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--YAP6/AWRI1631--YAP6.fa
  
  Database contains 807 sequences, 324873 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        RGTTCGA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCGTACAT
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCKCTMCC
        8
        GCTCTACC
       
        GCCTTAMC
        8
        GCCTTAAC
       
        GTGRTA
        6
        GTGATA
       
        AGMAG
        5
        AGAAG
       
        GGCSCAA
        7
        GGCCCAA
       
        AKCGTGA
        7
        ATCGTGA
       
        CACGGYG
        7
        CACGGTG
       
        ATGGCAAC
        8
        ATGGCAAC
       
        CGCGGGS
        7
        CGCGGGG
       
        AATMCAAC
        8
        AATCCAAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
RGTTCGA	7	GGTTCGA
CCRTACAY	8	CCGTACAT
CTBGGCCA	8	CTCGGCCA
GCKCTMCC	8	GCTCTACC
GCCTTAMC	8	GCCTTAAC
GTGRTA	6	GTGATA
AGMAG	5	AGAAG
GGCSCAA	7	GGCCCAA
AKCGTGA	7	ATCGTGA
CACGGYG	7	CACGGTG
ATGGCAAC	8	ATGGCAAC
CGCGGGS	7	CGCGGGG
AATMCAAC	8	AATCCAAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 43 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
AKCGTGA	DREME-9	chrVI	-	30238	30244	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrX	+	59048	59054	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	+	68397	68403	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXVI	-	75689	75695	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrIII	+	82500	82506	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	-	85833	85839	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrX	+	115977	115983	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	-	140979	140985	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	-	140979	140985	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	+	141056	141062	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	+	141056	141062	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	-	177124	177130	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXVI	+	210230	210236	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXIII	-	290826	290832	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	+	317140	317146	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	328608	328614	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	-	354959	354965	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	-	355064	355070	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrIX	-	370442	370448	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrX	-	374622	374628	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXI	-	379772	379778	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	+	401565	401571	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	-	431194	431200	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	438154	438160	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	438872	438878	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXV	+	444890	444896	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXV	+	444890	444896	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	460622	460628	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrV	+	487369	487375	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	541875	541881	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrIV	+	555914	555920	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXIV	-	577352	577358	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrX	+	620508	620514	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrII	-	645192	645198	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXIII	-	702379	702385	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXIII	+	762092	762098	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	795016	795022	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	795016	795022	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	795016	795022	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	795016	795022	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	797203	797209	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrXV	-	900128	900134	4.01e-05	0.596	AGCGTGA
AKCGTGA	DREME-9	chrIV	-	1402269	1402275	4.01e-05	0.596	AGCGTGA

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--YAP6/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/background --motif AKCGTGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/AWRI1631--YAP6.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/AWRI1631--YAP6.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/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--YAP6/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/AWRI1631--YAP6.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--YAP6/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