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/BY4741--RPB2/BY4741--RPB2.fa
  
  Database contains 1939 sequences, 3150839 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TCTTB
        5
        TCTTT
       
        GGTAD
        5
        GGTAA
       
        GCTKCY
        6
        GCTTCT
       
        CCAAAK
        6
        CCAAAT
       
        TGATR
        5
        TGATA
       
        ACCABC
        6
        ACCACC
       
        GTRTGGAA
        8
        GTATGGAA
       
        ATGGAAAC
        8
        ATGGAAAC
       
        AAVGTTG
        7
        AAAGTTG
       
        TGACTCYA
        8
        TGACTCCA
       
        TATRTRTA
        8
        TATATATA
       
        CCTSTAGA
        8
        CCTGTAGA
       
        CAATGGCA
        8
        CAATGGCA
       
        CAGCAGW
        7
        CAGCAGT
       
        CTACWAC
        7
        CTACAAC
       
        CGAYGAC
        7
        CGATGAC
       
        KACAGTAA
        8
        TACAGTAA
       
        ACCAA
        5
        ACCAA
       
        AAGARG
        6
        AAGAAG
       
        CCAAKTC
        7
        CCAATTC
       
        TGYTCAA
        7
        TGTTCAA
       
        TGTTGTTR
        8
        TGTTGTTG
       
        AATGGTAC
        8
        AATGGTAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
TCTTB	5	TCTTT
GGTAD	5	GGTAA
GCTKCY	6	GCTTCT
CCAAAK	6	CCAAAT
TGATR	5	TGATA
ACCABC	6	ACCACC
GTRTGGAA	8	GTATGGAA
ATGGAAAC	8	ATGGAAAC
AAVGTTG	7	AAAGTTG
TGACTCYA	8	TGACTCCA
TATRTRTA	8	TATATATA
CCTSTAGA	8	CCTGTAGA
CAATGGCA	8	CAATGGCA
CAGCAGW	7	CAGCAGT
CTACWAC	7	CTACAAC
CGAYGAC	7	CGATGAC
KACAGTAA	8	TACAGTAA
ACCAA	5	ACCAA
AAGARG	6	AAGAAG
CCAAKTC	7	CCAATTC
TGYTCAA	7	TGTTCAA
TGTTGTTR	8	TGTTGTTG
AATGGTAC	8	AATGGTAC

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/BY4741--RPB2/fimo_out_2 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/background --motif GGTAD /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/BY4741--RPB2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/fimo_out_2
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/BY4741--RPB2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/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/BY4741--RPB2/fimo_out_2	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/BY4741--RPB2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4741--RPB2/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