FIMO Results

Database and Motifs

High-scoring Motif Occurences

Debugging Information

Results in TSV Format

Results in GFF3 Format

FIMO - Motif search tool

FIMO version 5.1.1, (Release date: Wed Jan 29 15:00:42 2020 -0800)

For further information on how to interpret these results please access http://meme-suite.org//doc/fimo-output-format.html.
To get a copy of the FIMO software please access http://meme-suite.org

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 human-CoV.fasta
  
  Database contains 1 sequences, 27553 residues

  MOTIFS MEME.html (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TCTMAACTAAAC
        12
        TCTCAACTAAAC
       
        RGMRSSTGTTGT
        12
        GGAGGCTGTTGT
       
        MTRGTGYTGTC
        11
        CTGGTGCTGTC
       
Random model letter frequencies (--nrdb--):

A 0.282 C 0.222 G 0.229 T 0.267

MOTIF	WIDTH	BEST POSSIBLE MATCH
TCTMAACTAAAC	12	TCTCAACTAAAC
RGMRSSTGTTGT	12	GGAGGCTGTTGT
MTRGTGYTGTC	11	CTGGTGCTGTC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 14 motif occurences with a p-value less than 1e-05. The full set of motif occurences can be seen in the TSV (tab-delimited values) output file fimo.tsv, the GFF3 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
TCTMAACTAAAC	MEME-1	NC_005831	+	62	73	8.25e-08	0.00152	tctcaactaaac
TCTMAACTAAAC	MEME-1	NC_005831	+	25429	25440	1.87e-07	0.00152	tctaaactaaac
TCTMAACTAAAC	MEME-1	NC_005831	+	26118	26129	1.87e-07	0.00152	tctaaactaaac
TCTMAACTAAAC	MEME-1	NC_005831	+	25184	25195	3.36e-07	0.00205	tctcaactatac
RGMRSSTGTTGT	MEME-2	NC_005831	+	25156	25167	4.6e-07	0.00712	agagcctgttgt
TCTMAACTAAAC	MEME-1	NC_005831	+	20462	20473	5.34e-07	0.00261	tctcaactaaat
RGMRSSTGTTGT	MEME-2	NC_005831	+	24474	24485	5.63e-07	0.00712	cgaggctgttgt
MTRGTGYTGTC	MEME-3	NC_005831	+	83	93	6.54e-07	0.00863	ctagtgctgtc
MTRGTGYTGTC	MEME-3	NC_005831	+	25128	25138	8.49e-07	0.00863	atggtgctgtc
MTRGTGYTGTC	MEME-3	NC_005831	+	26061	26071	1e-06	0.00863	ctggtgttgcc
TCTMAACTAAAC	MEME-1	NC_005831	+	24493	24504	1.21e-06	0.00493	gttcaactaaac
RGMRSSTGTTGT	MEME-2	NC_005831	+	26077	26088	2.67e-06	0.0225	ggagggtgtttt
RGMRSSTGTTGT	MEME-2	NC_005831	+	20408	20419	8.72e-06	0.0471	gtaggttgttgt
RGMRSSTGTTGT	MEME-2	NC_005831	+	150	161	9.32e-06	0.0471	ggcaagtgttgt

DEBUGGING INFORMATION

Command line:

fimo --oc . --verbosity 1 --thresh 1.0E-5 --norc MEME.html human-CoV.fasta

Settings:


  
    output_directory = .
    MEME file name = MEME.html
    sequence file name = human-CoV.fasta
  
  
    background file name = --nrdb--
    alphabet = DNA
    max stored scores = 100000
  
  
    allow clobber = true
    compute q-values = true
    parse genomic coord. = false
  
  
    text only = false
    scan both strands = false
    max strand = false
  
  
    threshold type = p-value
    output theshold = 1e-05
    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 = .	MEME file name = MEME.html	sequence file name = human-CoV.fasta
background file name = --nrdb--	alphabet = DNA	max stored scores = 100000
allow clobber = true	compute q-values = true	parse genomic coord. = false
text only = false	scan both strands = false	max strand = false
threshold type = p-value	output theshold = 1e-05	pseudocount = 0.1
alpha = 1	verbosity = 1