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--CAT8/BY4742--CAT8.fa
  
  Database contains 560 sequences, 171142 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        AYCCRTAC
        8
        ACCCATAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        GCCWTAAC
        8
        GCCTTAAC
       
        GCKCTACC
        8
        GCGCTACC
       
        CGARCCC
        7
        CGAACCC
       
        CCASAC
        6
        CCACAC
       
        CACTAWA
        7
        CACTATA
       
        ATCSTTG
        7
        ATCCTTG
       
        CTTARACC
        8
        CTTAGACC
       
        GGYTATCA
        8
        GGCTATCA
       
        GCGCAR
        6
        GCGCAA
       
        SAAGAAA
        7
        GAAGAAA
       
        AATCSAAC
        8
        AATCCAAC
       
        CATYACGC
        8
        CATTACGC
       
        ACCCRTGC
        8
        ACCCATGC
       
        AMACCCAA
        8
        ACACCCAA
       
        GTAKCTCA
        8
        GTATCTCA
       
        TCTCCACR
        8
        TCTCCACG
       
        ACGGAKG
        7
        ACGGATG
       
        AGTCAKAC
        8
        AGTCATAC
       
        AAAAARAA
        8
        AAAAAAAA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
AYCCRTAC	8	ACCCATAC
CTBGGCCA	8	CTCGGCCA
GCCWTAAC	8	GCCTTAAC
GCKCTACC	8	GCGCTACC
CGARCCC	7	CGAACCC
CCASAC	6	CCACAC
CACTAWA	7	CACTATA
ATCSTTG	7	ATCCTTG
CTTARACC	8	CTTAGACC
GGYTATCA	8	GGCTATCA
GCGCAR	6	GCGCAA
SAAGAAA	7	GAAGAAA
AATCSAAC	8	AATCCAAC
CATYACGC	8	CATTACGC
ACCCRTGC	8	ACCCATGC
AMACCCAA	8	ACACCCAA
GTAKCTCA	8	GTATCTCA
TCTCCACR	8	TCTCCACG
ACGGAKG	7	ACGGATG
AGTCAKAC	8	AGTCATAC
AAAAARAA	8	AAAAAAAA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 31 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
ATCSTTG	DREME-8	chrVII	-	115540	115546	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVIII	-	134272	134278	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrIII	-	142841	142847	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVI	-	162201	162207	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVIII	-	175114	175120	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	-	232587	232593	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVII	-	346210	346216	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrIV	-	359629	359635	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	-	374548	374554	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXV	-	438695	438701	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXIV	-	495414	495420	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXI	-	579017	579023	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrII	-	605960	605966	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVII	-	701042	701048	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVII	-	701146	701152	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXVI	-	769296	769302	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	-	796610	796616	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	-	875428	875434	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXV	-	978933	978939	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrX	+	73583	73589	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVII	+	115486	115492	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVIII	+	133175	133181	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrIV	+	359575	359581	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	+	369416	369422	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrII	+	405715	405721	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXV	+	438641	438647	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXI	+	578963	578969	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXVI	+	653982	653988	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrVII	+	700988	700994	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXVI	+	769242	769248	6.35e-05	0.687	ATCCTTG
ATCSTTG	DREME-8	chrXII	+	875374	875380	6.35e-05	0.687	ATCCTTG

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--CAT8/fimo_out_7 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/background --motif ATCSTTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/fimo_out_7
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/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--CAT8/fimo_out_7	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/BY4742--CAT8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CAT8/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