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/BY4742--INO80/BY4742--INO80.fa
  
  Database contains 529 sequences, 202507 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        CTWRACC
        7
        CTTAACC
       
        CCVTACA
        7
        CCATACA
       
        GCKCTMCC
        8
        GCGCTACC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        TAGTGTAR
        8
        TAGTGTAG
       
        CYTGCGC
        7
        CTTGCGC
       
        AAGAAAW
        7
        AAGAAAA
       
        CCGTGSA
        7
        CCGTGGA
       
        ACACSC
        6
        ACACCC
       
        ATCGTRAG
        8
        ATCGTGAG
       
        GTGATAGY
        8
        GTGATAGC
       
        ACTRCGCC
        8
        ACTGCGCC
       
        CSCATGC
        7
        CCCATGC
       
        CGCCTTAS
        8
        CGCCTTAG
       
        GCGCCMA
        7
        GCGCCAA
       
        TAKCTCA
        7
        TAGCTCA
       
        AATCAKAA
        8
        AATCATAA
       
        ATCTGYTG
        8
        ATCTGTTG
       
        AGTTCGAW
        8
        AGTTCGAT
       
        RCGGGGA
        7
        ACGGGGA
       
        AAGATTTC
        8
        AAGATTTC
       
        ATSTGGAG
        8
        ATGTGGAG
       
        CKAGAATC
        8
        CGAGAATC
       
        AGTCGCMC
        8
        AGTCGCAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
CTWRACC	7	CTTAACC
CCVTACA	7	CCATACA
GCKCTMCC	8	GCGCTACC
CTBGGCCA	8	CTCGGCCA
ATGGCAWC	8	ATGGCAAC
TAGTGTAR	8	TAGTGTAG
CYTGCGC	7	CTTGCGC
AAGAAAW	7	AAGAAAA
CCGTGSA	7	CCGTGGA
ACACSC	6	ACACCC
ATCGTRAG	8	ATCGTGAG
GTGATAGY	8	GTGATAGC
ACTRCGCC	8	ACTGCGCC
CSCATGC	7	CCCATGC
CGCCTTAS	8	CGCCTTAG
GCGCCMA	7	GCGCCAA
TAKCTCA	7	TAGCTCA
AATCAKAA	8	AATCATAA
ATCTGYTG	8	ATCTGTTG
AGTTCGAW	8	AGTTCGAT
RCGGGGA	7	ACGGGGA
AAGATTTC	8	AAGATTTC
ATSTGGAG	8	ATGTGGAG
CKAGAATC	8	CGAGAATC
AGTCGCMC	8	AGTCGCAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 28 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
ATSTGGAG	DREME-24	chrXIV	+	104841	104848	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrXV	+	113838	113845	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrIX	+	175067	175074	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrII	+	266414	266421	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrXII	+	282832	282839	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrIII	+	295520	295527	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrIX	+	325784	325791	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrXVI	+	572433	572440	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrX	-	59127	59134	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrVIII	-	116134	116141	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrXV	-	354068	354075	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrIV	-	434291	434298	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrXIV	-	560720	560727	1.22e-05	0.375	ATGTGGAG
ATSTGGAG	DREME-24	chrII	+	36452	36459	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrV	+	53632	53639	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXIII	+	352334	352341	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXIV	+	374923	374930	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrVI	-	157943	157950	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrVIII	-	237875	237882	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrVIII	-	358505	358512	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXII	-	370876	370883	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrVII	-	440743	440750	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXVI	-	560225	560232	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXVI	-	622567	622574	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrVII	-	856973	856980	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrIV	-	1095397	1095404	2.45e-05	0.375	ATCTGGAG
ATSTGGAG	DREME-24	chrXV	+	274610	274617	6.37e-05	0.905	ATTTGGAG
ATSTGGAG	DREME-24	chrVII	+	535149	535156	6.37e-05	0.905	ATTTGGAG

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/BY4742--INO80/fimo_out_22 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/background --motif ATSTGGAG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/fimo_out_22
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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/BY4742--INO80/fimo_out_22	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/BY4742--INO80.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--INO80/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