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 38 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
TCYGTACA	DREME-9	chrXV	-	93113	93120	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrVI	-	224058	224065	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXIII	-	224216	224223	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrIV	-	341444	341451	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXVI	-	378841	378848	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXIV	-	444606	444613	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXIV	-	495396	495403	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrVII	-	649150	649157	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrVII	-	661849	661856	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXV	-	679011	679018	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrX	-	702799	702806	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXII	-	713373	713380	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXII	-	932260	932267	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXII	-	932268	932275	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXII	-	932276	932283	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXV	-	1028908	1028915	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrII	+	45172	45179	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrIX	+	68352	68359	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXI	+	108923	108930	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrVIII	+	126104	126111	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrIII	+	178492	178499	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXIII	+	225547	225554	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrXII	+	241809	241816	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrV	+	396381	396388	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrV	+	423274	423281	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrII	+	477217	477224	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrII	+	604287	604294	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrIV	+	1359598	1359605	1.2e-05	0.221	TCCGTACA
TCYGTACA	DREME-9	chrII	-	61074	61081	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrXI	-	141732	141739	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrIII	-	178473	178480	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrIX	+	257535	257542	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrVII	+	310688	310695	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrX	-	541492	541499	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrXIII	-	551544	551551	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrII	+	604303	604310	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrXVI	+	821949	821956	3.16e-05	0.431	TCTGTACA
TCYGTACA	DREME-9	chrIV	+	1175813	1175820	3.16e-05	0.431	TCTGTACA

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_10 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--IES2/background --motif TCYGTACA /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_10
    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_10	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