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 38 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
AGCGWGA	DREME-17	chrXI	-	140979	140985	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrV	-	177124	177130	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXIII	-	290826	290832	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVII	-	328608	328614	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVII	-	328608	328614	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrV	-	354959	354965	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVII	-	364866	364872	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrIX	-	370442	370448	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrV	-	431194	431200	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVII	-	438872	438878	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXII	-	460622	460628	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVII	-	541875	541881	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXIV	-	577352	577358	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrII	-	645192	645198	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXII	-	795016	795022	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXII	-	797203	797209	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrX	+	59048	59054	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrIII	+	82500	82506	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrX	+	115977	115983	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVIII	+	134176	134182	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrXI	+	141056	141062	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrV	+	487369	487375	3.6e-05	0.538	AGCGTGA
AGCGWGA	DREME-17	chrVIII	-	116020	116026	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrI	-	139175	139181	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrX	-	228316	228322	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXV	-	301120	301126	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXI	-	308289	308295	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrII	-	332636	332642	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXV	-	464473	464479	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIV	-	547117	547123	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIV	-	568138	568144	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXV	-	976523	976529	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrIII	+	123617	123623	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIII	+	196139	196145	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIV	+	241497	241503	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrVIII	+	388964	388970	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIV	+	443147	443153	7.21e-05	0.623	AGCGAGA
AGCGWGA	DREME-17	chrXIV	+	631886	631892	7.21e-05	0.623	AGCGAGA

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_14 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--NOT3/background --motif AGCGWGA /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_14
    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_14	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