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 a549_max_memeout/a549_max.fa
  
  Database contains 28950 sequences, 20527529 residues

  MOTIFS a549_max_memeout/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RTGASTMA
        8
        ATGACTCA
       
        CNGGRA
        6
        CAGGGA
       
        CACRTGB
        7
        CACATGG
       
        GGGHGGGR
        8
        GGGCGGGG
       
        RNAAAYA
        7
        ACAAACA
       
        CCDCCKCC
        8
        CCGCCGCC
       
        AGRAA
        5
        AGAAA
       
        TGARTMA
        7
        TGAATCA
       
        AGRDGGCG
        8
        AGGGGGCG
       
        TGACSTCR
        8
        TGACCTCA
       
        GCNGCYGC
        8
        GCTGCTGC
       
        CACRCVCA
        8
        CACACACA
       
        DAAATR
        6
        AAAATG
       
        CAGCSTGG
        8
        CAGCCTGG
       
        CRGCCTC
        7
        CAGCCTC
       
        CGCABGCG
        8
        CGCAGGCG
       
        GCCTKTAA
        8
        GCCTGTAA
       
        CTCCWGS
        7
        CTCCTGC
       
        CACGTD
        6
        CACGTT
       
        ATTGGCYG
        8
        ATTGGCTG
       
        GGAAD
        5
        GGAAG
       
        TTWAWA
        6
        TTAAAA
       
        CASMGCC
        7
        CAGAGCC
       
        AAAMAAAA
        8
        AAAAAAAA
       
        CCACRCCC
        8
        CCACGCCC
       
        CTCCDCCC
        8
        CTCCGCCC
       
        AAATAH
        6
        AAATAA
       
        CCRCGY
        6
        CCGCGC
       
        CCCAGCCY
        8
        CCCAGCCC
       
        ATTCATTC
        8
        ATTCATTC
       
        CCAGGA
        6
        CCAGGA
       
        CWGCAGCC
        8
        CTGCAGCC
       
        CATGGCGR
        8
        CATGGCGG
       
        CASACAC
        7
        CAGACAC
       
        CACTTTGG
        8
        CACTTTGG
       
        AGGACRC
        7
        AGGACAC
       
        AGRTGGCA
        8
        AGGTGGCA
       
        CGTCTCYA
        8
        CGTCTCCA
       
        ACGTCAY
        7
        ACGTCAC
       
        CGGAGCYG
        8
        CGGAGCCG
       
        GAGTCATM
        8
        GAGTCATC
       
        TGATGTMA
        8
        TGATGTCA
       
Random model letter frequencies (a549_max_memeout/background):

A 0.207 C 0.293 G 0.293 T 0.207

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 a549_max_memeout/fimo_out_7 --bgfile a549_max_memeout/background --motif AGRAA a549_max_memeout/dreme_out/dreme.xml a549_max_memeout/a549_max.fa

Settings:


  
    output_directory = a549_max_memeout/fimo_out_7
    MEME file name = a549_max_memeout/dreme_out/dreme.xml
    sequence file name = a549_max_memeout/a549_max.fa
  
  
    background file name = a549_max_memeout/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.