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--MOT1/AWRI1631--MOT1.fa
  
  Database contains 685 sequences, 217269 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGHTCGA
        7
        GGTTCGA
       
        ACCCANAC
        8
        ACCCATAC
       
        CTBGGCCA
        8
        CTCGGCCA
       
        CGCSTTA
        7
        CGCCTTA
       
        GCKCTACC
        8
        GCGCTACC
       
        AACCACTW
        8
        AACCACTT
       
        SAAGA
        5
        CAAGA
       
        ATGYACGG
        8
        ATGTACGG
       
        TGGCGYA
        7
        TGGCGCA
       
        ACGRTG
        6
        ACGATG
       
        ATGWGATA
        8
        ATGTGATA
       
        AGTCAKAC
        8
        AGTCATAC
       
        CTWGACC
        7
        CTAGACC
       
        AAAGCGWG
        8
        AAAGCGTG
       
        AATGGTCA
        8
        AATGGTCA
       
        CTTAAYCA
        8
        CTTAATCA
       
        ATAGTGTA
        8
        ATAGTGTA
       
        GGTCTCY
        7
        GGTCTCC
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/background):

A 0.301 C 0.199 G 0.199 T 0.301

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGHTCGA	7	GGTTCGA
ACCCANAC	8	ACCCATAC
CTBGGCCA	8	CTCGGCCA
CGCSTTA	7	CGCCTTA
GCKCTACC	8	GCGCTACC
AACCACTW	8	AACCACTT
SAAGA	5	CAAGA
ATGYACGG	8	ATGTACGG
TGGCGYA	7	TGGCGCA
ACGRTG	6	ACGATG
ATGWGATA	8	ATGTGATA
AGTCAKAC	8	AGTCATAC
CTWGACC	7	CTAGACC
AAAGCGWG	8	AAAGCGTG
AATGGTCA	8	AATGGTCA
CTTAAYCA	8	CTTAATCA
ATAGTGTA	8	ATAGTGTA
GGTCTCY	7	GGTCTCC

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
AATGGTCA	DREME-15	chrX	+	204747	204754	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrVI	+	223474	223481	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrX	+	233951	233958	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrX	+	355468	355475	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	+	374367	374374	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrII	+	405972	405979	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrII	+	405972	405979	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	+	427144	427151	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXI	+	490980	490987	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrX	+	541520	541527	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrIV	+	568976	568983	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXV	+	571970	571977	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	+	576219	576226	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	+	793930	793937	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	+	811536	811543	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrIII	-	58184	58191	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrV	-	85144	85151	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXIV	-	102823	102830	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrIX	-	324353	324360	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXI	-	334722	334729	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXV	-	340350	340357	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrX	-	374474	374481	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrV	-	492403	492410	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXI	-	513382	513389	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXIV	-	519149	519156	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrVII	-	544627	544634	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrIV	-	620020	620027	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrX	-	652423	652430	1.95e-05	0.285	AATGGTCA
AATGGTCA	DREME-15	chrXII	-	951213	951220	1.95e-05	0.285	AATGGTCA

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--MOT1/fimo_out_12 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/background --motif AATGGTCA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/AWRI1631--MOT1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/fimo_out_12
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/AWRI1631--MOT1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/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--MOT1/fimo_out_12	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/AWRI1631--MOT1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/AWRI1631--MOT1/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