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--HIR1/BY4742--HIR1.fa
  
  Database contains 902 sequences, 328555 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        TGTAYGGR
        8
        TGTATGGA
       
        CTYGGCC
        7
        CTTGGCC
       
        ARAAAWA
        7
        AAAAAAA
       
        CTWAACCA
        8
        CTTAACCA
       
        GCKCTACC
        8
        GCGCTACC
       
        GCGCM
        5
        GCGCA
       
        ACATYAC
        7
        ACATCAC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        AGTGGTTA
        8
        AGTGGTTA
       
        CDTTGGGC
        8
        CTTTGGGC
       
        GTCYCCA
        7
        GTCTCCA
       
        GARTCATA
        8
        GAATCATA
       
        CCGTGMTA
        8
        CCGTGATA
       
        ACTAGACC
        8
        ACTAGACC
       
        ACCCAVAC
        8
        ACCCACAC
       
        CCAAMAGA
        8
        CCAAAAGA
       
        TRTAYA
        6
        TATATA
       
        ACAAAGCA
        8
        ACAAAGCA
       
        CTCTCSC
        7
        CTCTCCC
       
        ACTGAGCT
        8
        ACTGAGCT
       
        ATRCTAAG
        8
        ATGCTAAG
       
        GGAWTTGA
        8
        GGAATTGA
       
        ATCAKAAG
        8
        ATCATAAG
       
        ACACGCCC
        8
        ACACGCCC
       
        SATCGTGA
        8
        CATCGTGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/background):

A 0.318 C 0.182 G 0.182 T 0.318

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
TGTAYGGR	8	TGTATGGA
CTYGGCC	7	CTTGGCC
ARAAAWA	7	AAAAAAA
CTWAACCA	8	CTTAACCA
GCKCTACC	8	GCGCTACC
GCGCM	5	GCGCA
ACATYAC	7	ACATCAC
ATGGCAWC	8	ATGGCAAC
AGTGGTTA	8	AGTGGTTA
CDTTGGGC	8	CTTTGGGC
GTCYCCA	7	GTCTCCA
GARTCATA	8	GAATCATA
CCGTGMTA	8	CCGTGATA
ACTAGACC	8	ACTAGACC
ACCCAVAC	8	ACCCACAC
CCAAMAGA	8	CCAAAAGA
TRTAYA	6	TATATA
ACAAAGCA	8	ACAAAGCA
CTCTCSC	7	CTCTCCC
ACTGAGCT	8	ACTGAGCT
ATRCTAAG	8	ATGCTAAG
GGAWTTGA	8	GGAATTGA
ATCAKAAG	8	ATCATAAG
ACACGCCC	8	ACACGCCC
SATCGTGA	8	CATCGTGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
ACTGAGCT	DREME-21	chrII	-	36405	36412	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVII	-	115495	115502	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXIII	-	220871	220878	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXIII	-	352287	352294	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	-	359584	359591	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXIV	-	374876	374883	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrX	-	422944	422951	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXV	-	438650	438657	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	-	539334	539341	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXI	-	578972	578979	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXII	-	875383	875390	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	-	884368	884375	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXV	-	976428	976435	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	-	1175836	1175843	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	-	1524464	1524471	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVI	+	157991	157998	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVIII	+	237923	237930	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXIII	+	298402	298409	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVIII	+	358553	358560	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrX	+	391099	391106	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVII	+	440791	440798	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrX	+	517948	517955	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXVI	+	560273	560280	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXIII	+	572939	572946	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXII	+	605416	605423	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXVI	+	622615	622622	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrVII	+	701032	701039	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrXVI	+	769286	769293	1.12e-05	0.25	ACTGAGCT
ACTGAGCT	DREME-21	chrIV	+	1095445	1095452	1.12e-05	0.25	ACTGAGCT

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--HIR1/fimo_out_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/background --motif ACTGAGCT /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/BY4742--HIR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/fimo_out_17
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/BY4742--HIR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/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--HIR1/fimo_out_17	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/BY4742--HIR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--HIR1/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