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--MAC1/BY4742--MAC1.fa
  
  Database contains 759 sequences, 310680 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GRVTCGAA
        8
        GAATCGAA
       
        AGTGGTW
        7
        AGTGGTT
       
        TGTAYGGR
        8
        TGTATGGA
       
        AACTKGGC
        8
        AACTTGGC
       
        AARAAAWA
        8
        AAAAAAAA
       
        GCKCTACC
        8
        GCGCTACC
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ACCCAVAC
        8
        ACCCACAC
       
        GYGGTCTA
        8
        GTGGTCTA
       
        AGAYCGGG
        8
        AGATCGGG
       
        CCTTAAMC
        8
        CCTTAACC
       
        ACACTATA
        8
        ACACTATA
       
        GCGCCA
        6
        GCGCCA
       
        CTATCACR
        8
        CTATCACA
       
        CASACGC
        7
        CACACGC
       
        CRTGCTAA
        8
        CGTGCTAA
       
        CGCGGGSA
        8
        CGCGGGGA
       
        AAAGCRTG
        8
        AAAGCGTG
       
        TAKCTCA
        7
        TATCTCA
       
        GGCCMAAC
        8
        GGCCCAAC
       
        CTKCGGTC
        8
        CTTCGGTC
       
        GAYCTCCA
        8
        GATCTCCA
       
        TCCGTGSA
        8
        TCCGTGGA
       
        CCAAMAGA
        8
        CCAACAGA
       
        TCTAATCW
        8
        TCTAATCA
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background):

A 0.313 C 0.187 G 0.187 T 0.313

MOTIF	WIDTH	BEST POSSIBLE MATCH
GRVTCGAA	8	GAATCGAA
AGTGGTW	7	AGTGGTT
TGTAYGGR	8	TGTATGGA
AACTKGGC	8	AACTTGGC
AARAAAWA	8	AAAAAAAA
GCKCTACC	8	GCGCTACC
ATGGCAWC	8	ATGGCAAC
ACCCAVAC	8	ACCCACAC
GYGGTCTA	8	GTGGTCTA
AGAYCGGG	8	AGATCGGG
CCTTAAMC	8	CCTTAACC
ACACTATA	8	ACACTATA
GCGCCA	6	GCGCCA
CTATCACR	8	CTATCACA
CASACGC	7	CACACGC
CRTGCTAA	8	CGTGCTAA
CGCGGGSA	8	CGCGGGGA
AAAGCRTG	8	AAAGCGTG
TAKCTCA	7	TATCTCA
GGCCMAAC	8	GGCCCAAC
CTKCGGTC	8	CTTCGGTC
GAYCTCCA	8	GATCTCCA
TCCGTGSA	8	TCCGTGGA
CCAAMAGA	8	CCAACAGA
TCTAATCW	8	TCTAATCA

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 43 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
TAKCTCA	DREME-19	chrII	+	36404	36410	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	+	115494	115500	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	+	282583	282589	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXIII	+	352286	352292	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrIV	+	359583	359589	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXIV	+	374875	374881	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrX	+	422943	422949	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXV	+	438649	438655	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	+	535122	535128	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXI	+	578971	578977	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrII	+	645334	645340	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	+	645822	645828	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	+	645822	645828	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	799641	799647	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	837743	837749	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	837743	837749	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	837743	837749	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	875382	875388	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrIV	+	884367	884373	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	+	975947	975953	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXV	+	976427	976433	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrIV	+	1175835	1175841	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrV	-	99974	99980	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	-	122225	122231	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVI	-	157993	157999	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXV	-	216509	216515	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVIII	-	237925	237931	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXIII	-	298573	298579	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXIII	-	298573	298579	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVIII	-	358555	358561	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrX	-	391101	391107	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrII	-	393056	393062	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrII	-	393056	393062	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	-	440793	440799	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	-	560275	560281	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXIII	-	572941	572947	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	-	605418	605424	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	-	622617	622623	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	-	701034	701040	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrVII	-	701034	701040	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXVI	-	769288	769294	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrXII	-	781710	781716	6.28e-05	0.894	TAGCTCA
TAKCTCA	DREME-19	chrIV	-	1095447	1095453	6.28e-05	0.894	TAGCTCA

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--MAC1/fimo_out_18 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/background --motif TAKCTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/fimo_out_18
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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--MAC1/fimo_out_18	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/BY4742--MAC1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--MAC1/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