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--SWI1/BY4741--SWI1.fa
  
  Database contains 923 sequences, 390882 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CGCSTTA
        7
        CGCCTTA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GGTTCGA
        7
        GGTTCGA
       
        ACCACKA
        7
        ACCACTA
       
        ATGGGYG
        7
        ATGGGTG
       
        TCCGBACA
        8
        TCCGTACA
       
        GCKCTACC
        8
        GCGCTACC
       
        TTTCTTB
        7
        TTTCTTT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACGGYG
        7
        CACGGTG
       
        CCCAYACA
        8
        CCCACACA
       
        CTATCAC
        7
        CTATCAC
       
        GATTWGAA
        8
        GATTAGAA
       
        CCACACSC
        8
        CCACACCC
       
        ATCKTGAG
        8
        ATCGTGAG
       
        AYTCTCG
        7
        ATTCTCG
       
        CTGAGCTA
        8
        CTGAGCTA
       
        CAWATATA
        8
        CATATATA
       
        TCKCCCA
        7
        TCTCCCA
       
        ACCACTTK
        8
        ACCACTTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background):

A 0.320 C 0.180 G 0.180 T 0.320

MOTIF	WIDTH	BEST POSSIBLE MATCH
CGCSTTA	7	CGCCTTA
CTBGGCCA	8	CTCGGCCA
GGTTCGA	7	GGTTCGA
ACCACKA	7	ACCACTA
ATGGGYG	7	ATGGGTG
TCCGBACA	8	TCCGTACA
GCKCTACC	8	GCGCTACC
TTTCTTB	7	TTTCTTT
ATGGCAWC	8	ATGGCAAC
CACGGYG	7	CACGGTG
CCCAYACA	8	CCCACACA
CTATCAC	7	CTATCAC
GATTWGAA	8	GATTAGAA
CCACACSC	8	CCACACCC
ATCKTGAG	8	ATCGTGAG
AYTCTCG	7	ATTCTCG
CTGAGCTA	8	CTGAGCTA
CAWATATA	8	CATATATA
TCKCCCA	7	TCTCCCA
ACCACTTK	8	ACCACTTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 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-17	chrII	-	36404	36411	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	-	115494	115501	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	-	115494	115501	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXIII	-	352286	352293	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrIV	-	359583	359590	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXIV	-	374875	374882	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXIV	-	374875	374882	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrX	-	422943	422950	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXV	-	438649	438656	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXV	-	438649	438656	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXI	-	578971	578978	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXII	-	875382	875389	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrIV	-	884367	884374	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXV	-	976427	976434	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrIV	-	1175835	1175842	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrX	+	119455	119462	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVI	+	157992	157999	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVIII	+	237924	237931	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVIII	+	358554	358561	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrX	+	391100	391107	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	+	440792	440799	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXVI	+	560274	560281	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXIII	+	572940	572947	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	+	574914	574921	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXII	+	605417	605424	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXVI	+	622616	622623	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	+	701033	701040	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrXVI	+	769287	769294	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrVII	+	800048	800055	1.1e-05	0.281	CTGAGCTA
CTGAGCTA	DREME-17	chrIV	+	1095446	1095453	1.1e-05	0.281	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/BY4741--SWI1/fimo_out_14 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/background --motif CTGAGCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/fimo_out_14
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/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--SWI1/fimo_out_14	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/BY4741--SWI1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--SWI1/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