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--PDR8/AWRI1631--PDR8.fa
  
  Database contains 483 sequences, 151442 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        TGTAYGGR
        8
        TGTATGGG
       
        ACTBGGCC
        8
        ACTTGGCC
       
        CGCSTTA
        7
        CGCCTTA
       
        AGTGRTA
        7
        AGTGGTA
       
        AARAAAW
        7
        AAAAAAA
       
        TAGTGTR
        7
        TAGTGTA
       
        CAASGATG
        8
        CAACGATG
       
        AGCGCV
        6
        AGCGCG
       
        ACCCAVAC
        8
        ACCCACAC
       
        GATTRGAA
        8
        GATTAGAA
       
        CACGGTGM
        8
        CACGGTGA
       
        KTAGCTCA
        8
        TTAGCTCA
       
        CATYACGC
        8
        CATCACGC
       
        AGACCACR
        8
        AGACCACA
       
        ACCATTRA
        8
        ACCATTAA
       
        ATTGSGCC
        8
        ATTGCGCC
       
        GAGACC
        6
        GAGACC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
TGTAYGGR	8	TGTATGGG
ACTBGGCC	8	ACTTGGCC
CGCSTTA	7	CGCCTTA
AGTGRTA	7	AGTGGTA
AARAAAW	7	AAAAAAA
TAGTGTR	7	TAGTGTA
CAASGATG	8	CAACGATG
AGCGCV	6	AGCGCG
ACCCAVAC	8	ACCCACAC
GATTRGAA	8	GATTAGAA
CACGGTGM	8	CACGGTGA
KTAGCTCA	8	TTAGCTCA
CATYACGC	8	CATCACGC
AGACCACR	8	AGACCACA
ACCATTRA	8	ACCATTAA
ATTGSGCC	8	ATTGCGCC
GAGACC	6	GAGACC

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
KTAGCTCA	DREME-13	chrII	+	36403	36410	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVII	+	115493	115500	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXIII	+	352285	352292	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrIV	+	359582	359589	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXIV	+	374874	374881	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXV	+	438648	438655	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVII	+	535121	535128	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXI	+	578970	578977	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXII	+	875381	875388	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXII	+	975946	975953	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVI	-	157993	158000	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXV	-	216509	216516	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVIII	-	237925	237932	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVIII	-	358555	358562	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVII	-	440793	440800	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXVI	-	560275	560282	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXVI	-	622617	622624	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrVII	-	701034	701041	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXVI	-	769288	769295	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrXII	-	781710	781717	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrIV	-	1095447	1095454	1.96e-05	0.276	TTAGCTCA
KTAGCTCA	DREME-13	chrX	+	422942	422949	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrIV	+	884366	884373	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrXV	+	976426	976433	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrIV	+	1175834	1175841	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrX	-	391101	391108	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrXIII	-	572941	572948	3.2e-05	0.338	GTAGCTCA
KTAGCTCA	DREME-13	chrXII	-	605418	605425	3.2e-05	0.338	GTAGCTCA

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--PDR8/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/background --motif KTAGCTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/AWRI1631--PDR8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/AWRI1631--PDR8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/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--PDR8/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/AWRI1631--PDR8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--PDR8/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