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/cutnotseq.fa
  
  Database contains 16563 sequences, 12454848 residues

  MOTIFS cutnotseq_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGGCGGRR
        8
        GGGCGGGG
       
        HTTYCY
        6
        CTTTCT
       
        AAATRY
        6
        AAATGT
       
        CCASYAGG
        8
        CCACCAGG
       
        CYCCWCCC
        8
        CCCCTCCC
       
        CMCGCCYC
        8
        CCCGCCTC
       
        CTVCAGS
        7
        CTCCAGG
       
        CRCWG
        5
        CACAG
       
        ATGYWAAT
        8
        ATGCAAAT
       
        CHGGRA
        6
        CTGGGA
       
        ATTGGCYR
        8
        ATTGGCTG
       
        AWAAYAAA
        8
        AAAATAAA
       
        CTSCCTCY
        8
        CTCCCTCC
       
        TKTAWA
        6
        TTTAAA
       
        CACCRCS
        7
        CACCGCC
       
        CASGTR
        6
        CAGGTG
       
        AGAAA
        5
        AGAAA
       
        CCAATCAS
        8
        CCAATCAG
       
        KTCATTY
        7
        TTCATTT
       
        ACASACAY
        8
        ACACACAC
       
        GCCACRCC
        8
        GCCACGCC
       
        GAGTSAC
        7
        GAGTGAC
       
        CCDCCTCC
        8
        CCACCTCC
       
        CCACTAGA
        8
        CCACTAGA
       
        GAATGY
        6
        GAATGT
       
        ACCAATMG
        8
        ACCAATAG
       
        ACAAAGVC
        8
        ACAAAGGC
       
        GRACTACA
        8
        GAACTACA
       
        ACSGAGA
        7
        ACGGAGA
       
Random model letter frequencies (cutnotseq_memechip_out/background):

A 0.260 C 0.240 G 0.240 T 0.260

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGGCGGRR	8	GGGCGGGG
HTTYCY	6	CTTTCT
AAATRY	6	AAATGT
CCASYAGG	8	CCACCAGG
CYCCWCCC	8	CCCCTCCC
CMCGCCYC	8	CCCGCCTC
CTVCAGS	7	CTCCAGG
CRCWG	5	CACAG
ATGYWAAT	8	ATGCAAAT
CHGGRA	6	CTGGGA
ATTGGCYR	8	ATTGGCTG
AWAAYAAA	8	AAAATAAA
CTSCCTCY	8	CTCCCTCC
TKTAWA	6	TTTAAA
CACCRCS	7	CACCGCC
CASGTR	6	CAGGTG
AGAAA	5	AGAAA
CCAATCAS	8	CCAATCAG
KTCATTY	7	TTCATTT
ACASACAY	8	ACACACAC
GCCACRCC	8	GCCACGCC
GAGTSAC	7	GAGTGAC
CCDCCTCC	8	CCACCTCC
CCACTAGA	8	CCACTAGA
GAATGY	6	GAATGT
ACCAATMG	8	ACCAATAG
ACAAAGVC	8	ACAAAGGC
GRACTACA	8	GAACTACA
ACSGAGA	7	ACGGAGA

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_15 --bgfile cutnotseq_memechip_out/background --motif TKTAWA cutnotseq_memechip_out/dreme_out/dreme.xml cutnotseq_memechip_out/cutnotseq.fa

Settings:


  
    output_directory = cutnotseq_memechip_out/fimo_out_15
    MEME file name = cutnotseq_memechip_out/dreme_out/dreme.xml
    sequence file name = cutnotseq_memechip_out/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_15	MEME file name = cutnotseq_memechip_out/dreme_out/dreme.xml	sequence file name = cutnotseq_memechip_out/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