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/AWRI1631--ACE2/AWRI1631--ACE2.fa
  
  Database contains 484 sequences, 161033 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        AGTGGTW
        7
        AGTGGTT
       
        CAYCCRTA
        8
        CACCCATA
       
        CAACTKGG
        8
        CAACTTGG
       
        CGCSTTA
        7
        CGCCTTA
       
        CCABAC
        6
        CCACAC
       
        CGCKCTAC
        8
        CGCGCTAC
       
        AARAAA
        6
        AAAAAA
       
        CCAAVAGA
        8
        CCAAGAGA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CAASGATG
        8
        CAACGATG
       
        GTGGAGA
        7
        GTGGAGA
       
        ATTAASAG
        8
        ATTAAGAG
       
        TGCGCCA
        7
        TGCGCCA
       
        AGMATGGG
        8
        AGAATGGG
       
        CCGTGCW
        7
        CCGTGCT
       
        AAGCGWGA
        8
        AAGCGTGA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        GCAACGY
        7
        GCAACGT
       
        AMACCCA
        7
        AAACCCA
       
        ACCGAWG
        7
        ACCGATG
       
        GCAYGCGA
        8
        GCACGCGA
       
        GRGTTCAA
        8
        GGGTTCAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
AGTGGTW	7	AGTGGTT
CAYCCRTA	8	CACCCATA
CAACTKGG	8	CAACTTGG
CGCSTTA	7	CGCCTTA
CCABAC	6	CCACAC
CGCKCTAC	8	CGCGCTAC
AARAAA	6	AAAAAA
CCAAVAGA	8	CCAAGAGA
ATAGTKTA	8	ATAGTGTA
CAASGATG	8	CAACGATG
GTGGAGA	7	GTGGAGA
ATTAASAG	8	ATTAAGAG
TGCGCCA	7	TGCGCCA
AGMATGGG	8	AGAATGGG
CCGTGCW	7	CCGTGCT
AAGCGWGA	8	AAGCGTGA
ACTGAGCT	8	ACTGAGCT
GCAACGY	7	GCAACGT
AMACCCA	7	AAACCCA
ACCGAWG	7	ACCGATG
GCAYGCGA	8	GCACGCGA
GRGTTCAA	8	GGGTTCAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 35 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-17	chrIII	+	82499	82506	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrX	+	115976	115983	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrXI	+	141055	141062	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrXVI	+	210229	210236	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrVII	+	401564	401571	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrV	+	487368	487375	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrV	-	177124	177131	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrXIII	-	290826	290833	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrVII	-	328608	328615	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrV	-	354959	354966	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrIX	-	370442	370449	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrX	-	374622	374629	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrVII	-	541875	541882	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrXIV	-	577352	577359	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrII	-	645192	645199	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrXII	-	797203	797210	1.24e-05	0.243	AAGCGTGA
AAGCGWGA	DREME-17	chrIII	+	123616	123623	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXIII	+	196138	196145	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrVIII	+	388963	388970	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXIV	+	631885	631892	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXII	-	92571	92578	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrVI	-	101399	101406	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrI	-	139175	139182	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXV	-	301120	301127	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXV	-	464473	464480	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXIV	-	568138	568145	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXV	-	976523	976530	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrXV	-	980706	980713	2.47e-05	0.278	AAGCGAGA
AAGCGWGA	DREME-17	chrIII	+	178365	178372	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrIX	+	257435	257442	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrV	+	270426	270433	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrXI	-	5836	5843	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrII	-	332555	332562	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrXII	-	460120	460127	4.03e-05	0.363	AAGCGGGA
AAGCGWGA	DREME-17	chrXII	-	897913	897920	4.03e-05	0.363	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/AWRI1631--ACE2/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/background --motif AAGCGWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/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/AWRI1631--ACE2/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/AWRI1631--ACE2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--ACE2/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