0.734	CCGGGCTA
CCGTGMTA	DREME-20	chrIV	-	1175909	1175916	9.6e-05	0.734	CCGTGCTC

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/BY4742--NOT3/fimo_out_18 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif CCGTGMTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_18
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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/BY4742--NOT3/fimo_out_18	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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