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 MOA24_loss_diff.fa
  
  Database contains 1297 sequences, 31439 residues

  MOTIFS meme_out/meme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TCCATTCSATTCCAT
        15
        TCCATTCGATTCCAT
       
        CCDCCTCDGCCTCCC
        15
        CCGCCTCGGCCTCCC
       
Random model letter frequencies (./background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
TCCATTCSATTCCAT	15	TCCATTCGATTCCAT
CCDCCTCDGCCTCCC	15	CCGCCTCGGCCTCCC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 18 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
CCDCCTCDGCCTCCC	MEME-2	chr4	-	22479221	22479235	4.19e-11	1.1e-06	CCGCCTCGGCCTCCC
CCDCCTCDGCCTCCC	MEME-2	chr19	+	4871524	4871538	3.56e-10	4.66e-06	ccgcctctgcctccc
CCDCCTCDGCCTCCC	MEME-2	chr17	+	47296478	47296492	6.02e-10	5.25e-06	ctgcctcggcctccc
CCDCCTCDGCCTCCC	MEME-2	chr12	+	7040409	7040423	2.45e-09	1.28e-05	ctgcctcagcctccc
CCDCCTCDGCCTCCC	MEME-2	chr14	+	35234928	35234942	2.45e-09	1.28e-05	ccaccttggcctccc
CCDCCTCDGCCTCCC	MEME-2	chr11	+	65155341	65155355	3.99e-09	1.74e-05	ccgcctcggcttccc
CCDCCTCDGCCTCCC	MEME-2	chr10	+	101025452	101025466	5.68e-09	2.12e-05	ctgccttggcctccc
CCDCCTCDGCCTCCC	MEME-2	chr5	+	150583088	150583102	8.03e-09	2.63e-05	ccacctcaacctccc
CCDCCTCDGCCTCCC	MEME-2	chr12	+	19683172	19683186	1.16e-08	3.36e-05	cctcctcaacctccc
CCDCCTCDGCCTCCC	MEME-2	chr17	-	51169160	51169174	4.56e-08	0.000119	CCACCTCGCCCAGCC
CCDCCTCDGCCTCCC	MEME-2	chr20	+	5644329	5644343	9.01e-08	0.000214	cctccttaccctctc
CCDCCTCDGCCTCCC	MEME-2	chr11	+	114483234	114483248	1.8e-07	0.000393	ccagctctgccactc
CCDCCTCDGCCTCCC	MEME-2	chr17	+	17919337	17919351	4.95e-07	0.000995	CCTCCTCTCCCATTC
CCDCCTCDGCCTCCC	MEME-2	chr6	+	166576083	166576097	1.78e-05	0.0332	ctgcctttgcttctt
CCDCCTCDGCCTCCC	MEME-2	chr16	-	85050696	85050710	4.74e-05	0.0819	CCAACTCTACCACAC
CCDCCTCDGCCTCCC	MEME-2	chr4	-	157464628	157464642	5.01e-05	0.0819	TCTTCTCTCCCTCTC
CCDCCTCDGCCTCCC	MEME-2	chr8	-	118567654	118567668	5.55e-05	0.0854	GCTACTTGGCCTGCC
CCDCCTCDGCCTCCC	MEME-2	chr12	-	1023626	1023640	9.29e-05	0.135	CTGCCTCCACCAGCT

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_4 --bgfile ./background --motif CCDCCTCDGCCTCCC meme_out/meme.xml MOA24_loss_diff.fa

Settings:


  
    output_directory = fimo_out_4
    MEME file name = meme_out/meme.xml
    sequence file name = MOA24_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_4	MEME file name = meme_out/meme.xml	sequence file name = MOA24_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