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/YJM789--CUP9/YJM789--CUP9.fa
  
  Database contains 645 sequences, 205800 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGG
       
        SGGTTCGA
        8
        GGGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CGCCTTA
        7
        CGCCTTA
       
        CACTANA
        7
        CACTAAA
       
        ACCCAVAC
        8
        ACCCACAC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        CACATYAC
        8
        CACATCAC
       
        TGGCGYA
        7
        TGGCGCA
       
        ATCKTGA
        7
        ATCTTGA
       
        ATGGGYG
        7
        ATGGGTG
       
        CCGTGMTA
        8
        CCGTGATA
       
        CWGAAGA
        7
        CAGAAGA
       
        CGSTCTCC
        8
        CGGTCTCC
       
        AGTCAKAC
        8
        AGTCATAC
       
        ACTGAGCT
        8
        ACTGAGCT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGG
SGGTTCGA	8	GGGTTCGA
CTBGGCCA	8	CTCGGCCA
CGCCTTA	7	CGCCTTA
CACTANA	7	CACTAAA
ACCCAVAC	8	ACCCACAC
ATGGCAWC	8	ATGGCAAC
GCKCTACC	8	GCGCTACC
CACATYAC	8	CACATCAC
TGGCGYA	7	TGGCGCA
ATCKTGA	7	ATCTTGA
ATGGGYG	7	ATGGGTG
CCGTGMTA	8	CCGTGATA
CWGAAGA	7	CAGAAGA
CGSTCTCC	8	CGGTCTCC
AGTCAKAC	8	AGTCATAC
ACTGAGCT	8	ACTGAGCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 24 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
ACTGAGCT	DREME-17	chrII	-	36405	36412	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVII	-	115495	115502	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVI	+	157991	157998	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVIII	+	237923	237930	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVIII	+	358553	358560	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXIV	-	374876	374883	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrX	+	391099	391106	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrX	-	422944	422951	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXV	-	438650	438657	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVII	+	440791	440798	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrX	+	517948	517955	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXVI	+	560273	560280	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXIII	+	572939	572946	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXI	-	578972	578979	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXII	+	605416	605423	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXVI	+	622615	622622	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVII	+	701032	701039	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrVII	+	701032	701039	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXVI	+	769286	769293	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXII	-	875383	875390	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrIV	-	884368	884375	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrXV	-	976428	976435	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrIV	+	1095445	1095452	1.24e-05	0.209	ACTGAGCT
ACTGAGCT	DREME-17	chrIV	-	1175836	1175843	1.24e-05	0.209	ACTGAGCT

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/YJM789--CUP9/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/background --motif ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/YJM789--CUP9.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/YJM789--CUP9.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--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/YJM789--CUP9/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--CUP9/YJM789--CUP9.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--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