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--HAA1/AWRI1631--HAA1.fa
  
  Database contains 430 sequences, 127200 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        ACTBGGCC
        8
        ACTTGGCC
       
        CCRTACAY
        8
        CCGTACAT
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AGTGGTWA
        8
        AGTGGTTA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CCASAC
        6
        CCACAC
       
        ACCACTWG
        8
        ACCACTTG
       
        CACCGTGS
        8
        CACCGTGG
       
        CAMGGA
        6
        CACGGA
       
        AAGATWT
        7
        AAGATTT
       
        AYTGCGCC
        8
        ATTGCGCC
       
        GACTSTTA
        8
        GACTCTTA
       
        ATAGTKTA
        8
        ATAGTGTA
       
        CTTSTA
        6
        CTTCTA
       
        CTGAGCTA
        8
        CTGAGCTA
       
        AACACSC
        7
        AACACCC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
ACTBGGCC	8	ACTTGGCC
CCRTACAY	8	CCGTACAT
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
AGTGGTWA	8	AGTGGTTA
ATGGCAWC	8	ATGGCAAC
CCASAC	6	CCACAC
ACCACTWG	8	ACCACTTG
CACCGTGS	8	CACCGTGG
CAMGGA	6	CACGGA
AAGATWT	7	AAGATTT
AYTGCGCC	8	ATTGCGCC
GACTSTTA	8	GACTCTTA
ATAGTKTA	8	ATAGTGTA
CTTSTA	6	CTTCTA
CTGAGCTA	8	CTGAGCTA
AACACSC	7	AACACCC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 25 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
GACTSTTA	DREME-14	chrVII	+	122297	122304	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrX	+	414994	415001	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrVII	+	544667	544674	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrVII	+	876422	876429	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrIV	+	1201778	1201785	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrVII	-	122381	122388	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrV	-	135460	135467	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrVII	-	185749	185756	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrVI	-	226723	226730	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrIX	-	300263	300270	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrV	-	435787	435794	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrXII	-	448849	448856	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrXIII	-	480656	480663	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrIV	-	1352501	1352508	1.96e-05	0.348	GACTCTTA
GACTSTTA	DREME-14	chrXI	+	74653	74660	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXIV	+	102745	102752	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrIII	+	127745	127752	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXV	+	228360	228367	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXVI	+	282487	282494	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXIV	+	632628	632635	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrVII	+	731166	731173	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXVI	+	810705	810712	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrVI	-	137521	137528	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXII	-	605212	605219	3.93e-05	0.39	GACTGTTA
GACTSTTA	DREME-14	chrXII	-	976018	976025	3.93e-05	0.39	GACTGTTA

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--HAA1/fimo_out_11 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/background --motif GACTSTTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/AWRI1631--HAA1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/fimo_out_11
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/AWRI1631--HAA1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/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--HAA1/fimo_out_11	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/AWRI1631--HAA1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HAA1/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