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--HSF1/AWRI1631--HSF1.fa
  
  Database contains 486 sequences, 163716 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        CCRTACAY
        8
        CCATACAT
       
        CTBGGCCA
        8
        CTCGGCCA
       
        TAAGGCR
        7
        TAAGGCG
       
        GCKCTMCC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        RCACCCA
        7
        ACACCCA
       
        GGTCTCY
        7
        GGTCTCC
       
        AAGATTTM
        8
        AAGATTTC
       
        ACATCH
        6
        ACATCA
       
        ACTARACC
        8
        ACTAGACC
       
        ACTGAGCT
        8
        ACTGAGCT
       
        ACAAGGMT
        8
        ACAAGGCT
       
        TAATCAKA
        8
        TAATCATA
       
        TAAKCGCA
        8
        TAATCGCA
       
        AAGAAAMA
        8
        AAGAAAAA
       
        AGTCAKAC
        8
        AGTCATAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
CCRTACAY	8	CCATACAT
CTBGGCCA	8	CTCGGCCA
TAAGGCR	7	TAAGGCG
GCKCTMCC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
ATAGTKTA	8	ATAGTGTA
RCACCCA	7	ACACCCA
GGTCTCY	7	GGTCTCC
AAGATTTM	8	AAGATTTC
ACATCH	6	ACATCA
ACTARACC	8	ACTAGACC
ACTGAGCT	8	ACTGAGCT
ACAAGGMT	8	ACAAGGCT
TAATCAKA	8	TAATCATA
TAAKCGCA	8	TAATCGCA
AAGAAAMA	8	AAGAAAAA
AGTCAKAC	8	AGTCATAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 37 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
ACAAGGMT	DREME-14	chrV	+	117918	117925	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrVII	-	122267	122274	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrV	+	135490	135497	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrIII	+	151349	151356	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrVII	+	185779	185786	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrXI	-	202997	203004	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrIX	+	300293	300300	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrII	+	408856	408863	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrX	-	414964	414971	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrXII	-	427022	427029	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrV	+	435817	435824	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrXIII	+	480686	480693	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrXVI	+	481546	481553	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrXVI	-	582060	582067	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrX	-	651590	651597	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrVII	-	876392	876399	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrIV	-	1201748	1201755	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrIV	+	1352531	1352538	1.24e-05	0.22	ACAAGGCT
ACAAGGMT	DREME-14	chrVII	-	115486	115493	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXII	+	232586	232593	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXII	+	283356	283363	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrIV	-	359575	359582	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXV	-	438641	438648	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXIV	+	525123	525130	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXI	-	578963	578970	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrVII	+	701041	701048	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXVI	+	769295	769302	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXII	-	875374	875381	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXV	+	978932	978939	3.2e-05	0.353	ACAAGGAT
ACAAGGMT	DREME-14	chrXV	-	79872	79879	6.39e-05	0.554	ACAAGGTT
ACAAGGMT	DREME-14	chrVII	+	205420	205427	6.39e-05	0.554	ACAAGGGT
ACAAGGMT	DREME-14	chrXVI	+	303475	303482	6.39e-05	0.554	ACAAGGGT
ACAAGGMT	DREME-14	chrXVI	+	407156	407163	6.39e-05	0.554	ACAAGGTT
ACAAGGMT	DREME-14	chrX	-	415089	415096	6.39e-05	0.554	ACAAGGTT
ACAAGGMT	DREME-14	chrXV	+	594255	594262	6.39e-05	0.554	ACAAGGGT
ACAAGGMT	DREME-14	chrXVI	-	769114	769121	6.39e-05	0.554	ACAAGGTT
ACAAGGMT	DREME-14	chrXV	+	883308	883315	6.39e-05	0.554	ACAAGGTT

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--HSF1/fimo_out_13 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/background --motif ACAAGGMT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/AWRI1631--HSF1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/fimo_out_13
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/AWRI1631--HSF1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/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--HSF1/fimo_out_13	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/AWRI1631--HSF1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--HSF1/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