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_gain_diff.fa
  
  Database contains 1289 sequences, 33082 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-YCTSCTG
        7
        CCTGCTG
       
        2-CWGCCA
        6
        CAGCCA
       
        3-MTGASTCAK
        9
        ATGAGTCAT
       
        4-CTGGCCA
        7
        CTGGCCA
       
        5-CCCCCTWGMG
        10
        CCCCCTTGAG
       
Random model letter frequencies (./background):

A 0.262 C 0.238 G 0.238 T 0.262

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-YCTSCTG	7	CCTGCTG
2-CWGCCA	6	CAGCCA
3-MTGASTCAK	9	ATGAGTCAT
4-CTGGCCA	7	CTGGCCA
5-CCCCCTWGMG	10	CCCCCTTGAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 22 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-YCTSCTG	STREME-1	chr19	-	1837788	1837794	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr19	-	4523470	4523476	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr3	-	8095938	8095944	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr12	+	25387639	25387645	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr16	-	28321922	28321928	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr15	-	36883823	36883829	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr20	+	38221274	38221280	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr5	+	42583443	42583449	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr21	-	43684593	43684599	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr20	+	43692139	43692145	5.26e-05	0.119	cctgCTG
1-YCTSCTG	STREME-1	chr19	-	45326374	45326380	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr6	+	52663832	52663838	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr11	-	61747853	61747859	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr10	-	62264953	62264959	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr15	-	75509120	75509126	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr15	+	78241115	78241121	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr9	+	78821283	78821289	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr15	+	88834509	88834515	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr7	-	98831834	98831840	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr12	-	110024510	110024516	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr6	+	143010178	143010184	5.26e-05	0.119	CCTGCTG
1-YCTSCTG	STREME-1	chr2	+	178914449	178914455	5.26e-05	0.119	CCTGCTG

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-YCTSCTG streme_out/streme.xml MOA24_gain_diff.fa

Settings:


  
    output_directory = fimo_out_1
    MEME file name = streme_out/streme.xml
    sequence file name = MOA24_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_1	MEME file name = streme_out/streme.xml	sequence file name = MOA24_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