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/BY4742--MIG2/BY4742--MIG2.fa
  
  Database contains 935 sequences, 414756 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        ATGTAYGG
        8
        ATGTATGG
       
        AARAAAWA
        8
        AAAAAAAA
       
        CCWTAACC
        8
        CCTTAACC
       
        ACCACTAH
        8
        ACCACTAA
       
        ACTYGGCC
        8
        ACTTGGCC
       
        GCKCTACC
        8
        GCGCTACC
       
        ACCCANAC
        8
        ACCCACAC
       
        CATYACGC
        8
        CATTACGC
       
        AGAAATCT
        8
        AGAAATCT
       
        TCCACGGW
        8
        TCCACGGT
       
        CTWGACC
        7
        CTAGACC
       
        CWGACGC
        7
        CAGACGC
       
        CTCCMTTA
        8
        CTCCATTA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
ATGTAYGG	8	ATGTATGG
AARAAAWA	8	AAAAAAAA
CCWTAACC	8	CCTTAACC
ACCACTAH	8	ACCACTAA
ACTYGGCC	8	ACTTGGCC
GCKCTACC	8	GCGCTACC
ACCCANAC	8	ACCCACAC
CATYACGC	8	CATTACGC
AGAAATCT	8	AGAAATCT
TCCACGGW	8	TCCACGGT
CTWGACC	7	CTAGACC
CWGACGC	7	CAGACGC
CTCCMTTA	8	CTCCATTA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 52 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
AGAAATCT	DREME-10	chrXIII	+	24797	24804	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	+	24797	24804	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	+	24797	24804	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	+	24797	24804	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	+	24797	24804	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrX	+	76119	76126	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	+	84419	84426	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrV	+	86636	86643	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVIII	-	110179	110186	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVIII	-	133066	133073	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVIII	+	160405	160412	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	+	165397	165404	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrI	-	182562	182569	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXVI	+	192756	192763	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	+	227107	227114	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	+	227107	227114	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	229727	229734	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	229727	229734	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	-	232718	232725	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	-	232718	232725	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	-	232718	232725	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	-	232718	232725	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXII	-	232718	232725	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	-	259198	259205	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrV	-	269443	269450	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrV	-	269443	269450	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	-	301484	301491	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXI	-	326766	326773	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXI	-	326766	326773	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXI	-	326766	326773	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXI	-	326766	326773	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	332584	332591	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXVI	+	372401	372408	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIX	-	386796	386803	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	-	386891	386898	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	-	415817	415824	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	437804	437811	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXV	+	438608	438615	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	465301	465308	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVII	-	477662	477669	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrX	-	520264	520271	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrX	-	524052	524059	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXIII	+	552593	552600	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVII	-	561702	561709	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrII	-	605225	605232	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	-	620043	620050	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrXV	+	621557	621564	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVII	-	787166	787173	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrVII	-	787166	787173	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	-	981014	981021	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	1305662	1305669	3.1e-05	0.486	AGAAATCT
AGAAATCT	DREME-10	chrIV	+	1492301	1492308	3.1e-05	0.486	AGAAATCT

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/BY4742--MIG2/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/background --motif AGAAATCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/BY4742--MIG2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/BY4742--MIG2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/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/BY4742--MIG2/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/BY4742--MIG2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MIG2/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