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--INO80/BY4742--INO80.fa
  
  Database contains 529 sequences, 202507 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        CTWRACC
        7
        CTTAACC
       
        CCVTACA
        7
        CCATACA
       
        GCKCTMCC
        8
        GCGCTACC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TAGTGTAR
        8
        TAGTGTAG
       
        CYTGCGC
        7
        CTTGCGC
       
        AAGAAAW
        7
        AAGAAAA
       
        CCGTGSA
        7
        CCGTGGA
       
        ACACSC
        6
        ACACCC
       
        ATCGTRAG
        8
        ATCGTGAG
       
        GTGATAGY
        8
        GTGATAGC
       
        ACTRCGCC
        8
        ACTGCGCC
       
        CSCATGC
        7
        CCCATGC
       
        CGCCTTAS
        8
        CGCCTTAG
       
        GCGCCMA
        7
        GCGCCAA
       
        TAKCTCA
        7
        TAGCTCA
       
        AATCAKAA
        8
        AATCATAA
       
        ATCTGYTG
        8
        ATCTGTTG
       
        AGTTCGAW
        8
        AGTTCGAT
       
        RCGGGGA
        7
        ACGGGGA
       
        AAGATTTC
        8
        AAGATTTC
       
        ATSTGGAG
        8
        ATGTGGAG
       
        CKAGAATC
        8
        CGAGAATC
       
        AGTCGCMC
        8
        AGTCGCAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
CTWRACC	7	CTTAACC
CCVTACA	7	CCATACA
GCKCTMCC	8	GCGCTACC
CTBGGCCA	8	CTCGGCCA
ATGGCAWC	8	ATGGCAAC
TAGTGTAR	8	TAGTGTAG
CYTGCGC	7	CTTGCGC
AAGAAAW	7	AAGAAAA
CCGTGSA	7	CCGTGGA
ACACSC	6	ACACCC
ATCGTRAG	8	ATCGTGAG
GTGATAGY	8	GTGATAGC
ACTRCGCC	8	ACTGCGCC
CSCATGC	7	CCCATGC
CGCCTTAS	8	CGCCTTAG
GCGCCMA	7	GCGCCAA
TAKCTCA	7	TAGCTCA
AATCAKAA	8	AATCATAA
ATCTGYTG	8	ATCTGTTG
AGTTCGAW	8	AGTTCGAT
RCGGGGA	7	ACGGGGA
AAGATTTC	8	AAGATTTC
ATSTGGAG	8	ATGTGGAG
CKAGAATC	8	CGAGAATC
AGTCGCMC	8	AGTCGCAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 56 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
AGTTCGAW	DREME-21	chrVII	-	73842	73849	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrVIII	-	85311	85318	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXI	-	308157	308164	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXIII	-	372458	372465	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrX	+	378411	378418	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXI	+	379731	379738	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXVI	+	404779	404786	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrVII	-	412307	412314	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXIII	-	420601	420608	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXVI	-	435906	435913	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrV	+	438751	438758	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrV	+	469508	469515	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrVIII	-	475719	475726	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXIII	-	586649	586656	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrII	-	643020	643027	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXV	-	663825	663832	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXII	-	687872	687879	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrVII	-	707121	707128	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXII	+	710806	710813	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXVI	+	731950	731957	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrXVI	-	775778	775785	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrVII	+	823533	823540	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrIV	-	1075485	1075492	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrIV	+	1355960	1355967	1.96e-05	0.3	AGTTCGAT
AGTTCGAW	DREME-21	chrII	+	9644	9651	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXI	+	84269	84276	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIII	-	92031	92038	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrI	+	181232	181239	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXVI	+	188628	188635	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrVII	+	205612	205619	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIII	-	225467	225474	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrII	-	326805	326812	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrII	+	347664	347671	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrII	-	347795	347802	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrX	-	391056	391063	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrX	+	422987	422994	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrVII	+	423183	423190	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrX	-	424445	424452	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIV	+	443097	443104	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXI	+	458648	458655	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrIV	-	488810	488817	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIII	+	504986	504993	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrIV	+	519804	519811	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIII	-	572896	572903	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXII	+	628475	628482	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIV	-	726147	726154	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXIII	-	808259	808266	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrVII	-	857391	857398	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXII	-	962985	962992	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXV	+	976471	976478	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrIV	+	1175879	1175886	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrIV	-	1461728	1461735	3.92e-05	0.3	AGTTCGAA
AGTTCGAW	DREME-21	chrXII	+	794026	794033	6.37e-05	0.452	AGTTCGAC
AGTTCGAW	DREME-21	chrXI	-	513250	513257	6.37e-05	0.452	AGTTCGAG
AGTTCGAW	DREME-21	chrXV	-	572053	572060	6.37e-05	0.452	AGTTCGAG
AGTTCGAW	DREME-21	chrXII	-	903613	903620	6.37e-05	0.452	AGTTCGAG

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--INO80/fimo_out_19 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background --motif AGTTCGAW /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/fimo_out_19
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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--INO80/fimo_out_19	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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