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--SMP1/RM11-1A--SMP1.fa
  
  Database contains 470 sequences, 152367 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCRA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        ACCCADAC
        8
        ACCCATAC
       
        AACTKGGC
        8
        AACTTGGC
       
        ATCCGTRC
        8
        ATCCGTAC
       
        GCKCTACC
        8
        GCGCTACC
       
        AARAAAW
        7
        AAAAAAA
       
        GTGATAGY
        8
        GTGATAGC
       
        CRCACGCC
        8
        CACACGCC
       
        GYGCCTTA
        8
        GCGCCTTA
       
        GATTAASA
        8
        GATTAAGA
       
        GGAGACC
        7
        GGAGACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TGGCGCW
        7
        TGGCGCA
       
        TCGGYCAA
        8
        TCGGCCAA
       
        ATCTTYTG
        8
        ATCTTCTG
       
        CTAWATC
        7
        CTATATC
       
        GACAASC
        7
        GACAACC
       
        GCATGGGW
        8
        GCATGGGT
       
        CGATCTKG
        8
        CGATCTGG
       
        CGCGGGSA
        8
        CGCGGGGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCRA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
ACCCADAC	8	ACCCATAC
AACTKGGC	8	AACTTGGC
ATCCGTRC	8	ATCCGTAC
GCKCTACC	8	GCGCTACC
AARAAAW	7	AAAAAAA
GTGATAGY	8	GTGATAGC
CRCACGCC	8	CACACGCC
GYGCCTTA	8	GCGCCTTA
GATTAASA	8	GATTAAGA
GGAGACC	7	GGAGACC
ATGGCAWC	8	ATGGCAAC
TGGCGCW	7	TGGCGCA
TCGGYCAA	8	TCGGCCAA
ATCTTYTG	8	ATCTTCTG
CTAWATC	7	CTATATC
GACAASC	7	GACAACC
GCATGGGW	8	GCATGGGT
CGATCTKG	8	CGATCTGG
CGCGGGSA	8	CGCGGGGA

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--SMP1/fimo_out_18 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/background --motif CTAWATC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/RM11-1A--SMP1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/fimo_out_18
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/RM11-1A--SMP1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/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 = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/fimo_out_18	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/RM11-1A--SMP1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--SMP1/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