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--IES2/YJM789--IES2.fa
  
  Database contains 762 sequences, 264687 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        BTAAGGCG
        8
        TTAAGGCG
       
        CTBGGCCA
        8
        CTCGGCCA
       
        SAAGA
        5
        CAAGA
       
        CTATCACR
        8
        CTATCACA
       
        CGGTABC
        7
        CGGTAGC
       
        CCCATDC
        7
        CCCATAC
       
        CGRTGAAA
        8
        CGGTGAAA
       
        TCYGTACA
        8
        TCCGTACA
       
        ACACTATA
        8
        ACACTATA
       
        ACTARACC
        8
        ACTAGACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        GCTCTMCC
        8
        GCTCTACC
       
        GCTTCY
        6
        GCTTCC
       
        ACCCAMAC
        8
        ACCCACAC
       
        ACGCSACA
        8
        ACGCGACA
       
        GCYAGA
        6
        GCCAGA
       
        AGTCAKAC
        8
        AGTCATAC
       
        CTGAGCTA
        8
        CTGAGCTA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/background):

A 0.311 C 0.189 G 0.189 T 0.311

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
BTAAGGCG	8	TTAAGGCG
CTBGGCCA	8	CTCGGCCA
SAAGA	5	CAAGA
CTATCACR	8	CTATCACA
CGGTABC	7	CGGTAGC
CCCATDC	7	CCCATAC
CGRTGAAA	8	CGGTGAAA
TCYGTACA	8	TCCGTACA
ACACTATA	8	ACACTATA
ACTARACC	8	ACTAGACC
ATGGCAWC	8	ATGGCAAC
GCTCTMCC	8	GCTCTACC
GCTTCY	6	GCTTCC
ACCCAMAC	8	ACCCACAC
ACGCSACA	8	ACGCGACA
GCYAGA	6	GCCAGA
AGTCAKAC	8	AGTCATAC
CTGAGCTA	8	CTGAGCTA

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	chrVI	+	157992	157999	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVIII	+	237924	237931	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVIII	+	358554	358561	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrX	+	391100	391107	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	440792	440799	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	560274	560281	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXIII	+	572940	572947	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXII	+	605417	605424	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	622616	622623	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	701033	701040	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	701033	701040	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	+	748818	748825	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXVI	+	769287	769294	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	+	1095446	1095453	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrII	-	36404	36411	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrVII	-	115494	115501	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXV	-	305602	305609	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXIII	-	352286	352293	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	359583	359590	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXIV	-	374875	374882	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrX	-	422943	422950	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXV	-	438649	438656	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXI	-	578971	578978	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXII	-	875382	875389	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	884367	884374	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrXV	-	976427	976434	1.2e-05	0.23	CTGAGCTA
CTGAGCTA	DREME-19	chrIV	-	1175835	1175842	1.2e-05	0.23	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/YJM789--IES2/fimo_out_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/background --motif CTGAGCTA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/YJM789--IES2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/fimo_out_17
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/YJM789--IES2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/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--IES2/fimo_out_17	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/YJM789--IES2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/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