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 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
  
  Database contains 698 sequences, 222543 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        CCRTRCA
        7
        CCATACA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCKCTACC
        8
        GCGCTACC
       
        GCCWTAAC
        8
        GCCTTAAC
       
        AARAAAW
        7
        AAAAAAA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        AGATCGKG
        8
        AGATCGGG
       
        ACTARACC
        8
        ACTAGACC
       
        CGSTCTCC
        8
        CGGTCTCC
       
        CAASGATG
        8
        CAACGATG
       
        TAATCAKA
        8
        TAATCATA
       
        GCGCAAK
        7
        GCGCAAG
       
        GTGGSGTA
        8
        GTGGCGTA
       
        GGYTATCA
        8
        GGCTATCA
       
        AAAGCRTG
        8
        AAAGCGTG
       
        GARTCATA
        8
        GAGTCATA
       
        ATGGTCA
        7
        ATGGTCA
       
        ATTTCSTA
        8
        ATTTCGTA
       
        ACTGAGCT
        8
        ACTGAGCT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/background):

A 0.302 C 0.198 G 0.198 T 0.302

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
CCRTRCA	7	CCATACA
CTBGGCCA	8	CTCGGCCA
GCKCTACC	8	GCGCTACC
GCCWTAAC	8	GCCTTAAC
AARAAAW	7	AAAAAAA
ATAGTKTA	8	ATAGTGTA
AGATCGKG	8	AGATCGGG
ACTARACC	8	ACTAGACC
CGSTCTCC	8	CGGTCTCC
CAASGATG	8	CAACGATG
TAATCAKA	8	TAATCATA
GCGCAAK	7	GCGCAAG
GTGGSGTA	8	GTGGCGTA
GGYTATCA	8	GGCTATCA
AAAGCRTG	8	AAAGCGTG
GARTCATA	8	GAGTCATA
ATGGTCA	7	ATGGTCA
ATTTCSTA	8	ATTTCGTA
ACTGAGCT	8	ACTGAGCT

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 /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/background --motif AARAAAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/RM11-1A--PHD1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/RM11-1A--PHD1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--PHD1/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