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--INO80/AWRI1631--INO80.fa
  
  Database contains 664 sequences, 207100 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AGTGGTH
        7
        AGTGGTT
       
        GGHTCGA
        7
        GGTTCGA
       
        ACCCABAC
        8
        ACCCATAC
       
        AASGCG
        6
        AAGGCG
       
        AACTKGGC
        8
        AACTTGGC
       
        SAAGA
        5
        CAAGA
       
        GCKCTACC
        8
        GCGCTACC
       
        TGTACGGR
        8
        TGTACGGA
       
        CACGGYG
        7
        CACGGTG
       
        GATTRGAA
        8
        GATTAGAA
       
        CTATCACR
        8
        CTATCACA
       
        AAACCCAW
        8
        AAACCCAA
       
        CACTATAK
        8
        CACTATAT
       
        ATTRCGCC
        8
        ATTGCGCC
       
        AAAGCGWG
        8
        AAAGCGTG
       
        RAAAAAA
        7
        AAAAAAA
       
        GATKGCAA
        8
        GATGGCAA
       
        CACGCCC
        7
        CACGCCC
       
        CTGAGCTA
        8
        CTGAGCTA
       
        ACCGARAG
        8
        ACCGAAAG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
AGTGGTH	7	AGTGGTT
GGHTCGA	7	GGTTCGA
ACCCABAC	8	ACCCATAC
AASGCG	6	AAGGCG
AACTKGGC	8	AACTTGGC
SAAGA	5	CAAGA
GCKCTACC	8	GCGCTACC
TGTACGGR	8	TGTACGGA
CACGGYG	7	CACGGTG
GATTRGAA	8	GATTAGAA
CTATCACR	8	CTATCACA
AAACCCAW	8	AAACCCAA
CACTATAK	8	CACTATAT
ATTRCGCC	8	ATTGCGCC
AAAGCGWG	8	AAAGCGTG
RAAAAAA	7	AAAAAAA
GATKGCAA	8	GATGGCAA
CACGCCC	7	CACGCCC
CTGAGCTA	8	CTGAGCTA
ACCGARAG	8	ACCGAAAG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 27 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
CTGAGCTA	DREME-19	chrXIII	-	20331	20338	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrII	-	36404	36411	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	-	115494	115501	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVI	+	157992	157999	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVIII	+	237924	237931	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXIII	-	352286	352293	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVIII	+	358554	358561	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	359583	359590	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXIV	-	374875	374882	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrX	+	391100	391107	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrX	-	422943	422950	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXV	-	438649	438656	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	440792	440799	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	560274	560281	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXIII	+	572940	572947	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXI	-	578971	578978	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXI	-	578971	578978	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXII	+	605417	605424	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	622616	622623	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	701033	701040	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	701033	701040	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	769287	769294	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXII	-	875382	875389	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	884367	884374	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrXV	-	976427	976434	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	+	1095446	1095453	1.23e-05	0.185	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	1175835	1175842	1.23e-05	0.185	CTGAGCTA

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--INO80/fimo_out_18 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/background --motif CTGAGCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/AWRI1631--INO80.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/fimo_out_18
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/AWRI1631--INO80.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/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--INO80/fimo_out_18	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/AWRI1631--INO80.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--INO80/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