FIMO Results

Database and Motifs

High-scoring Motif Occurences

Debugging Information

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 intersect_memechip_out/idr.intersect.fa
  
  Database contains 29682 sequences, 5691754 residues

  MOTIFS intersect_memechip_out/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGRKGGCR
        8
        AGGGGGCA
       
        CCASYAGR
        8
        CCACCAGG
       
        DTTTCY
        6
        TTTTCT
       
        KGTGGY
        6
        TGTGGC
       
        AGRKGGAG
        8
        AGGGGGAG
       
        ATTHY
        5
        ATTCT
       
        KHACTGCA
        8
        GCACTGCA
       
        GCGCCBCC
        8
        GCGCCCCC
       
        CKBCCTCC
        8
        CTGCCTCC
       
        RGRAA
        5
        AGGAA
       
        CCKCTAGR
        8
        CCTCTAGG
       
        MGTGGYCA
        8
        AGTGGCCA
       
        ACAGYGVC
        8
        ACAGTGAC
       
        AAAMAAAA
        8
        AAAAAAAA
       
        AAATRY
        6
        AAATGC
       
        ACAGCABC
        8
        ACAGCAGC
       
        CACTAGAK
        8
        CACTAGAG
       
        RGWGACA
        7
        AGAGACA
       
        GYGGCCGY
        8
        GCGGCCGC
       
        GGACRC
        6
        GGACAC
       
        CTGYAG
        6
        CTGCAG
       
        CGCCKCC
        7
        CGCCTCC
       
        TWTAAAW
        7
        TTTAAAA
       
        GGGCAGYA
        8
        GGGCAGCA
       
        GGGCGGGR
        8
        GGGCGGGG
       
        ACABACAC
        8
        ACACACAC
       
        CCGCCAGR
        8
        CCGCCAGG
       
        CAGAGAM
        7
        CAGAGAA
       
        GTGGWA
        6
        GTGGAA
       
        GTGGCWGA
        8
        GTGGCTGA
       
        ATAAATRA
        8
        ATAAATGA
       
        AAACTRCA
        8
        AAACTGCA
       
        CAGCVTC
        7
        CAGCCTC
       
        ACGT
        4
        ACGT
       
        GTAKATAC
        8
        GTAGATAC
       
        GWAAACA
        7
        GTAAACA
       
        AGAKGGTG
        8
        AGAGGGTG
       
        GAYATTGC
        8
        GACATTGC
       
Random model letter frequencies (intersect_memechip_out/background):

A 0.249 C 0.251 G 0.251 T 0.249

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 intersect_memechip_out/fimo_out_10 --bgfile intersect_memechip_out/background --motif ATTHY intersect_memechip_out/dreme_out/dreme.xml intersect_memechip_out/idr.intersect.fa

Settings:


  
    output_directory = intersect_memechip_out/fimo_out_10
    MEME file name = intersect_memechip_out/dreme_out/dreme.xml
    sequence file name = intersect_memechip_out/idr.intersect.fa
  
  
    background file name = intersect_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.