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--YKL222C/BY4742--YKL222C.fa
  
  Database contains 546 sequences, 159391 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        BTAAGGCG
        8
        TTAAGGCG
       
        GCKCTACC
        8
        GCGCTACC
       
        CCCANAC
        7
        CCCACAC
       
        CTARACCA
        8
        CTAGACCA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        TAKCTCA
        7
        TATCTCA
       
        TGGCGYA
        7
        TGGCGCA
       
        CTKGCGC
        7
        CTTGCGC
       
        AGAARA
        6
        AGAAAA
       
        SGGTTCGA
        8
        GGGTTCGA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GTGGTTAK
        8
        GTGGTTAT
       
        ATCCKTGC
        8
        ATCCGTGC
       
        GTATKAC
        7
        GTATGAC
       
        CCCATKC
        7
        CCCATGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGA
CTBGGCCA	8	CTCGGCCA
BTAAGGCG	8	TTAAGGCG
GCKCTACC	8	GCGCTACC
CCCANAC	7	CCCACAC
CTARACCA	8	CTAGACCA
ATAGTKTA	8	ATAGTGTA
TAKCTCA	7	TATCTCA
TGGCGYA	7	TGGCGCA
CTKGCGC	7	CTTGCGC
AGAARA	6	AGAAAA
SGGTTCGA	8	GGGTTCGA
ATGGCAWC	8	ATGGCAAC
GTGGTTAK	8	GTGGTTAT
ATCCKTGC	8	ATCCGTGC
GTATKAC	7	GTATGAC
CCCATKC	7	CCCATGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 32 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-8	chrII	+	36404	36410	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrM	+	59640	59646	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrV	-	99974	99980	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVII	+	115494	115500	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVII	-	122225	122231	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrX	+	140339	140345	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVI	-	157993	157999	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXV	-	216509	216515	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVIII	-	237925	237931	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXIII	+	352286	352292	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVIII	-	358555	358561	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrIV	+	359583	359589	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXIV	+	374875	374881	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrX	-	391101	391107	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrX	+	422943	422949	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXV	+	438649	438655	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVII	-	440793	440799	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVII	+	535122	535128	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXVI	-	560275	560281	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXIII	-	572941	572947	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXI	+	578971	578977	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXII	-	605418	605424	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXVI	-	622617	622623	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrVII	-	701034	701040	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXVI	-	769288	769294	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXII	-	781710	781716	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXII	+	875382	875388	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrIV	+	884367	884373	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXII	+	975947	975953	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrXV	+	976427	976433	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrIV	-	1095447	1095453	6.33e-05	0.617	TAGCTCA
TAKCTCA	DREME-8	chrIV	+	1175835	1175841	6.33e-05	0.617	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/BY4742--YKL222C/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/background --motif TAKCTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/BY4742--YKL222C.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/BY4742--YKL222C.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/BY4742--YKL222C.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--YKL222C/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