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/RM11-1A--CAD1/RM11-1A--CAD1.fa
  
  Database contains 468 sequences, 146138 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGDTCGA
        7
        GGTTCGA
       
        AYCCRTAC
        8
        ACCCATAC
       
        AGTGGTW
        7
        AGTGGTT
       
        CGCSTTA
        7
        CGCCTTA
       
        CCAACTK
        7
        CCAACTT
       
        ATGGCAWC
        8
        ATGGCAAC
       
        CTATCACR
        8
        CTATCACA
       
        CGGTAGC
        7
        CGGTAGC
       
        AKCGTGA
        7
        ATCGTGA
       
        CGTGGMG
        7
        CGTGGAG
       
        SAAGAAA
        7
        GAAGAAA
       
        CRCCCA
        6
        CACCCA
       
        AGTCAKAC
        8
        AGTCATAC
       
        CGTGYTAA
        8
        CGTGTTAA
       
        CTTGTTRG
        8
        CTTGTTGG
       
        GCSACAA
        7
        GCGACAA
       
        TAAKCGCA
        8
        TAAGCGCA
       
        AATCTTYT
        8
        AATCTTCT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/background):

A 0.308 C 0.192 G 0.192 T 0.308

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGDTCGA	7	GGTTCGA
AYCCRTAC	8	ACCCATAC
AGTGGTW	7	AGTGGTT
CGCSTTA	7	CGCCTTA
CCAACTK	7	CCAACTT
ATGGCAWC	8	ATGGCAAC
CTATCACR	8	CTATCACA
CGGTAGC	7	CGGTAGC
AKCGTGA	7	ATCGTGA
CGTGGMG	7	CGTGGAG
SAAGAAA	7	GAAGAAA
CRCCCA	6	CACCCA
AGTCAKAC	8	AGTCATAC
CGTGYTAA	8	CGTGTTAA
CTTGTTRG	8	CTTGTTGG
GCSACAA	7	GCGACAA
TAAKCGCA	8	TAAGCGCA
AATCTTYT	8	AATCTTCT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 22 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
AKCGTGA	DREME-9	chrIII	+	82500	82506	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrX	+	115977	115983	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXI	+	141056	141062	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXVI	+	210230	210236	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrVII	+	401565	401571	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	+	487369	487375	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	-	85833	85839	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXI	-	140979	140985	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	-	177124	177130	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXIII	-	290826	290832	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	328608	328614	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	-	354959	354965	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	-	355064	355070	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrIX	-	370442	370448	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrX	-	374622	374628	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXI	-	379772	379778	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrV	-	431194	431200	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	438872	438878	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	460622	460628	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrVII	-	541875	541881	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrII	-	645192	645198	3.97e-05	0.517	AGCGTGA
AKCGTGA	DREME-9	chrXII	-	797203	797209	3.97e-05	0.517	AGCGTGA

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/RM11-1A--CAD1/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/background --motif AKCGTGA /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/RM11-1A--CAD1.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/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/RM11-1A--CAD1/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/RM11-1A--CAD1.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/RM11-1A--CAD1/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