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--NOT3/BY4742--NOT3.fa
  
  Database contains 513 sequences, 171825 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTYGGTW
        8
        AGTTGGTT
       
        CCRTACAY
        8
        CCATACAT
       
        GGTTCRA
        7
        GGTTCGA
       
        ACCACTM
        7
        ACCACTA
       
        CGCSTTA
        7
        CGCCTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATGGGNG
        7
        ATGGGTG
       
        GCGCTHCC
        8
        GCGCTACC
       
        AAGAAAWA
        8
        AAGAAAAA
       
        ATMCAAC
        7
        ATACAAC
       
        CCASAC
        6
        CCACAC
       
        GRTCTCCA
        8
        GGTCTCCA
       
        CYATGGCC
        8
        CTATGGCC
       
        AATCTTYT
        8
        AATCTTTT
       
        GCGCAAK
        7
        GCGCAAG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAGRTTAG
        8
        AAGGTTAG
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CCAASAG
        7
        CCAAGAG
       
        CCGTGMTA
        8
        CCGTGATA
       
        GGCTAYC
        7
        GGCTATC
       
        CGCGRGC
        7
        CGCGAGC
       
        GCGTGCSA
        8
        GCGTGCGA
       
        ACTSACG
        7
        ACTGACG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTYGGTW	8	AGTTGGTT
CCRTACAY	8	CCATACAT
GGTTCRA	7	GGTTCGA
ACCACTM	7	ACCACTA
CGCSTTA	7	CGCCTTA
ATGGCAWC	8	ATGGCAAC
ATGGGNG	7	ATGGGTG
GCGCTHCC	8	GCGCTACC
AAGAAAWA	8	AAGAAAAA
ATMCAAC	7	ATACAAC
CCASAC	6	CCACAC
GRTCTCCA	8	GGTCTCCA
CYATGGCC	8	CTATGGCC
AATCTTYT	8	AATCTTTT
GCGCAAK	7	GCGCAAG
AGTCAKAC	8	AGTCATAC
AAGRTTAG	8	AAGGTTAG
AAGCGWGA	8	AAGCGTGA
CCAASAG	7	CCAAGAG
CCGTGMTA	8	CCGTGATA
GGCTAYC	7	GGCTATC
CGCGRGC	7	CGCGAGC
GCGTGCSA	8	GCGTGCGA
ACTSACG	7	ACTGACG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 34 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
AAGCGWGA	DREME-18	chrIII	+	82499	82506	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrX	+	115976	115983	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrXI	+	141055	141062	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrXVI	+	210229	210236	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrVII	+	401564	401571	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrXV	+	444889	444896	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrV	+	487368	487375	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrV	-	177124	177131	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrXIII	-	290826	290833	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrVII	-	328608	328615	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrV	-	354959	354966	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrIX	-	370442	370449	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrVII	-	541875	541882	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrII	-	645192	645199	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrXII	-	797203	797210	1.25e-05	0.281	AAGCGTGA
AAGCGWGA	DREME-18	chrIII	+	123616	123623	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXIII	+	196138	196145	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrVIII	+	388963	388970	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXIV	+	631885	631892	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXII	-	92571	92578	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrVI	-	101399	101406	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXIII	-	124372	124379	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrI	-	139175	139182	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXV	-	301120	301127	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXV	-	464473	464480	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXIV	-	547117	547124	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXIV	-	568138	568145	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXV	-	976523	976530	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrXV	-	980706	980713	2.51e-05	0.291	AAGCGAGA
AAGCGWGA	DREME-18	chrIX	+	257435	257442	4.11e-05	0.407	AAGCGGGA
AAGCGWGA	DREME-18	chrV	+	270426	270433	4.11e-05	0.407	AAGCGGGA
AAGCGWGA	DREME-18	chrV	-	6203	6210	4.11e-05	0.407	AAGCGCGA
AAGCGWGA	DREME-18	chrII	-	332555	332562	4.11e-05	0.407	AAGCGGGA
AAGCGWGA	DREME-18	chrXII	-	897913	897920	4.11e-05	0.407	AAGCGCGA

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--NOT3/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/background --motif AAGCGWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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--NOT3/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/BY4742--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NOT3/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