FIMO Results

Database and Motifs

High-scoring Motif Occurences

Debugging Information

Results in TSV Format

Results in GFF3 Format

FIMO - Motif search tool

FIMO version 5.5.2, (Release date: Sun Jan 29 10:33:12 2023 -0800)

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 GSM6573515_CC119h_Translocation_dsb_meme-chip/GSM6573515_CC119h_Translocation_dsb.hg19.summits_200.fa
  
  Database contains 9 sequences, 3600 residues

  MOTIFS GSM6573515_CC119h_Translocation_dsb_meme-chip/streme_out/streme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        1-AAMAATRVWWATAA
        14
        AAAAATACTAATAA
       
        2-CCTGGYCAA
        9
        CCTGGCCAA
       
        3-GTGAAA
        6
        GTGAAA
       
        4-CWGTCTCCY
        9
        CTGTCTCCC
       
        5-MATCTGAGCT
        10
        AATCTGAGCT
       
Random model letter frequencies (GSM6573515_CC119h_Translocation_dsb_meme-chip/background):

A 0.283 C 0.217 G 0.217 T 0.283

MOTIF	WIDTH	BEST POSSIBLE MATCH
1-AAMAATRVWWATAA	14	AAAAATACTAATAA
2-CCTGGYCAA	9	CCTGGCCAA
3-GTGAAA	6	GTGAAA
4-CWGTCTCCY	9	CTGTCTCCC
5-MATCTGAGCT	10	AATCTGAGCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 10 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
5-MATCTGAGCT	STREME-5	chr1	-	209639188	209639197	1.14e-06	0.00796	AATCTGAGCT
5-MATCTGAGCT	STREME-5	chr10	+	15963683	15963692	1.73e-05	0.0387	catctgaggt
5-MATCTGAGCT	STREME-5	chr6	+	42702990	42702999	2.35e-05	0.0387	aatcttggct
5-MATCTGAGCT	STREME-5	chr17	+	19326081	19326090	2.88e-05	0.0387	aatcccagct
5-MATCTGAGCT	STREME-5	chr10	-	15963601	15963610	3.12e-05	0.0387	CATCTTGGCT
5-MATCTGAGCT	STREME-5	chr12	+	5877669	5877678	3.32e-05	0.0387	CGTCTGTGCT
5-MATCTGAGCT	STREME-5	chr10	+	908578	908587	7.64e-05	0.0681	agtcccagct
5-MATCTGAGCT	STREME-5	chr10	+	908501	908510	7.98e-05	0.0681	catcctggct
5-MATCTGAGCT	STREME-5	chr17	+	19325948	19325957	9.74e-05	0.0681	aatcccagca
5-MATCTGAGCT	STREME-5	chr6	-	42702880	42702889	9.74e-05	0.0681	AATCCCAGCA

DEBUGGING INFORMATION

Command line:

fimo --parse-genomic-coord --verbosity 1 --oc GSM6573515_CC119h_Translocation_dsb_meme-chip/fimo_out_5 --bgfile GSM6573515_CC119h_Translocation_dsb_meme-chip/background --motif 5-MATCTGAGCT GSM6573515_CC119h_Translocation_dsb_meme-chip/streme_out/streme.xml GSM6573515_CC119h_Translocation_dsb_meme-chip/GSM6573515_CC119h_Translocation_dsb.hg19.summits_200.fa

Settings:


  
    output_directory = GSM6573515_CC119h_Translocation_dsb_meme-chip/fimo_out_5
    MEME file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/streme_out/streme.xml
    sequence file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/GSM6573515_CC119h_Translocation_dsb.hg19.summits_200.fa
  
  
    background file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/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 = GSM6573515_CC119h_Translocation_dsb_meme-chip/fimo_out_5	MEME file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/streme_out/streme.xml	sequence file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/GSM6573515_CC119h_Translocation_dsb.hg19.summits_200.fa
background file name = GSM6573515_CC119h_Translocation_dsb_meme-chip/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