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/RM11-1A--ACE2/RM11-1A--ACE2.fa
  
  Database contains 484 sequences, 155576 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ACCCADAC
        8
        ACCCATAC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        ATCCGTRC
        8
        ATCCGTAC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GGTCTM
        6
        GGTCTC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        RGCSCAA
        7
        GGCGCAA
       
        AARAAA
        6
        AAAAAA
       
        GTGATARC
        8
        GTGATAGC
       
        ARTCATAC
        8
        AGTCATAC
       
        GCCASAC
        7
        GCCACAC
       
        CGCGGGS
        7
        CGCGGGG
       
        ACTGAGCT
        8
        ACTGAGCT
       
        ATCAKAAG
        8
        ATCAGAAG
       
        GAGTTCRA
        8
        GAGTTCAA
       
        TCTCCCA
        7
        TCTCCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CTBGGCCA	8	CTCGGCCA
ACCCADAC	8	ACCCATAC
GCCTTAMC	8	GCCTTAAC
GCKCTACC	8	GCGCTACC
ATCCGTRC	8	ATCCGTAC
ATGGCAWC	8	ATGGCAAC
GGTCTM	6	GGTCTC
ATAGTKTA	8	ATAGTGTA
RGCSCAA	7	GGCGCAA
AARAAA	6	AAAAAA
GTGATARC	8	GTGATAGC
ARTCATAC	8	AGTCATAC
GCCASAC	7	GCCACAC
CGCGGGS	7	CGCGGGG
ACTGAGCT	8	ACTGAGCT
ATCAKAAG	8	ATCAGAAG
GAGTTCRA	8	GAGTTCAA
TCTCCCA	7	TCTCCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 33 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
ATCAKAAG	DREME-17	chrXIV	+	89486	89493	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrV	+	138701	138708	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrIV	+	229663	229670	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	+	278030	278037	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrX	+	355409	355416	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	+	405505	405512	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrII	+	405913	405920	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrIV	+	568917	568924	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrX	+	608825	608832	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrXVI	+	701544	701551	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	+	736375	736382	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrXIII	-	131852	131859	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrXI	-	158313	158320	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrXI	-	162514	162521	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrX	-	374533	374540	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	-	405431	405438	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrIV	-	434335	434342	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrXIII	-	747919	747926	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	-	828750	828757	1.96e-05	0.314	ATCAGAAG
ATCAKAAG	DREME-17	chrVII	+	122305	122312	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrXIII	+	379542	379549	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrX	+	415002	415009	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrXVI	+	582098	582105	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrVII	+	876430	876437	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrIV	+	1201786	1201793	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrV	-	135452	135459	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrIII	-	151311	151318	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrVII	-	185741	185748	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrVI	-	226715	226722	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrIX	-	300255	300262	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrV	-	435779	435786	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrXIII	-	480648	480655	5.05e-05	0.466	ATCATAAG
ATCAKAAG	DREME-17	chrIV	-	1352493	1352500	5.05e-05	0.466	ATCATAAG

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/RM11-1A--ACE2/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/background --motif ATCAKAAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/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/RM11-1A--ACE2/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/RM11-1A--ACE2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/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