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--CAD1/BY4742--CAD1.fa
  
  Database contains 590 sequences, 242506 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGHTCGA
        7
        GGTTCGA
       
        CCRTRCA
        7
        CCATACA
       
        ACCACTM
        7
        ACCACTA
       
        TAAGGCR
        7
        TAAGGCG
       
        CAACTKGG
        8
        CAACTTGG
       
        GCKCTACC
        8
        GCGCTACC
       
        AARAAAW
        7
        AAAAAAA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GATTWGAA
        8
        GATTAGAA
       
        ACSCAGA
        7
        ACCCAGA
       
        TAKCTCA
        7
        TATCTCA
       
        CASACGC
        7
        CACACGC
       
        CCAAVAGA
        8
        CCAAGAGA
       
        AYTGCGCC
        8
        ACTGCGCC
       
        CTCTCSCA
        8
        CTCTCCCA
       
        TCTCCACR
        8
        TCTCCACG
       
        ATTAASAG
        8
        ATTAAGAG
       
        CGCGTGSC
        8
        CGCGTGCC
       
        CGTTAYAC
        8
        CGTTACAC
       
        AWGTGATA
        8
        ATGTGATA
       
        CCCGCGY
        7
        CCCGCGC
       
        ACCCAHAC
        8
        ACCCACAC
       
        ACYCCGAT
        8
        ACTCCGAT
       
        ATCKTGA
        7
        ATCTTGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/background):

A 0.311 C 0.189 G 0.189 T 0.311

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGHTCGA	7	GGTTCGA
CCRTRCA	7	CCATACA
ACCACTM	7	ACCACTA
TAAGGCR	7	TAAGGCG
CAACTKGG	8	CAACTTGG
GCKCTACC	8	GCGCTACC
AARAAAW	7	AAAAAAA
ATGGCAWC	8	ATGGCAAC
GATTWGAA	8	GATTAGAA
ACSCAGA	7	ACCCAGA
TAKCTCA	7	TATCTCA
CASACGC	7	CACACGC
CCAAVAGA	8	CCAAGAGA
AYTGCGCC	8	ACTGCGCC
CTCTCSCA	8	CTCTCCCA
TCTCCACR	8	TCTCCACG
ATTAASAG	8	ATTAAGAG
CGCGTGSC	8	CGCGTGCC
CGTTAYAC	8	CGTTACAC
AWGTGATA	8	ATGTGATA
CCCGCGY	7	CCCGCGC
ACCCAHAC	8	ACCCACAC
ACYCCGAT	8	ACTCCGAT
ATCKTGA	7	ATCTTGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 33 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
CGTTAYAC	DREME-19	chrIII	+	82516	82523	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrX	+	115993	116000	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXI	+	141072	141079	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrV	-	177107	177114	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrIX	-	197600	197607	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXVI	+	210246	210253	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXIII	-	290809	290816	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrVII	-	328591	328598	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrVII	-	328591	328598	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrV	-	354942	354949	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrV	-	354942	354949	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrIX	-	370425	370432	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrVII	+	401581	401588	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrV	+	487385	487392	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrVII	-	541858	541865	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXII	-	605236	605243	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrII	-	645175	645182	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXII	+	687952	687959	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrXII	-	797186	797193	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrIV	+	1017261	1017268	1.19e-05	0.284	CGTTACAC
CGTTAYAC	DREME-19	chrVII	+	645	652	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrI	+	665	672	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrXV	+	712	719	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrIV	+	768	775	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrVIII	+	5369	5376	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrV	+	138867	138874	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrII	+	682090	682097	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrV	-	85219	85226	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrVIII	-	556232	556239	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrXIV	-	783405	783412	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrXIII	-	923666	923673	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrXV	-	960243	960250	3.16e-05	0.456	CGTTATAC
CGTTAYAC	DREME-19	chrIV	-	1524752	1524759	3.16e-05	0.456	CGTTATAC

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--CAD1/fimo_out_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/background --motif CGTTAYAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/BY4742--CAD1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/fimo_out_17
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/BY4742--CAD1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/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--CAD1/fimo_out_17	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/BY4742--CAD1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAD1/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