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--HAA1/YJM789--HAA1.fa
  
  Database contains 452 sequences, 137896 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        CTBGGCCA
        8
        CTCGGCCA
       
        SGGTTCRA
        8
        GGGTTCGA
       
        CGCSTTA
        7
        CGCCTTA
       
        CCRTACA
        7
        CCATACA
       
        CABACGC
        7
        CACACGC
       
        GTGATAR
        7
        GTGATAG
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTCTHCC
        7
        CTCTCCC
       
        TACACTAW
        8
        TACACTAT
       
        CRCCCA
        6
        CACCCA
       
        AGCKCGC
        7
        AGCGCGC
       
        TCAKAA
        6
        TCAGAA
       
        TACCACTA
        8
        TACCACTA
       
        TGGCGCAR
        8
        TGGCGCAA
       
        AARAAA
        6
        AAAAAA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        CACGGTGM
        8
        CACGGTGA
       
        ATCSTTG
        7
        ATCCTTG
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/background):

A 0.309 C 0.191 G 0.191 T 0.309

MOTIF	WIDTH	BEST POSSIBLE MATCH
CTBGGCCA	8	CTCGGCCA
SGGTTCRA	8	GGGTTCGA
CGCSTTA	7	CGCCTTA
CCRTACA	7	CCATACA
CABACGC	7	CACACGC
GTGATAR	7	GTGATAG
ATGGCAWC	8	ATGGCAAC
CTCTHCC	7	CTCTCCC
TACACTAW	8	TACACTAT
CRCCCA	6	CACCCA
AGCKCGC	7	AGCGCGC
TCAKAA	6	TCAGAA
TACCACTA	8	TACCACTA
TGGCGCAR	8	TGGCGCAA
AARAAA	6	AAAAAA
ACTGAGCT	8	ACTGAGCT
CACGGTGM	8	CACGGTGA
ATCSTTG	7	ATCCTTG

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 23 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-18	chrVII	-	115540	115546	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVIII	-	134272	134278	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrIII	-	142841	142847	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVI	-	162201	162207	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVIII	-	175114	175120	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXV	-	438695	438701	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXIV	-	495414	495420	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXI	-	579017	579023	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVII	-	701042	701048	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVII	-	701146	701152	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXVI	-	769296	769302	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXII	-	796610	796616	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXII	-	875428	875434	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXV	-	978933	978939	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrX	+	73583	73589	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVII	+	115486	115492	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVIII	+	133175	133181	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrII	+	405715	405721	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXV	+	438641	438647	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXI	+	578963	578969	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrVII	+	700988	700994	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXVI	+	769242	769248	6.35e-05	0.746	ATCCTTG
ATCSTTG	DREME-18	chrXII	+	875374	875380	6.35e-05	0.746	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/YJM789--HAA1/fimo_out_17 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/background --motif ATCSTTG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/YJM789--HAA1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/fimo_out_17
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/YJM789--HAA1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/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--HAA1/fimo_out_17	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/YJM789--HAA1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--HAA1/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