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--CIN5/BY4742--CIN5.fa
  
  Database contains 971 sequences, 478765 residues

  MOTIFS /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/dreme_out/dreme.xml (DNA)
  
        MOTIF
        WIDTH
        
         BEST POSSIBLE MATCH
        
        GGWTCGA
        7
        GGTTCGA
       
        TGTAYGGR
        8
        TGTATGGA
       
        CTBGGCCA
        8
        CTCGGCCA
       
        BTAAGGCG
        8
        TTAAGGCG
       
        GCKCTACC
        8
        GCGCTACC
       
        AGAARA
        6
        AGAAAA
       
        TAGTGGTW
        8
        TAGTGGTA
       
        CAWAACCG
        8
        CATAACCG
       
        CRCCCA
        6
        CACCCA
       
        CTATCACR
        8
        CTATCACG
       
        TTACRTAA
        8
        TTACATAA
       
        ATTAASAG
        8
        ATTAAGAG
       
        CTCTCSCA
        8
        CTCTCCCA
       
        GCKTCTGA
        8
        GCTTCTGA
       
        AGATCGKG
        8
        AGATCGGG
       
        ATSTGTTG
        8
        ATGTGTTG
       
        CGCGGGSA
        8
        CGCGGGGA
       
        ATGGCAAC
        8
        ATGGCAAC
       
        GATGATRA
        8
        GATGATGA
       
        ACTGAGCT
        8
        ACTGAGCT
       
        GRCCACGA
        8
        GACCACGA
       
        GTGGAGAY
        8
        GTGGAGAT
       
Random model letter frequencies (/srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/background):

A 0.310 C 0.190 G 0.190 T 0.310

MOTIF	WIDTH	BEST POSSIBLE MATCH
GGWTCGA	7	GGTTCGA
TGTAYGGR	8	TGTATGGA
CTBGGCCA	8	CTCGGCCA
BTAAGGCG	8	TTAAGGCG
GCKCTACC	8	GCGCTACC
AGAARA	6	AGAAAA
TAGTGGTW	8	TAGTGGTA
CAWAACCG	8	CATAACCG
CRCCCA	6	CACCCA
CTATCACR	8	CTATCACG
TTACRTAA	8	TTACATAA
ATTAASAG	8	ATTAAGAG
CTCTCSCA	8	CTCTCCCA
GCKTCTGA	8	GCTTCTGA
AGATCGKG	8	AGATCGGG
ATSTGTTG	8	ATGTGTTG
CGCGGGSA	8	CGCGGGGA
ATGGCAAC	8	ATGGCAAC
GATGATRA	8	GATGATGA
ACTGAGCT	8	ACTGAGCT
GRCCACGA	8	GACCACGA
GTGGAGAY	8	GTGGAGAT

SECTION I: HIGH-SCORING MOTIF OCCURENCES

There were 87 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
CAWAACCG	DREME-8	chrVII	+	192	199	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXI	+	219	226	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXV	+	261	268	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrIV	+	307	314	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrIII	+	524	531	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	5747	5754	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIV	+	6848	6855	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXII	+	11510	11517	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	24668	24675	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	24668	24675	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	24668	24675	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	24668	24675	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVII	+	73878	73885	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVIII	+	85347	85354	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXI	+	308193	308200	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVII	+	365561	365568	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	372494	372501	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVII	+	412343	412350	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	420637	420644	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXV	+	663861	663868	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXII	+	687908	687915	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrII	+	796776	796783	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIII	+	914970	914977	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVIII	-	103912	103919	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrX	-	378375	378382	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXI	-	379695	379702	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrV	-	438715	438722	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrV	-	469472	469479	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVIII	-	556693	556700	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXI	-	666479	666486	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXII	-	674133	674140	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXIV	-	783858	783865	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrVII	-	823497	823504	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXII	-	856854	856861	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrXII	-	1064866	1064873	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrIV	-	1525198	1525205	1.2e-05	0.314	CATAACCG
CAWAACCG	DREME-8	chrV	+	131117	131124	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrV	+	157824	157831	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrV	+	157824	157831	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrIII	+	168336	168343	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXIV	+	241512	241519	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	+	448685	448692	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrIV	+	645188	645195	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrIV	+	802766	802773	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	+	837752	837759	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	+	837752	837759	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	+	837752	837759	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	+	837752	837759	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXIII	+	887421	887428	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrVIII	-	134348	134355	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrV	-	250313	250320	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrII	-	350854	350861	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXII	-	427002	427009	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrVII	-	481525	481532	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrVII	-	481525	481532	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrVII	-	481525	481532	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrIV	-	520999	521006	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrXV	-	621881	621888	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrIV	-	1345552	1345559	2.41e-05	0.338	CAAAACCG
CAWAACCG	DREME-8	chrI	+	72429	72436	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrI	+	72429	72436	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXII	+	167142	167149	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrX	+	204574	204581	3.88e-05	0.42	CACAACCG
CAWAACCG	DREME-8	chrXIII	+	303032	303039	3.88e-05	0.42	CACAACCG
CAWAACCG	DREME-8	chrII	+	606008	606015	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXV	+	620640	620647	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXIII	+	808281	808288	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrXVI	-	339004	339011	3.88e-05	0.42	CACAACCG
CAWAACCG	DREME-8	chrXVI	-	572500	572507	3.88e-05	0.42	CACAACCG
CAWAACCG	DREME-8	chrVII	-	649190	649197	3.88e-05	0.42	CAGAACCG
CAWAACCG	DREME-8	chrIV	-	915931	915938	3.88e-05	0.42	CAGAACCG

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--CIN5/fimo_out_9 --bgfile /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/background --motif CAWAACCG /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/dreme_out/dreme.xml /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/BY4742--CIN5.fa

Settings:


  
    output_directory = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/fimo_out_9
    MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/dreme_out/dreme.xml
    sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/BY4742--CIN5.fa
  
  
    background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/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/BY4742--CIN5/fimo_out_9	MEME file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/dreme_out/dreme.xml	sequence file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/BY4742--CIN5.fa
background file name = /srv/www/kundaje/amr1/yeastvar/meme_results/results/aa_results/BY4742--CIN5/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