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--NRG1/BY4742--NRG1.fa
  
  Database contains 908 sequences, 357542 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGTTCRA
        7
        GGTTCGA
       
        ATGTAHGG
        8
        ATGTATGG
       
        CTBGGCCA
        8
        CTCGGCCA
       
        TTTCTTB
        7
        TTTCTTT
       
        TAAGGCR
        7
        TAAGGCG
       
        AGTGGTWW
        8
        AGTGGTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CACCCAK
        7
        CACCCAT
       
        CTATCACR
        8
        CTATCACA
       
        ATCKTGAG
        8
        ATCGTGAG
       
        ATTAASAG
        8
        ATTAAGAG
       
        CTATATCK
        8
        CTATATCT
       
        CCGGWCTC
        8
        CCGGTCTC
       
        CASACGC
        7
        CACACGC
       
        GKGGCCCA
        8
        GGGGCCCA
       
        CCAACWGA
        8
        CCAACAGA
       
        TGGCGCAR
        8
        TGGCGCAG
       
        CCAGWTCG
        8
        CCAGATCG
       
        GGRGATCA
        8
        GGGGATCA
       
        ARAAAAAA
        8
        AAAAAAAA
       
        CCGTRCAC
        8
        CCGTACAC
       
        AGMATGGG
        8
        AGAATGGG
       
        CGTGYTAA
        8
        CGTGTTAA
       
        ACTAGAC
        7
        ACTAGAC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/background):

A 0.306 C 0.194 G 0.194 T 0.306

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGTTCRA	7	GGTTCGA
ATGTAHGG	8	ATGTATGG
CTBGGCCA	8	CTCGGCCA
TTTCTTB	7	TTTCTTT
TAAGGCR	7	TAAGGCG
AGTGGTWW	8	AGTGGTTA
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
CACCCAK	7	CACCCAT
CTATCACR	8	CTATCACA
ATCKTGAG	8	ATCGTGAG
ATTAASAG	8	ATTAAGAG
CTATATCK	8	CTATATCT
CCGGWCTC	8	CCGGTCTC
CASACGC	7	CACACGC
GKGGCCCA	8	GGGGCCCA
CCAACWGA	8	CCAACAGA
TGGCGCAR	8	TGGCGCAG
CCAGWTCG	8	CCAGATCG
GGRGATCA	8	GGGGATCA
ARAAAAAA	8	AAAAAAAA
CCGTRCAC	8	CCGTACAC
AGMATGGG	8	AGAATGGG
CGTGYTAA	8	CGTGTTAA
ACTAGAC	7	ACTAGAC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 49 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
CCGGWCTC	DREME-14	chrIII	+	82483	82490	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXIV	+	89100	89107	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrX	+	115960	115967	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXI	+	141039	141046	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrV	-	177140	177147	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrIX	-	197633	197640	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXVI	+	210213	210220	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXIII	-	290842	290849	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrVII	-	328624	328631	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrV	-	354975	354982	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrV	-	354975	354982	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrIX	-	370458	370465	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrVII	+	401548	401555	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrVII	-	483497	483504	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrV	+	487352	487359	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrVII	-	541891	541898	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrII	-	645208	645215	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXII	-	797219	797226	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXV	-	866928	866935	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrXII	+	1004698	1004705	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrIV	+	1017228	1017235	5.03e-06	0.168	CCGGTCTC
CCGGWCTC	DREME-14	chrVIII	-	146246	146253	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrX	-	197317	197324	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrVI	-	204928	204935	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXI	+	219954	219961	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXIII	-	321151	321158	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXV	+	391806	391813	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrIV	+	410438	410445	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXI	+	518047	518054	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXII	-	656938	656945	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrIV	+	721895	721902	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXV	+	762267	762274	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXIII	-	768373	768380	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrVII	+	774408	774415	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrVII	+	774408	774415	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXVI	+	856961	856968	1.01e-05	0.196	CCGGACTC
CCGGWCTC	DREME-14	chrXI	-	99866	99873	1.64e-05	0.289	CCGGCCTC
CCGGWCTC	DREME-14	chrIX	+	129924	129931	1.64e-05	0.289	CCGGCCTC
CCGGWCTC	DREME-14	chrIX	+	324498	324505	1.64e-05	0.289	CCGGCCTC
CCGGWCTC	DREME-14	chrXVI	+	880493	880500	1.64e-05	0.289	CCGGCCTC
CCGGWCTC	DREME-14	chrXII	+	84191	84198	2.79e-05	0.399	CCGGTCAC
CCGGWCTC	DREME-14	chrXIII	+	91726	91733	2.79e-05	0.399	CCGGTCGC
CCGGWCTC	DREME-14	chrXIII	+	91726	91733	2.79e-05	0.399	CCGGTCGC
CCGGWCTC	DREME-14	chrXV	-	160078	160085	2.79e-05	0.399	CCGGTCAC
CCGGWCTC	DREME-14	chrXV	-	160078	160085	2.79e-05	0.399	CCGGTCAC
CCGGWCTC	DREME-14	chrXVI	-	450987	450994	2.79e-05	0.399	CCGGTCCC
CCGGWCTC	DREME-14	chrVII	-	661876	661883	2.79e-05	0.399	CCGGTCGC
CCGGWCTC	DREME-14	chrXII	-	737993	738000	2.79e-05	0.399	CCGGTCAC
CCGGWCTC	DREME-14	chrIV	+	1080615	1080622	2.79e-05	0.399	CCGGTCGC

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--NRG1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/background --motif CCGGWCTC /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/BY4742--NRG1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/BY4742--NRG1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--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.

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output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--NRG1/BY4742--NRG1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--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