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--MGA2/AWRI1631--MGA2.fa
  
  Database contains 458 sequences, 144354 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCATACAT
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        TAGTGGTW
        8
        TAGTGGTA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CRCCCA
        6
        CACCCA
       
        GTGATAGY
        8
        GTGATAGC
       
        TGGCGYA
        7
        TGGCGCA
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CACTTKCG
        8
        CACTTGCG
       
        CCGTGSA
        7
        CCGTGGA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        GTCAKAC
        7
        GTCATAC
       
        ATCAKAAG
        8
        ATCATAAG
       
        ATCTKTTG
        8
        ATCTGTTG
       
        GYGCCAGA
        8
        GTGCCAGA
       
        SAAAAAA
        7
        GAAAAAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
CCRTACAY	8	CCATACAT
CTBGGCCA	8	CTCGGCCA
CGCSTTA	7	CGCCTTA
TAGTGGTW	8	TAGTGGTA
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
CRCCCA	6	CACCCA
GTGATAGY	8	GTGATAGC
TGGCGYA	7	TGGCGCA
AAGCGWGA	8	AAGCGTGA
CACTTKCG	8	CACTTGCG
CCGTGSA	7	CCGTGGA
ACTGAGCT	8	ACTGAGCT
GTCAKAC	7	GTCATAC
ATCAKAAG	8	ATCATAAG
ATCTKTTG	8	ATCTGTTG
GYGCCAGA	8	GTGCCAGA
SAAAAAA	7	GAAAAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 25 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
GTCAKAC	DREME-15	chrXIII	+	131865	131871	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrV	-	138689	138695	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXI	+	162527	162533	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrII	-	181446	181452	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrIV	-	217381	217387	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXV	-	253195	253201	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXVI	+	281059	281065	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXVI	+	281059	281065	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXV	+	301223	301229	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrX	-	355397	355403	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrX	+	374546	374552	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrVIII	-	383029	383035	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrVII	-	405493	405499	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrII	-	405901	405907	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXIV	-	519069	519075	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrIV	-	568905	568911	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrII	-	605902	605908	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXII	+	628551	628557	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXV	-	710316	710322	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXII	-	734894	734900	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrVII	-	736363	736369	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXIII	+	747932	747938	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrXIII	-	808464	808470	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrVII	+	828763	828769	3.94e-05	0.447	GTCAGAC
GTCAKAC	DREME-15	chrIV	-	836018	836024	3.94e-05	0.447	GTCAGAC

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--MGA2/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/background --motif GTCAKAC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/AWRI1631--MGA2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/AWRI1631--MGA2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/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--MGA2/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/AWRI1631--MGA2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MGA2/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