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--AFT2/YJM789--AFT2.fa
  
  Database contains 485 sequences, 150880 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        TGTAYGGR
        8
        TGTATGGG
       
        BGGTTCGA
        8
        GGGTTCGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CTWRACC
        7
        CTTAACC
       
        GCKCTACC
        8
        GCGCTACC
       
        CRCCCA
        6
        CACCCA
       
        ATGGCAWC
        8
        ATGGCAAC
       
        ATAGTKTA
        8
        ATAGTGTA
       
        GGYTATCA
        8
        GGCTATCA
       
        GTCTGRC
        7
        GTCTGAC
       
        CACCGTGS
        8
        CACCGTGG
       
        AAGGCGCM
        8
        AAGGCGCC
       
        TTTCTTB
        7
        TTTCTTT
       
        GGATTTKA
        8
        GGATTTTA
       
        TGGCGYA
        7
        TGGCGCA
       
        TAATCAKA
        8
        TAATCATA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        CYTGCGC
        7
        CTTGCGC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/background):

A 0.307 C 0.193 G 0.193 T 0.307

MOTIF	WIDTH	BEST POSSIBLE MATCH
TGTAYGGR	8	TGTATGGG
BGGTTCGA	8	GGGTTCGA
CTBGGCCA	8	CTCGGCCA
CTWRACC	7	CTTAACC
GCKCTACC	8	GCGCTACC
CRCCCA	6	CACCCA
ATGGCAWC	8	ATGGCAAC
ATAGTKTA	8	ATAGTGTA
GGYTATCA	8	GGCTATCA
GTCTGRC	7	GTCTGAC
CACCGTGS	8	CACCGTGG
AAGGCGCM	8	AAGGCGCC
TTTCTTB	7	TTTCTTT
GGATTTKA	8	GGATTTTA
TGGCGYA	7	TGGCGCA
TAATCAKA	8	TAATCATA
ACTGAGCT	8	ACTGAGCT
CYTGCGC	7	CTTGCGC

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 29 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
TAATCAKA	DREME-16	chrXIII	-	131854	131861	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrV	+	138699	138706	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrXI	-	162516	162523	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrX	+	355407	355414	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrX	+	355407	355414	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrX	-	374535	374542	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrVII	+	405503	405510	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrII	+	405911	405918	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrIV	+	568915	568922	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrXII	-	673964	673971	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrVII	+	736373	736380	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrXIII	-	747921	747928	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrVII	-	828752	828759	3.13e-05	0.711	TAATCAGA
TAATCAKA	DREME-16	chrVII	+	122303	122310	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrV	-	135454	135461	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrIII	-	151313	151320	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrVII	-	185743	185750	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrVI	-	226717	226724	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrIX	-	257586	257593	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrIX	-	300257	300264	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrX	+	415000	415007	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrV	+	431464	431471	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrV	-	435781	435788	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrXI	+	458761	458768	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrXIII	-	480650	480657	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrVII	+	561556	561563	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrVII	+	876428	876435	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrIV	+	1201784	1201791	8.14e-05	0.828	TAATCATA
TAATCAKA	DREME-16	chrIV	-	1352495	1352502	8.14e-05	0.828	TAATCATA

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--AFT2/fimo_out_16 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/background --motif TAATCAKA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/fimo_out_16
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/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--AFT2/fimo_out_16	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/YJM789--AFT2.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/YJM789--AFT2/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