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/BY4741--PDR8/BY4741--PDR8.fa
  
  Database contains 863 sequences, 320858 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        TGTAYGGR
        8
        TGTATGGA
       
        ACTBGGCC
        8
        ACTCGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        AGAAAMAA
        8
        AGAAAAAA
       
        GCKCTACC
        8
        GCGCTACC
       
        ACCCAVAC
        8
        ACCCACAC
       
        AASCACT
        7
        AACCACT
       
        CTWGACC
        7
        CTAGACC
       
        CAASGATG
        8
        CAACGATG
       
        CACCGTGS
        8
        CACCGTGG
       
        TGGCGYA
        7
        TGGCGCA
       
        ARAAWA
        6
        AAAAAA
       
        CAGAYGC
        7
        CAGATGC
       
        TAKCTCA
        7
        TATCTCA
       
        GARTCATA
        8
        GAATCATA
       
        CAGTCTKG
        8
        CAGTCTGG
       
        CTCTYCC
        7
        CTCTCCC
       
        CRCCCA
        6
        CACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/background):

A 0.321 C 0.179 G 0.179 T 0.321

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
TGTAYGGR	8	TGTATGGA
ACTBGGCC	8	ACTCGGCC
CGCSTTA	7	CGCCTTA
AGAAAMAA	8	AGAAAAAA
GCKCTACC	8	GCGCTACC
ACCCAVAC	8	ACCCACAC
AASCACT	7	AACCACT
CTWGACC	7	CTAGACC
CAASGATG	8	CAACGATG
CACCGTGS	8	CACCGTGG
TGGCGYA	7	TGGCGCA
ARAAWA	6	AAAAAA
CAGAYGC	7	CAGATGC
TAKCTCA	7	TATCTCA
GARTCATA	8	GAATCATA
CAGTCTKG	8	CAGTCTGG
CTCTYCC	7	CTCTCCC
CRCCCA	6	CACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 41 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
TAKCTCA	DREME-15	chrXV	-	22311	22317	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrV	-	99974	99980	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	-	122225	122231	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVIII	-	126812	126818	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIX	-	132042	132048	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVI	-	157993	157999	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXV	-	216509	216515	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVIII	-	237925	237931	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXIII	-	298573	298579	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVIII	-	358555	358561	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrX	-	391101	391107	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	-	440793	440799	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXVI	-	560275	560281	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXIII	-	572941	572947	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXVI	-	622617	622623	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	-	701034	701040	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	-	701034	701040	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXVI	-	769288	769294	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXII	-	781710	781716	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	-	800049	800055	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIV	-	1095447	1095453	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrII	+	36404	36410	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrM	+	59640	59646	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	+	115494	115500	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXVI	+	282583	282589	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXIII	+	352286	352292	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIV	+	359583	359589	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXIV	+	374875	374881	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrX	+	422943	422949	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXV	+	438649	438655	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXV	+	438649	438655	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIV	+	453889	453895	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrII	+	504565	504571	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrVII	+	535122	535128	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXI	+	578971	578977	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrII	+	645334	645340	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXII	+	875382	875388	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIV	+	884367	884373	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXII	+	975947	975953	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrXV	+	976427	976433	6.1e-05	0.939	TAGCTCA
TAKCTCA	DREME-15	chrIV	+	1175835	1175841	6.1e-05	0.939	TAGCTCA

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/BY4741--PDR8/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/background --motif TAKCTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/BY4741--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/BY4741--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/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/BY4741--PDR8/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/BY4741--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--PDR8/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