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_gain_diff.fa
  
  Database contains 600 sequences, 14571 residues

  MOTIFS streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-CAGGAAR
        7
        CAGGAAG
       
        2-TGCCCA
        6
        TGCCCA
       
        3-DCWGCWGH
        8
        TCTGCAGA
       
        4-ATGACTCACT
        10
        ATGACTCACT
       
Random model letter frequencies (./background):

A 0.270 C 0.230 G 0.230 T 0.270

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-CAGGAAR	7	CAGGAAG
2-TGCCCA	6	TGCCCA
3-DCWGCWGH	8	TCTGCAGA
4-ATGACTCACT	10	ATGACTCACT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
4-ATGACTCACT	STREME-4	chr22	+	38178201	38178210	1.09e-06	0.017	ATGactcact
4-ATGACTCACT	STREME-4	chr5	-	111556702	111556711	2.01e-06	0.017	ATGACTCACC
4-ATGACTCACT	STREME-4	chr10	+	110188673	110188682	3.28e-06	0.017	atgactcatt
4-ATGACTCACT	STREME-4	chr11	+	119166504	119166513	5.45e-06	0.017	ATGACTCACA
4-ATGACTCACT	STREME-4	chr9	-	34150417	34150426	7.46e-06	0.017	ATGACTCAGC
4-ATGACTCACT	STREME-4	chr9	+	124054803	124054812	7.46e-06	0.017	ATGACTCAGC
4-ATGACTCACT	STREME-4	chr4	+	174154656	174154665	7.46e-06	0.017	atgactcagc
4-ATGACTCACT	STREME-4	chr2	+	230687818	230687827	7.46e-06	0.017	ATGACTCAGC
4-ATGACTCACT	STREME-4	chr2	+	181791355	181791364	8.39e-06	0.017	ATGACTCACG
4-ATGACTCACT	STREME-4	chr7	-	149985059	149985068	1.09e-05	0.02	ATGACTAACT
4-ATGACTCACT	STREME-4	chr7	+	35762506	35762515	1.31e-05	0.0218	ATGACTCATA
4-ATGACTCACT	STREME-4	chr11	+	105719642	105719651	1.88e-05	0.0286	ATGACTCATG
4-ATGACTCACT	STREME-4	chr11	+	125128624	125128633	2.73e-05	0.0346	atgattcaca
4-ATGACTCACT	STREME-4	chr1	+	183608473	183608482	2.73e-05	0.0346	atgattcaca
4-ATGACTCACT	STREME-4	chr3	+	143135240	143135249	2.84e-05	0.0346	ATGAGTCACT
4-ATGACTCACT	STREME-4	chr18	-	67783811	67783820	3.15e-05	0.0355	ATGTCTCACT
4-ATGACTCACT	STREME-4	chr3	-	143135239	143135248	3.64e-05	0.0355	GTGACTCATT
4-ATGACTCACT	STREME-4	chr1	+	172325777	172325786	3.64e-05	0.0355	GTGACTCATT
4-ATGACTCACT	STREME-4	chr9	+	108951770	108951779	3.95e-05	0.0355	gtgactcaca
4-ATGACTCACT	STREME-4	chr11	-	119811034	119811043	3.95e-05	0.0355	GTGACTCACA
4-ATGACTCACT	STREME-4	chr20	+	58342467	58342476	4.08e-05	0.0355	ATGATTCATC
4-ATGACTCACT	STREME-4	chr17	-	82531750	82531759	4.42e-05	0.0367	CTGACTCACC
4-ATGACTCACT	STREME-4	chr4	+	4260412	4260421	4.65e-05	0.037	atgacttagt
4-ATGACTCACT	STREME-4	chr6	-	131789335	131789344	4.9e-05	0.0373	ATGAGTCACC
4-ATGACTCACT	STREME-4	chr8	-	92818520	92818529	5.96e-05	0.0419	ATGATTAACT
4-ATGACTCACT	STREME-4	chr5	+	120803510	120803519	5.96e-05	0.0419	ATGATTaact
4-ATGACTCACT	STREME-4	chr11	-	66578220	66578229	7.26e-05	0.0489	ATGACTCCTT
4-ATGACTCACT	STREME-4	chr2	+	170052241	170052250	7.5e-05	0.0489	TTGACTCATT
4-ATGACTCACT	STREME-4	chr1	-	172325776	172325785	8.56e-05	0.0539	ATGAGTCACA

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_5 --bgfile ./background --motif 4-ATGACTCACT streme_out/streme.xml MOA3_gain_diff.fa

Settings:


  
    output_directory = fimo_out_5
    MEME file name = streme_out/streme.xml
    sequence file name = MOA3_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 = MOA3_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