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--RIM101/AWRI1631--RIM101.fa
  
  Database contains 408 sequences, 112450 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTGGTW
        7
        AGTGGTT
       
        CCRTACA
        7
        CCATACA
       
        AASGCG
        6
        AAGGCG
       
        SGGTTCGA
        8
        GGGTTCGA
       
        CAACTKGG
        8
        CAACTTGG
       
        TGGCGYA
        7
        TGGCGTA
       
        CGCGCTWC
        8
        CGCGCTAC
       
        ACGKTGCC
        8
        ACGTTGCC
       
        SAAGA
        5
        CAAGA
       
        AWAGCCG
        7
        ATAGCCG
       
        GWCTCCA
        7
        GACTCCA
       
        ACCCABA
        7
        ACCCATA
       
        GACTSTTA
        8
        GACTCTTA
       
        ACACTAK
        7
        ACACTAT
       
        CTCTMCCA
        8
        CTCTCCCA
       
        AAGCGWGA
        8
        AAGCGTGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTGGTW	7	AGTGGTT
CCRTACA	7	CCATACA
AASGCG	6	AAGGCG
SGGTTCGA	8	GGGTTCGA
CAACTKGG	8	CAACTTGG
TGGCGYA	7	TGGCGTA
CGCGCTWC	8	CGCGCTAC
ACGKTGCC	8	ACGTTGCC
SAAGA	5	CAAGA
AWAGCCG	7	ATAGCCG
GWCTCCA	7	GACTCCA
ACCCABA	7	ACCCATA
GACTSTTA	8	GACTCTTA
ACACTAK	7	ACACTAT
CTCTMCCA	8	CTCTCCCA
AAGCGWGA	8	AAGCGTGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 42 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
AWAGCCG	DREME-10	chrXII	-	65528	65534	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIII	+	82511	82517	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrX	+	115988	115994	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrXI	+	141067	141073	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	-	177113	177119	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIX	-	197606	197612	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIII	-	227992	227998	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIX	+	248730	248736	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrXIII	-	290815	290821	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrVII	-	328597	328603	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	-	354948	354954	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIX	-	370431	370437	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	-	442205	442211	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	-	442205	442211	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	-	442205	442211	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrVIII	+	475756	475762	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	+	487380	487386	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrXVI	+	520302	520308	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrVII	-	541864	541870	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrXI	-	619080	619086	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrII	-	645181	645187	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrXII	-	797192	797198	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIV	+	1017256	1017262	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIV	+	1075522	1075528	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrIV	+	1233881	1233887	4.02e-05	0.352	ATAGCCG
AWAGCCG	DREME-10	chrV	+	42197	42203	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXIII	+	91956	91962	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXI	-	108868	108874	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrVII	-	115515	115521	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrIII	-	163583	163589	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrV	+	435704	435710	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXVI	+	435842	435848	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXV	-	438670	438676	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXI	-	578992	578998	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrVII	+	701013	701019	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXVI	+	769267	769273	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXII	-	875403	875409	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrIV	-	946429	946435	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXV	+	968112	968118	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrXV	+	968137	968143	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrIV	+	1233803	1233809	8.05e-05	0.419	AAAGCCG
AWAGCCG	DREME-10	chrIV	-	1451064	1451070	8.05e-05	0.419	AAAGCCG

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--RIM101/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/background --motif AWAGCCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/AWRI1631--RIM101.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/AWRI1631--RIM101.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/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--RIM101/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/AWRI1631--RIM101.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--RIM101/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