FIMO Results

FIMO - Motif search tool

FIMO version 5.5.5, (Release date: Thu Sep 14 08:48:04 2023 +1000)

For further information on how to interpret these results please access https://meme-suite.org/meme/doc/fimo-output-format.html.
To get a copy of the FIMO software please access https://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 MOA1_gain_diff.fa
  
  Database contains 751 sequences, 18143 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-CAGGAAGT
        8
        CAGGAAGT
       
        2-CASCAG
        6
        CAGCAG
       
        3-TGASTCA
        7
        TGAGTCA
       
        4-TCAGCA
        6
        TCAGCA
       
        5-CAGAGGS
        7
        CAGAGGC
       
Random model letter frequencies (./background):

A 0.260 C 0.240 G 0.240 T 0.260

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-CAGGAAGT	8	CAGGAAGT
2-CASCAG	6	CAGCAG
3-TGASTCA	7	TGAGTCA
4-TCAGCA	6	TCAGCA
5-CAGAGGS	7	CAGAGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 20 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	Alt ID	Sequence Name	Strand	Start	End	p-value	q-value	Matched Sequence
1-CAGGAAGT	STREME-1	chr11	+	79015028	79015035	1.52e-05	0.0761	CAGGAAGT
1-CAGGAAGT	STREME-1	chr8	-	107703527	107703534	1.52e-05	0.0761	CAGGAAGT
1-CAGGAAGT	STREME-1	chr8	+	108835351	108835358	1.52e-05	0.0761	caggaagt
1-CAGGAAGT	STREME-1	chr2	+	131085639	131085646	1.52e-05	0.0761	CAGGAAGT
1-CAGGAAGT	STREME-1	chr6	+	146311246	146311253	1.52e-05	0.0761	CAGGAAGT
1-CAGGAAGT	STREME-1	chr8	+	73483972	73483979	2.92e-05	0.0856	CAGGAAGG
1-CAGGAAGT	STREME-1	chr3	-	171771330	171771337	2.92e-05	0.0856	CAGGAAGG
1-CAGGAAGT	STREME-1	chr14	-	68468859	68468866	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr12	+	111945412	111945419	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr11	-	115656187	115656194	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr10	+	122183382	122183389	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr2	-	174952722	174952729	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr2	+	201414340	201414347	4.44e-05	0.0856	CAGGATGT
1-CAGGAAGT	STREME-1	chr11	-	9906073	9906080	5.96e-05	0.0972	CAGGAAGA
1-CAGGAAGT	STREME-1	chr1	+	154810194	154810201	5.96e-05	0.0972	CAGGAAGA
1-CAGGAAGT	STREME-1	chr12	-	7280708	7280715	7.36e-05	0.0972	CAGGAAGC
1-CAGGAAGT	STREME-1	chr11	-	65334695	65334702	7.36e-05	0.0972	CAGGAAGC
1-CAGGAAGT	STREME-1	chr14	+	65833068	65833075	7.36e-05	0.0972	CAGGAAGC
1-CAGGAAGT	STREME-1	chr1	+	167939197	167939204	7.36e-05	0.0972	CAGGAAGC
1-CAGGAAGT	STREME-1	chr17	+	34510877	34510884	8.76e-05	0.11	CAGGGAGT

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif 1-CAGGAAGT streme_out/streme.xml MOA1_gain_diff.fa

Settings:


  
    output_directory = fimo_out_5
    MEME file name = streme_out/streme.xml
    sequence file name = MOA1_gain_diff.fa
  
  
    background file name = ./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 = fimo_out_5	MEME file name = streme_out/streme.xml	sequence file name = MOA1_gain_diff.fa
background file name = ./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