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 25 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-CAAAGTGC	STREME-4	chr6	-	37127983	37127990	1.35e-05	0.0855	CAAAGTGC
4-CAAAGTGC	STREME-4	chr17	+	39178641	39178648	1.35e-05	0.0855	caaagtgc
4-CAAAGTGC	STREME-4	chr11	-	43419534	43419541	1.35e-05	0.0855	CAAAGTGC
4-CAAAGTGC	STREME-4	chr11	+	65155355	65155362	1.35e-05	0.0855	caaagtgc
4-CAAAGTGC	STREME-4	chr9	+	95341789	95341796	1.35e-05	0.0855	caaagtgc
4-CAAAGTGC	STREME-4	chr11	-	120432292	120432299	1.35e-05	0.0855	CAAAGTGC
4-CAAAGTGC	STREME-4	chr9	-	124874449	124874456	1.35e-05	0.0855	CAAAGTGC
4-CAAAGTGC	STREME-4	chr8	-	134720655	134720662	3.24e-05	0.144	CAAGGTGC
4-CAAAGTGC	STREME-4	chr14	+	50778074	50778081	4.19e-05	0.144	CACAGTGC
4-CAAAGTGC	STREME-4	chr3	-	64550191	64550198	4.19e-05	0.144	CACAGTGC
4-CAAAGTGC	STREME-4	chr11	+	9475357	9475364	4.85e-05	0.144	caaggggc
4-CAAAGTGC	STREME-4	chr11	+	44818837	44818844	4.85e-05	0.144	caaggggc
4-CAAAGTGC	STREME-4	chr10	-	63518292	63518299	4.85e-05	0.144	CAAGGGGC
4-CAAAGTGC	STREME-4	chr11	-	73329257	73329264	4.85e-05	0.144	CAAGGGGC
4-CAAAGTGC	STREME-4	chr1	+	117823528	117823535	4.85e-05	0.144	caaggggc
4-CAAAGTGC	STREME-4	chr1	+	19097761	19097768	6.2e-05	0.152	CAAAGAGC
4-CAAAGTGC	STREME-4	chr3	-	112111996	112112003	6.2e-05	0.152	CAAAGAGC
4-CAAAGTGC	STREME-4	chr1	-	23100404	23100411	6.87e-05	0.152	CACAGGGC
4-CAAAGTGC	STREME-4	chr2	+	51516894	51516901	6.87e-05	0.152	cacagggc
4-CAAAGTGC	STREME-4	chr2	+	173884583	173884590	6.87e-05	0.152	CACAGGGC
4-CAAAGTGC	STREME-4	chr12	+	13063471	13063478	9.73e-05	0.173	CAAAGTTC
4-CAAAGTGC	STREME-4	chr12	-	24779086	24779093	9.73e-05	0.173	CAAAGTTC
4-CAAAGTGC	STREME-4	chr14	-	61716703	61716710	9.73e-05	0.173	CAAAGTTC
4-CAAAGTGC	STREME-4	chr17	-	61837410	61837417	9.73e-05	0.173	CAGAGTGC
4-CAAAGTGC	STREME-4	chr1	-	211779172	211779179	9.73e-05	0.173	CAAAGTTC

DEBUGGING INFORMATION

Command line:

fimo --verbosity 1 --oc fimo_out_2 --bgfile ./background --motif 4-CAAAGTGC streme_out/streme.xml MOA3_loss_diff.fa

Settings:


  
    output_directory = fimo_out_2
    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.

Go to top

output_directory = fimo_out_2	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