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--CAT8/AWRI1631--CAT8.fa
  
  Database contains 485 sequences, 160587 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        SGGTTCRA
        8
        GGGTTCGA
       
        ACCWCT
        6
        ACCACT
       
        CCRTACAY
        8
        CCATACAT
       
        AACTKGGC
        8
        AACTTGGC
       
        CGCCTTA
        7
        CGCCTTA
       
        GTSATA
        6
        GTGATA
       
        ACCCANAC
        8
        ACCCACAC
       
        CGCKCTAC
        8
        CGCGCTAC
       
        AAAAAAMT
        8
        AAAAAAAT
       
        CASACGC
        7
        CAGACGC
       
        CCATCGTK
        8
        CCATCGTT
       
        CACGGTGM
        8
        CACGGTGA
       
        CAAGAK
        6
        CAAGAT
       
        CAACGWTG
        8
        CAACGTTG
       
        GCCRTTAC
        8
        GCCGTTAC
       
        TCAKAA
        6
        TCAGAA
       
        ACTTSTAA
        8
        ACTTCTAA
       
        AYTGCGCC
        8
        ATTGCGCC
       
        CGCGGGSA
        8
        CGCGGGGA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/background):

A 0.305 C 0.195 G 0.195 T 0.305

MOTIF	WIDTH	BEST POSSIBLE MATCH
SGGTTCRA	8	GGGTTCGA
ACCWCT	6	ACCACT
CCRTACAY	8	CCATACAT
AACTKGGC	8	AACTTGGC
CGCCTTA	7	CGCCTTA
GTSATA	6	GTGATA
ACCCANAC	8	ACCCACAC
CGCKCTAC	8	CGCGCTAC
AAAAAAMT	8	AAAAAAAT
CASACGC	7	CAGACGC
CCATCGTK	8	CCATCGTT
CACGGTGM	8	CACGGTGA
CAAGAK	6	CAAGAT
CAACGWTG	8	CAACGTTG
GCCRTTAC	8	GCCGTTAC
TCAKAA	6	TCAGAA
ACTTSTAA	8	ACTTCTAA
AYTGCGCC	8	ATTGCGCC
CGCGGGSA	8	CGCGGGGA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 26 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
ACTTSTAA	DREME-17	chrXIII	-	131859	131866	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrV	+	138694	138701	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrXI	-	162521	162528	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrXIII	+	183855	183862	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrV	-	311734	311741	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrIV	-	341536	341543	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrX	+	355402	355409	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrX	+	355402	355409	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrX	-	374540	374547	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrVII	+	405498	405505	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrII	+	405906	405913	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrIV	+	568910	568917	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrVII	+	736368	736375	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrXIII	-	747926	747933	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrVII	-	828757	828764	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrXVI	-	919290	919297	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrIV	+	1095281	1095288	3.06e-05	0.565	ACTTCTAA
ACTTSTAA	DREME-17	chrXII	-	92533	92540	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrII	+	415714	415721	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrVIII	+	467018	467025	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrXV	-	506245	506252	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrVII	+	661777	661784	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrXVI	+	744312	744319	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrXII	-	796590	796597	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrIV	-	981060	981067	6.11e-05	0.739	ACTTGTAA
ACTTSTAA	DREME-17	chrVII	+	1004244	1004251	6.11e-05	0.739	ACTTGTAA

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--CAT8/fimo_out_15 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/background --motif ACTTSTAA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/fimo_out_15
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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/AWRI1631--CAT8/fimo_out_15	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--CAT8/AWRI1631--CAT8.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--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