FIMO Results

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 SeCoV_GER.fasta
  
  Database contains 1 sequences, 28050 residues

  MOTIFS motifs.meme (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1
        9
        GAACTAAAC
       
Random model letter frequencies (--nrdb--):

A 0.282 C 0.222 G 0.229 T 0.267

MOTIF	WIDTH	BEST POSSIBLE MATCH
1	9	GAACTAAAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 9 motif occurences with a p-value less than 0.0001. 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	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
1	LT545990.1	+	88	96	5.36e-06	0.0358	GAACTAAAC
1	LT545990.1	+	24647	24655	5.36e-06	0.0358	GAACTAAAC
1	LT545990.1	+	25632	25640	5.36e-06	0.0358	GAACTAAAC
1	LT545990.1	+	27587	27595	5.36e-06	0.0358	GAACTAAAC
1	LT545990.1	+	26430	26438	1.67e-05	0.0892	TAACTAAAC
1	LT545990.1	+	20321	20329	2.69e-05	0.12	TTACTAAAC
1	LT545990.1	+	25339	25347	4.51e-05	0.172	GTTCTAAAC
1	LT545990.1	+	20189	20197	9.11e-05	0.271	GTCCTAGAC
1	LT545990.1	+	24462	24470	9.11e-05	0.271	GTCCTAGAC

DEBUGGING INFORMATION

Command line:

fimo --oc . --verbosity 1 --thresh 1.0E-4 --norc motifs.meme SeCoV_GER.fasta

Settings:


  
    output_directory = .
    MEME file name = motifs.meme
    sequence file name = SeCoV_GER.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 = 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 = .	MEME file name = motifs.meme	sequence file name = SeCoV_GER.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 = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1