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 sequence_1.fasta
  
  Database contains 1 sequences, 27165 residues

  MOTIFS motifs.meme (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1
        11
        CTCAACTAAAC
       
Random model letter frequencies (--nrdb--):

A 0.275 C 0.225 G 0.225 T 0.275

MOTIF	WIDTH	BEST POSSIBLE MATCH
1	11	CTCAACTAAAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 13 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	NC_009988.1	+	66	76	3.04e-07	0.00762	CTCAACTAAAC
1	NC_009988.1	+	24520	24530	3.04e-07	0.00762	CTCAACTAAAC
1	NC_009988.1	+	24756	24766	1.04e-06	0.0105	CTAAACTAAAC
1	NC_009988.1	+	25454	25464	1.04e-06	0.0105	CTAAACTAAAC
1	NC_009988.1	+	26597	26607	1.04e-06	0.0105	TTCAACTAAAC
1	NC_009988.1	+	20467	20477	6.08e-06	0.0508	TACAACTAAAT
1	NC_009988.1	-	13461	13471	1.79e-05	0.128	CCAAACTAAAC
1	NC_009988.1	-	6960	6970	2.96e-05	0.165	CTAAACTCAAC
1	NC_009988.1	+	10109	10119	2.96e-05	0.165	TTCAACTATAC
1	NC_009988.1	-	4394	4404	4.23e-05	0.212	CACAACTAATC
1	NC_009988.1	+	71	81	9.68e-05	0.373	CTAAACGAAAT
1	NC_009988.1	-	2851	2861	9.68e-05	0.373	TTCAACAAAAT
1	NC_009988.1	-	26355	26365	9.68e-05	0.373	TTCAACAAAAT

DEBUGGING INFORMATION

Command line:

fimo --oc . --verbosity 1 --thresh 1.0E-4 motifs.meme sequence_1.fasta

Settings:


  
    output_directory = .
    MEME file name = motifs.meme
    sequence file name = sequence_1.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 = 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 = .	MEME file name = motifs.meme	sequence file name = sequence_1.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 = true	max strand = false
threshold type = p-value	output theshold = 0.0001	pseudocount = 0.1
alpha = 1	verbosity = 1