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--CUP9/BY4742--CUP9.fa
  
  Database contains 821 sequences, 427317 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        CCTTAVC
        7
        CCTTAAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        AAGAAAD
        7
        AAGAAAA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        GTGATAGY
        8
        GTGATAGT
       
        KAATCATA
        8
        TAATCATA
       
        ATAYAACA
        8
        ATACAACA
       
        ATCTTYTG
        8
        ATCTTTTG
       
        CCGTGSA
        7
        CCGTGGA
       
        GTGGTYTA
        8
        GTGGTCTA
       
        AGTCAKAC
        8
        AGTCATAC
       
        TAGTGTAR
        8
        TAGTGTAG
       
        CTGAGCTA
        8
        CTGAGCTA
       
        MACACCCA
        8
        CACACCCA
       
        ACTSACG
        7
        ACTCACG
       
        CAGWTAAC
        8
        CAGTTAAC
       
        ATGGTCAS
        8
        ATGGTCAG
       
        CCAGWTCG
        8
        CCAGTTCG
       
        CCTTARAC
        8
        CCTTAAAC
       
        CKTTGGGC
        8
        CGTTGGGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/background):

A 0.304 C 0.196 G 0.196 T 0.304

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
CCTTAVC	7	CCTTAAC
CTBGGCCA	8	CTCGGCCA
AAGAAAD	7	AAGAAAA
ATGGCAWC	8	ATGGCAAC
GCKCTACC	8	GCGCTACC
GTGATAGY	8	GTGATAGT
KAATCATA	8	TAATCATA
ATAYAACA	8	ATACAACA
ATCTTYTG	8	ATCTTTTG
CCGTGSA	7	CCGTGGA
GTGGTYTA	8	GTGGTCTA
AGTCAKAC	8	AGTCATAC
TAGTGTAR	8	TAGTGTAG
CTGAGCTA	8	CTGAGCTA
MACACCCA	8	CACACCCA
ACTSACG	7	ACTCACG
CAGWTAAC	8	CAGTTAAC
ATGGTCAS	8	ATGGTCAG
CCAGWTCG	8	CCAGTTCG
CCTTARAC	8	CCTTAAAC
CKTTGGGC	8	CGTTGGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
CTGAGCTA	DREME-16	chrII	-	36404	36411	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVII	-	115494	115501	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXV	-	232216	232223	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXIII	-	352286	352293	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrIV	-	359583	359590	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrX	-	422943	422950	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXV	-	438649	438656	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXV	-	438649	438656	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXI	-	578971	578978	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	-	837743	837750	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	-	837743	837750	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	-	837743	837750	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	-	837743	837750	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	-	875382	875389	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrIV	-	884367	884374	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXV	-	976427	976434	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrIV	-	1175835	1175842	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVI	+	157992	157999	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVIII	+	237924	237931	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVIII	+	358554	358561	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrX	+	391100	391107	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVII	+	440792	440799	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXVI	+	560274	560281	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXIII	+	572940	572947	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXII	+	605417	605424	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXVI	+	622616	622623	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrVII	+	701033	701040	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrXVI	+	769287	769294	1.26e-05	0.366	CTGAGCTA
CTGAGCTA	DREME-16	chrIV	+	1095446	1095453	1.26e-05	0.366	CTGAGCTA

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--CUP9/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/background --motif CTGAGCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/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--CUP9/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/BY4742--CUP9.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CUP9/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