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--NRG1/AWRI1631--NRG1.fa
  
  Database contains 629 sequences, 214275 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CCCATDC
        7
        CCCATAC
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        AARARAAA
        8
        AAAAAAAA
       
        GTAMGGA
        7
        GTACGGA
       
        CACGGTGM
        8
        CACGGTGA
       
        GATTRGAA
        8
        GATTAGAA
       
        GGYTATCA
        8
        GGCTATCA
       
        CCASAC
        6
        CCACAC
       
        ATGGCAW
        7
        ATGGCAA
       
        ATCKTGAG
        8
        ATCGTGAG
       
        CACGGAW
        7
        CACGGAT
       
        TACCACTA
        8
        TACCACTA
       
        AYTGCGCC
        8
        ACTGCGCC
       
        CKTTGGGC
        8
        CGTTGGGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/background):

A 0.303 C 0.197 G 0.197 T 0.303

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
CTBGGCCA	8	CTCGGCCA
CCCATDC	7	CCCATAC
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
ATAGTKTA	8	ATAGTGTA
AARARAAA	8	AAAAAAAA
GTAMGGA	7	GTACGGA
CACGGTGM	8	CACGGTGA
GATTRGAA	8	GATTAGAA
GGYTATCA	8	GGCTATCA
CCASAC	6	CCACAC
ATGGCAW	7	ATGGCAA
ATCKTGAG	8	ATCGTGAG
CACGGAW	7	CACGGAT
TACCACTA	8	TACCACTA
AYTGCGCC	8	ACTGCGCC
CKTTGGGC	8	CGTTGGGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 51 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
GTAMGGA	DREME-8	chrII	-	45172	45178	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIX	-	68352	68358	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	-	79899	79905	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	87002	87008	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	-	94672	94678	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXI	-	108923	108929	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVIII	-	126104	126110	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXI	-	162404	162410	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIII	-	178492	178498	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIII	-	225547	225553	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	-	229656	229662	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	241809	241815	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	282676	282682	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	282676	282682	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrV	-	396381	396387	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXVI	-	406373	406379	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrV	-	423274	423280	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrII	-	477217	477223	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	522305	522311	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	-	539087	539093	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	-	539243	539249	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrII	-	604287	604293	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	-	819001	819007	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	-	1359598	1359604	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	+	48905	48911	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	+	93114	93120	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	+	210523	210529	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVI	+	224059	224065	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	+	253980	253986	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIII	+	306580	306586	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIII	+	306580	306586	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	+	341445	341451	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVII	+	366221	366227	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXVI	+	378842	378848	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIV	+	444607	444613	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIV	+	444623	444629	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIV	+	495397	495403	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrX	+	538616	538622	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVII	+	625346	625352	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVII	+	649151	649157	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrVII	+	661850	661856	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	+	679012	679018	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	+	713374	713380	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXIII	+	808423	808429	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	+	931468	931474	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	+	932269	932275	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXII	+	932277	932283	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	+	976406	976412	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrXV	+	1028909	1028915	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	+	1451014	1451020	4.2e-05	0.347	GTACGGA
GTAMGGA	DREME-8	chrIV	+	1507310	1507316	4.2e-05	0.347	GTACGGA

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--NRG1/fimo_out_8 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/background --motif GTAMGGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/AWRI1631--NRG1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/fimo_out_8
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/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.

Go to top

output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/fimo_out_8	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/AWRI1631--NRG1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--NRG1/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