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--YKL222C/YJM789--YKL222C.fa
  
  Database contains 463 sequences, 158553 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CGCSTTA
        7
        CGCCTTA
       
        CAYCCRTA
        8
        CACCCATA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCKCTMCC
        8
        GCTCTACC
       
        CCCATDC
        7
        CCCATAC
       
        TAGTGGTW
        8
        TAGTGGTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GTSTGGS
        7
        GTCTGGG
       
        AARAAAW
        7
        AAAAAAA
       
        CTTAABCA
        8
        CTTAATCA
       
        GGTCTCY
        7
        GGTCTCC
       
        GYACGGA
        7
        GTACGGA
       
        CACATYAC
        8
        CACATCAC
       
        ATCKTGA
        7
        ATCTTGA
       
        AGTCAKAC
        8
        AGTCATAC
       
        ACTGAGCT
        8
        ACTGAGCT
       
        CCGTGMTA
        8
        CCGTGATA
       
        TAGTGTR
        7
        TAGTGTA
       
        SCACGCGA
        8
        GCACGCGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CGCSTTA	7	CGCCTTA
CAYCCRTA	8	CACCCATA
CTBGGCCA	8	CTCGGCCA
GCKCTMCC	8	GCTCTACC
CCCATDC	7	CCCATAC
TAGTGGTW	8	TAGTGGTA
ATGGCAWC	8	ATGGCAAC
GTSTGGS	7	GTCTGGG
AARAAAW	7	AAAAAAA
CTTAABCA	8	CTTAATCA
GGTCTCY	7	GGTCTCC
GYACGGA	7	GTACGGA
CACATYAC	8	CACATCAC
ATCKTGA	7	ATCTTGA
AGTCAKAC	8	AGTCATAC
ACTGAGCT	8	ACTGAGCT
CCGTGMTA	8	CCGTGATA
TAGTGTR	7	TAGTGTA
SCACGCGA	8	GCACGCGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
ATCKTGA	DREME-15	chrXI	+	74669	74675	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXIV	+	102761	102767	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	+	122221	122227	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrII	+	122905	122911	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrIII	+	127761	127767	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrV	+	138727	138733	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXV	+	228376	228382	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrX	+	355435	355441	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrX	+	355435	355441	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXII	+	366367	366373	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	+	405531	405537	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrII	+	405939	405945	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXVI	+	520454	520460	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrIV	+	568943	568949	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXIV	+	632644	632650	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	+	731182	731188	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	+	736401	736407	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXVI	+	810721	810727	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXIII	-	131827	131833	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVI	-	137506	137512	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXI	-	162489	162495	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXV	-	282310	282316	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrX	-	374508	374514	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrIV	-	491171	491177	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	-	731052	731058	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXIII	-	732245	732251	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXIII	-	747894	747900	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrVII	-	828725	828731	6.34e-05	0.681	ATCGTGA
ATCKTGA	DREME-15	chrXII	-	976003	976009	6.34e-05	0.681	ATCGTGA

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--YKL222C/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/background --motif ATCKTGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/YJM789--YKL222C.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/YJM789--YKL222C.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/YJM789--YKL222C.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YKL222C/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