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 cutnotseq_memechip_out/idr.cutnotseq.fa
  
  Database contains 6181 sequences, 4660326 residues

  MOTIFS cutnotseq_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRGGCGGR
        8
        GGGGCGGG
       
        CCACYAGR
        8
        CCACTAGG
       
        DTTTCY
        6
        TTTTCT
       
        CCMCRCCC
        8
        CCCCGCCC
       
        CWGKAA
        6
        CTGGAA
       
        AAATRM
        6
        AAATAA
       
        CASCWGG
        7
        CAGCTGG
       
        CAKCCTGG
        8
        CAGCCTGG
       
        STGGGA
        6
        CTGGGA
       
        TTTAAAAW
        8
        TTTAAAAA
       
        CWCTGY
        6
        CTCTGC
       
        CCWGKAG
        7
        CCTGGAG
       
        GGGCGGR
        7
        GGGCGGG
       
        AGGAAWG
        7
        AGGAAAG
       
        ACGTGD
        6
        ACGTGG
       
        ATGCWAAT
        8
        ATGCAAAT
       
        CCATGTYG
        8
        CCATGTTG
       
        AAATTAGC
        8
        AAATTAGC
       
        CTCCTBCC
        8
        CTCCTCCC
       
        CGGAAGTR
        8
        CGGAAGTG
       
        CCGCTAGA
        8
        CCGCTAGA
       
        CTGCRG
        6
        CTGCAG
       
        CGCAKGCG
        8
        CGCAGGCG
       
        TATATWCA
        8
        TATATACA
       
        ACADATGT
        8
        ACAAATGT
       
        CTCTACTA
        8
        CTCTACTA
       
        AGGCGKGG
        8
        AGGCGTGG
       
        TAACAKAA
        8
        TAACAGAA
       
Random model letter frequencies (cutnotseq_memechip_out/background):

A 0.268 C 0.232 G 0.232 T 0.268

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRGGCGGR	8	GGGGCGGG
CCACYAGR	8	CCACTAGG
DTTTCY	6	TTTTCT
CCMCRCCC	8	CCCCGCCC
CWGKAA	6	CTGGAA
AAATRM	6	AAATAA
CASCWGG	7	CAGCTGG
CAKCCTGG	8	CAGCCTGG
STGGGA	6	CTGGGA
TTTAAAAW	8	TTTAAAAA
CWCTGY	6	CTCTGC
CCWGKAG	7	CCTGGAG
GGGCGGR	7	GGGCGGG
AGGAAWG	7	AGGAAAG
ACGTGD	6	ACGTGG
ATGCWAAT	8	ATGCAAAT
CCATGTYG	8	CCATGTTG
AAATTAGC	8	AAATTAGC
CTCCTBCC	8	CTCCTCCC
CGGAAGTR	8	CGGAAGTG
CCGCTAGA	8	CCGCTAGA
CTGCRG	6	CTGCAG
CGCAKGCG	8	CGCAGGCG
TATATWCA	8	TATATACA
ACADATGT	8	ACAAATGT
CTCTACTA	8	CTCTACTA
AGGCGKGG	8	AGGCGTGG
TAACAKAA	8	TAACAGAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 0 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

DEBUGGING INFORMATION

Command line:

/software/meme/4.12.0/bin/fimo --parse-genomic-coord --verbosity 1 --oc cutnotseq_memechip_out/fimo_out_20 --bgfile cutnotseq_memechip_out/background --motif CTGCRG cutnotseq_memechip_out/dreme_out/dreme.xml cutnotseq_memechip_out/idr.cutnotseq.fa

Settings:


  
    output_directory = cutnotseq_memechip_out/fimo_out_20
    MEME file name = cutnotseq_memechip_out/dreme_out/dreme.xml
    sequence file name = cutnotseq_memechip_out/idr.cutnotseq.fa
  
  
    background file name = cutnotseq_memechip_out/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 = cutnotseq_memechip_out/fimo_out_20	MEME file name = cutnotseq_memechip_out/dreme_out/dreme.xml	sequence file name = cutnotseq_memechip_out/idr.cutnotseq.fa
background file name = cutnotseq_memechip_out/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