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/YJM789--NOT3/YJM789--NOT3.fa
  
  Database contains 504 sequences, 167254 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TBGGCCA
        7
        TCGGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        GGTTCRA
        7
        GGTTCGA
       
        ATGTAYGG
        8
        ATGTATGG
       
        TGGCGYA
        7
        TGGCGCA
       
        AGCGCV
        6
        AGCGCG
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTARACCA
        8
        CTAGACCA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CACGGA
        6
        CACGGA
       
        TAGCTCR
        7
        TAGCTCA
       
        TCTCCACR
        8
        TCTCCACA
       
        GTTGGK
        6
        GTTGGT
       
        ARAAARAA
        8
        AAAAAAAA
       
        ATTAASAG
        8
        ATTAAGAG
       
        TAATCWGA
        8
        TAATCAGA
       
        AGCGWGA
        7
        AGCGTGA
       
        RCACCCA
        7
        ACACCCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/background):

A 0.316 C 0.184 G 0.184 T 0.316

MOTIF	WIDTH	BEST POSSIBLE MATCH
TBGGCCA	7	TCGGCCA
CGCSTTA	7	CGCCTTA
GGTTCRA	7	GGTTCGA
ATGTAYGG	8	ATGTATGG
TGGCGYA	7	TGGCGCA
AGCGCV	6	AGCGCG
ATGGCAWC	8	ATGGCAAC
CTARACCA	8	CTAGACCA
ATAGTKTA	8	ATAGTGTA
CACGGA	6	CACGGA
TAGCTCR	7	TAGCTCA
TCTCCACR	8	TCTCCACA
GTTGGK	6	GTTGGT
ARAAARAA	8	AAAAAAAA
ATTAASAG	8	ATTAAGAG
TAATCWGA	8	TAATCAGA
AGCGWGA	7	AGCGTGA
RCACCCA	7	ACACCCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 67 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
ATAGTKTA	DREME-9	chrIII	-	82519	82526	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrX	-	115996	116003	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	-	131139	131146	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	+	134326	134333	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXI	-	141075	141082	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	-	146120	146127	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIII	-	168358	168365	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	177104	177111	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIX	+	197440	197447	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	250291	250298	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	+	290806	290813	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIX	-	316383	316390	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	+	328588	328595	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	+	328588	328595	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrII	+	350832	350839	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	354939	354946	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIX	+	370422	370429	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXI	-	431500	431507	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	436581	436588	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	-	448707	448714	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	-	475764	475771	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	-	487388	487395	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVIII	-	506118	506125	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	+	520977	520984	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrVII	+	541855	541862	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXIV	-	560648	560655	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrII	+	645172	645179	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXII	+	797183	797190	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	802788	802795	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXIII	-	808303	808310	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXV	+	1071391	1071398	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrXV	+	1071391	1071398	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	1075530	1075537	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrIV	-	1305583	1305590	3.38e-05	0.325	ATAGTGTA
ATAGTKTA	DREME-9	chrV	+	53671	53678	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	80721	80728	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXI	+	162368	162375	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVI	-	191639	191646	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	204740	204747	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	282811	282818	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrIX	-	324360	324367	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrIX	-	336406	336413	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355335	355342	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355335	355342	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355461	355468	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	355461	355468	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	-	374481	374488	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVIII	-	389025	389032	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrII	+	405965	405972	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	+	423264	423271	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	427137	427144	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	438537	438544	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	445939	445946	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	-	459666	459673	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXIII	+	463559	463566	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXI	-	513389	513396	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	+	531615	531622	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	+	541513	541520	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	-	544634	544641	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrIV	+	568969	568976	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrIV	+	568969	568976	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXV	+	571963	571970	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrX	-	670086	670093	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	734748	734755	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXVI	+	744190	744197	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrXII	+	793923	793930	9.2e-05	0.45	ATAGTTTA
ATAGTKTA	DREME-9	chrVII	-	794308	794315	9.2e-05	0.45	ATAGTTTA

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/YJM789--NOT3/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/background --motif ATAGTKTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--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/YJM789--NOT3/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/YJM789--NOT3.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--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