FIMO Results

FIMO - Motif search tool

FIMO version 4.12.0, (Release date: Tue Jun 27 16:22:50 2017 -0700)

For further information on how to interpret these results or to get a copy of the FIMO software please access http://meme.nbcr.net

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 memeout_fulv/fulv.fa
  
  Database contains 1453 sequences, 262495 residues

  MOTIFS memeout_fulv/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGACCB
        6
        TGACCT
       
        RYAAAYA
        7
        GCAAACA
       
        HATGTCA
        7
        AATGTCA
       
        AGATA
        5
        AGATA
       
        AGGGCR
        6
        AGGGCA
       
        AGGTKRC
        7
        AGGTGAC
       
        CWTTCC
        6
        CATTCC
       
        AGGTCGK
        7
        AGGTCGT
       
        GATGACM
        7
        GATGACA
       
        TGATAAAA
        8
        TGATAAAA
       
Random model letter frequencies (memeout_fulv/background):

A 0.270 C 0.230 G 0.230 T 0.270

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGACCB	6	TGACCT
RYAAAYA	7	GCAAACA
HATGTCA	7	AATGTCA
AGATA	5	AGATA
AGGGCR	6	AGGGCA
AGGTKRC	7	AGGTGAC
CWTTCC	6	CATTCC
AGGTCGK	7	AGGTCGT
GATGACM	7	GATGACA
TGATAAAA	8	TGATAAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 30 motif occurences with a p-value less than 0.0001. The full set of motif occurences can be seen in the tab-delimited plain text output file fimo.txt, the GFF 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
AGGTCGK	DREME-8	chr19	-	3736491	3736497	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr19	+	9957142	9957148	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr2	+	11262651	11262657	5.51e-05	0.932	aggtcgt
AGGTCGK	DREME-8	chr6	-	20210610	20210616	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr10	-	25673816	25673822	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr13	-	27552630	27552636	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr2	-	35522717	35522723	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr14	+	38119868	38119874	5.51e-05	0.932	aggtcgt
AGGTCGK	DREME-8	chr19	-	39205354	39205360	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr19	+	41427207	41427213	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr21	+	41816220	41816226	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr2	-	43016125	43016131	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr21	-	43796587	43796593	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr10	-	44092385	44092391	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr20	-	48901402	48901408	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr12	-	58312080	58312086	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr17	+	65553563	65553569	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chrX	-	70850896	70850902	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr17	-	80579306	80579312	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr16	+	85499791	85499797	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr8	-	102475163	102475169	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr9	-	115147325	115147331	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr6	+	125523557	125523563	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr9	-	130809711	130809717	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr5	-	137144784	137144790	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr7	-	152308177	152308183	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr4	+	169612983	169612989	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr4	-	186432105	186432111	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr2	+	216081754	216081760	5.51e-05	0.932	AGGTCGT
AGGTCGK	DREME-8	chr2	+	238467780	238467786	5.51e-05	0.932	AGGTCGT

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc memeout_fulv/fimo_out_10 --bgfile memeout_fulv/background --motif AGGTCGK memeout_fulv/dreme_out/dreme.xml memeout_fulv/fulv.fa

Settings:


  
    output_directory = memeout_fulv/fimo_out_10
    MEME file name = memeout_fulv/dreme_out/dreme.xml
    sequence file name = memeout_fulv/fulv.fa
  
  
    background file name = memeout_fulv/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 = memeout_fulv/fimo_out_10	MEME file name = memeout_fulv/dreme_out/dreme.xml	sequence file name = memeout_fulv/fulv.fa
background file name = memeout_fulv/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