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/YJM789--YRR1/YJM789--YRR1.fa
  
  Database contains 489 sequences, 129034 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CCAYAC
        6
        CCATAC
       
        TCGAACCB
        8
        TCGAACCC
       
        TBGGCCA
        7
        TCGGCCA
       
        BTAAGGCG
        8
        TTAAGGCG
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ACCACTAV
        8
        ACCACTAA
       
        ATCCGTRC
        8
        ATCCGTAC
       
        CTATCACR
        8
        CTATCACA
       
        GCKCTACC
        8
        GCGCTACC
       
        CACGGTGM
        8
        CACGGTGA
       
        AAGTGRT
        7
        AAGTGGT
       
        AAGCGWGA
        8
        AAGCGTGA
       
        CTCTCSCA
        8
        CTCTCCCA
       
        CACGCGAS
        8
        CACGCGAC
       
        CTGAGCTA
        8
        CTGAGCTA
       
        TTGTTGWA
        8
        TTGTTGAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
CCAYAC	6	CCATAC
TCGAACCB	8	TCGAACCC
TBGGCCA	7	TCGGCCA
BTAAGGCG	8	TTAAGGCG
ATGGCAWC	8	ATGGCAAC
ACCACTAV	8	ACCACTAA
ATCCGTRC	8	ATCCGTAC
CTATCACR	8	CTATCACA
GCKCTACC	8	GCGCTACC
CACGGTGM	8	CACGGTGA
AAGTGRT	7	AAGTGGT
AAGCGWGA	8	AAGCGTGA
CTCTCSCA	8	CTCTCCCA
CACGCGAS	8	CACGCGAC
CTGAGCTA	8	CTGAGCTA
TTGTTGWA	8	TTGTTGAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 33 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
AAGCGWGA	DREME-12	chrIII	+	82499	82506	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrX	+	115976	115983	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXI	+	141055	141062	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrV	-	177124	177131	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXVI	+	210229	210236	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXIII	-	290826	290833	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrVII	-	328608	328615	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrV	-	354959	354966	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrIX	-	370442	370449	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrVII	+	401564	401571	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrV	+	487368	487375	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXIV	-	493699	493706	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrVII	-	541875	541882	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXIV	-	577352	577359	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrII	-	645192	645199	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXII	-	797203	797210	1.23e-05	0.194	AAGCGTGA
AAGCGWGA	DREME-12	chrXII	-	92571	92578	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrIII	+	123616	123623	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrI	-	139175	139182	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXIII	+	196138	196145	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXV	-	301120	301127	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrVIII	+	388963	388970	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXV	-	464473	464480	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXIV	-	547117	547124	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXIV	-	568138	568145	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXIV	+	631885	631892	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXV	-	976523	976530	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrXV	-	980706	980713	2.47e-05	0.222	AAGCGAGA
AAGCGWGA	DREME-12	chrVI	+	64818	64825	4.02e-05	0.306	AAGCGGGA
AAGCGWGA	DREME-12	chrIX	+	257435	257442	4.02e-05	0.306	AAGCGGGA
AAGCGWGA	DREME-12	chrII	-	332555	332562	4.02e-05	0.306	AAGCGGGA
AAGCGWGA	DREME-12	chrXIV	-	575626	575633	4.02e-05	0.306	AAGCGGGA
AAGCGWGA	DREME-12	chrXII	-	897913	897920	4.02e-05	0.306	AAGCGCGA

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/YJM789--YRR1/fimo_out_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/background --motif AAGCGWGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/YJM789--YRR1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/fimo_out_10
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/YJM789--YRR1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/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/YJM789--YRR1/fimo_out_10	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/YJM789--YRR1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--YRR1/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