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 MOA3_loss_diff.fa
  
  Database contains 1332 sequences, 31796 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-CTGAAAAAN
        9
        CTGAAAAAT
       
        2-CCCAGG
        6
        CCCAGG
       
        3-CACYAGRKG
        9
        CACCAGGGG
       
        4-CAAAGTGC
        8
        CAAAGTGC
       
        5-CAAATACA
        8
        CAAATACA
       
Random model letter frequencies (./background):

A 0.294 C 0.206 G 0.206 T 0.294

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-CTGAAAAAN	9	CTGAAAAAT
2-CCCAGG	6	CCCAGG
3-CACYAGRKG	9	CACCAGGGG
4-CAAAGTGC	8	CAAAGTGC
5-CAAATACA	8	CAAATACA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 15 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-CTGAAAAAN	STREME-1	chr11	+	9118291	9118299	5.64e-06	0.0582	ctgaaaaac
1-CTGAAAAAN	STREME-1	chr15	-	37580096	37580104	5.64e-06	0.0582	CTGAAAAAC
1-CTGAAAAAN	STREME-1	chr14	+	98681655	98681663	5.64e-06	0.0582	ctgaaaaac
1-CTGAAAAAN	STREME-1	chr1	-	99168849	99168857	5.64e-06	0.0582	CTGAAAAAC
1-CTGAAAAAN	STREME-1	chr7	-	11632154	11632162	1.37e-05	0.113	CTGAAAAAT
1-CTGAAAAAN	STREME-1	chr11	+	6138253	6138261	1.93e-05	0.133	ctgaaaaag
1-CTGAAAAAN	STREME-1	chr10	+	114591742	114591750	3.13e-05	0.184	ctgaaacac
1-CTGAAAAAN	STREME-1	chr11	-	124329962	124329970	3.69e-05	0.19	CTGAAACAT
1-CTGAAAAAN	STREME-1	chr10	-	18019708	18019716	4.65e-05	0.192	CTGGAAAAT
1-CTGAAAAAN	STREME-1	chr3	+	184843919	184843927	4.65e-05	0.192	ctggaaaat
1-CTGAAAAAN	STREME-1	chr12	-	80336787	80336795	6.57e-05	0.226	CTGGAAAAA
1-CTGAAAAAN	STREME-1	chr12	+	121460252	121460260	6.57e-05	0.226	CTGGAAAAA
1-CTGAAAAAN	STREME-1	chr18	+	10227522	10227530	7.13e-05	0.227	CAGAAAAAC
1-CTGAAAAAN	STREME-1	chr16	-	11071526	11071534	7.93e-05	0.234	CAGAAAAAT
1-CTGAAAAAN	STREME-1	chr1	-	240069608	240069616	8.89e-05	0.245	CTGCAAAAT

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_3 --bgfile ./background --motif 1-CTGAAAAAN streme_out/streme.xml MOA3_loss_diff.fa

Settings:


  
    output_directory = fimo_out_3
    MEME file name = streme_out/streme.xml
    sequence file name = MOA3_loss_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_3	MEME file name = streme_out/streme.xml	sequence file name = MOA3_loss_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