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/AWRI1631--AFT1/AWRI1631--AFT1.fa
  
  Database contains 723 sequences, 230504 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        GGTTCRA
        7
        GGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        TAGTGGTW
        8
        TAGTGGTA
       
        MAGAW
        5
        AAGAA
       
        GMGCTAC
        7
        GCGCTAC
       
        CTCTMCCA
        8
        CTCTACCA
       
        AGTCAKAC
        8
        AGTCAGAC
       
        CAASGATG
        8
        CAACGATG
       
        CATYACGC
        8
        CATTACGC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATAGTKTA
        8
        ATAGTTTA
       
        AAACCSAA
        8
        AAACCCAA
       
        CGTGYTAA
        8
        CGTGCTAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
GCCTTAMC	8	GCCTTAAC
GGTTCRA	7	GGTTCGA
CTBGGCCA	8	CTCGGCCA
TAGTGGTW	8	TAGTGGTA
MAGAW	5	AAGAA
GMGCTAC	7	GCGCTAC
CTCTMCCA	8	CTCTACCA
AGTCAKAC	8	AGTCAGAC
CAASGATG	8	CAACGATG
CATYACGC	8	CATTACGC
GRTCTCCA	8	GGTCTCCA
CGCSTTA	7	CGCCTTA
ATAGTKTA	8	ATAGTTTA
AAACCSAA	8	AAACCCAA
CGTGYTAA	8	CGTGCTAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 35 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
CGTGYTAA	DREME-16	chrIX	-	183477	183484	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrII	+	197521	197528	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrIX	+	210692	210699	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrV	-	443239	443246	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrV	-	551322	551329	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXIV	-	569904	569911	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXIV	+	602339	602346	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrIV	-	668044	668051	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXII	+	734829	734836	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrVII	+	739149	739156	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXVI	+	819556	819563	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXVI	-	880333	880340	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrXII	-	1052108	1052115	1.24e-05	0.431	CGTGCTAA
CGTGYTAA	DREME-16	chrVIII	+	85331	85338	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrVIII	+	148996	149003	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrX	-	291114	291121	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXI	+	308177	308184	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXIII	+	372478	372485	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrX	-	378391	378398	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrVII	+	412327	412334	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXIII	+	420621	420628	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrV	-	438731	438738	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrV	-	469488	469495	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXIII	+	586669	586676	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXV	+	663845	663852	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXII	+	687892	687899	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrVII	-	823513	823520	3.2e-05	0.535	CGTGTTAA
CGTGYTAA	DREME-16	chrXI	-	11590	11597	6.4e-05	0.825	CGTGATAA
CGTGYTAA	DREME-16	chrV	+	42128	42135	6.4e-05	0.825	CGTGATAA
CGTGYTAA	DREME-16	chrVIII	+	120467	120474	6.4e-05	0.825	CGTGATAA
CGTGYTAA	DREME-16	chrIII	-	295560	295567	6.4e-05	0.825	CGTGATAA
CGTGYTAA	DREME-16	chrXI	-	365050	365057	6.4e-05	0.825	CGTGGTAA
CGTGYTAA	DREME-16	chrV	+	433301	433308	6.4e-05	0.825	CGTGGTAA
CGTGYTAA	DREME-16	chrVIII	-	488601	488608	6.4e-05	0.825	CGTGATAA
CGTGYTAA	DREME-16	chrXIV	-	494268	494275	6.4e-05	0.825	CGTGGTAA

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/AWRI1631--AFT1/fimo_out_14 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/background --motif CGTGYTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/AWRI1631--AFT1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/fimo_out_14
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/AWRI1631--AFT1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/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/AWRI1631--AFT1/fimo_out_14	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/AWRI1631--AFT1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--AFT1/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