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 streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-RVAGRAAAWR
        10
        ACAGGAAAAG
       
        2-ATSGAATGGAATSGA
        15
        ATCGAATGGAATCGA
       
        3-TGAAAACA
        8
        TGAAAACA
       
        4-AKGCMT
        6
        AGGCCT
       
Random model letter frequencies (./background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-RVAGRAAAWR	10	ACAGGAAAAG
2-ATSGAATGGAATSGA	15	ATCGAATGGAATCGA
3-TGAAAACA	8	TGAAAACA
4-AKGCMT	6	AGGCCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 26 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-RVAGRAAAWR	STREME-1	chr11	+	95149745	95149754	7.13e-07	0.0277	GCAGGAAAAG
1-RVAGRAAAWR	STREME-1	chr1	-	231682844	231682853	1.87e-06	0.0363	ACAGGAAAAG
1-RVAGRAAAWR	STREME-1	chr18	-	7790163	7790172	3.74e-06	0.0483	GGAGGAAAAG
1-RVAGRAAAWR	STREME-1	chr11	-	83815933	83815942	5.33e-06	0.0517	ACAGGAAATG
1-RVAGRAAAWR	STREME-1	chr8	-	106337704	106337713	8.8e-06	0.0679	GAAGGAAAAG
1-RVAGRAAAWR	STREME-1	chr11	-	336946	336955	1.23e-05	0.0679	ACAGGAGAAG
1-RVAGRAAAWR	STREME-1	chr13	-	75350834	75350843	1.23e-05	0.0679	ACAGGAGAAG
1-RVAGRAAAWR	STREME-1	chr1	-	39246148	39246157	1.83e-05	0.0888	GCAGGAGATG
1-RVAGRAAAWR	STREME-1	chr10	-	122806014	122806023	2.06e-05	0.0889	GCAGGAACTG
1-RVAGRAAAWR	STREME-1	chr3	-	104667947	104667956	2.51e-05	0.0973	GAAGGAAGAG
1-RVAGRAAAWR	STREME-1	chr17	-	4347930	4347939	3.5e-05	0.122	ACAGGAACTG
1-RVAGRAAAWR	STREME-1	chr11	-	89533754	89533763	4.26e-05	0.122	GCAGGAAAAT
1-RVAGRAAAWR	STREME-1	chr4	+	17654304	17654313	4.55e-05	0.122	acagAAAAAG
1-RVAGRAAAWR	STREME-1	chr10	-	15589235	15589244	5.34e-05	0.122	GCAGGAAATA
1-RVAGRAAAWR	STREME-1	chr2	+	100985630	100985639	6.07e-05	0.122	GGAGGAAAAA
1-RVAGRAAAWR	STREME-1	chr11	-	28750989	28750998	6.19e-05	0.122	ACAGGCAATG
1-RVAGRAAAWR	STREME-1	chr17	+	62579841	62579850	6.4e-05	0.122	ggaggaggag
1-RVAGRAAAWR	STREME-1	chr8	-	105658637	105658646	6.59e-05	0.122	ACAGGAAAAT
1-RVAGRAAAWR	STREME-1	chr11	+	128802798	128802807	6.59e-05	0.122	ACAGGAAAAT
1-RVAGRAAAWR	STREME-1	chr2	+	164678265	164678274	6.59e-05	0.122	acaggaaaat
1-RVAGRAAAWR	STREME-1	chr5	-	177268887	177268896	6.59e-05	0.122	ACAGGAAAAT
1-RVAGRAAAWR	STREME-1	chr7	-	22329169	22329178	7.47e-05	0.127	GCAGAAAGAG
1-RVAGRAAAWR	STREME-1	chr1	-	100228998	100229007	7.64e-05	0.127	GCAGGAGGGG
1-RVAGRAAAWR	STREME-1	chr11	-	87773545	87773554	8.17e-05	0.127	CCAGGAAAGG
1-RVAGRAAAWR	STREME-1	chr13	-	28695626	28695635	8.37e-05	0.127	ACTGGAAATG
1-RVAGRAAAWR	STREME-1	chr12	-	49463007	49463016	8.52e-05	0.127	GCAGAAAAGG

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_1 --bgfile ./background --motif 1-RVAGRAAAWR streme_out/streme.xml MOA24_loss_diff.fa

Settings:


  
    output_directory = fimo_out_1
    MEME file name = streme_out/streme.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_1	MEME file name = streme_out/streme.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