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 26 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
TCTCCCA	DREME-19	chrIII	+	408	414	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrII	-	36413	36419	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXV	+	80054	80060	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrV	-	131034	131040	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVIII	+	146270	146276	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVII	+	149179	149185	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVI	+	157984	157990	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrX	+	197341	197347	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXI	-	219931	219937	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXV	+	228250	228256	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVIII	+	237916	237922	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXIII	+	321175	321181	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXIII	-	352295	352301	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVIII	+	358546	358552	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXIV	-	374884	374890	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrIV	-	410415	410421	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVII	+	440784	440790	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXI	-	518024	518030	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXVI	+	560266	560272	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXVI	+	622608	622614	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXII	+	656962	656968	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXIII	+	768397	768403	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrVII	-	774385	774391	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXVI	-	856938	856944	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrXV	-	866910	866916	4.05e-05	0.474	TCTCCCA
TCTCCCA	DREME-19	chrIV	+	1095438	1095444	4.05e-05	0.474	TCTCCCA

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_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--ACE2/background --motif TCTCCCA /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_17
    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_17	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