RegulonDB

FeaR matrix and aligment

matrix-quality result

Command: 
FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality

Figures

Matrix logo

Decreasing cumulative distributions (dCDF)

Decreasing cumulative distributions (dCDF), logarithmic Y axis

ROC curve (logarithmic X axis)

Matrix information

; convert-matrix  -v 1 -from transfac -i FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality_logo
; Input files
;	input	FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality_matrix.tf
;	prior	FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29086
;		c	0.20809
;		g	0.20476
;		t	0.29629
A	0	0	0	0	3	0	4	0	0	0	1	2	1	4	3	3
C	0	1	1	3	0	4	0	2	4	0	0	2	3	0	0	0
G	1	3	1	0	1	0	0	2	0	1	3	0	0	0	1	1
T	3	0	2	1	0	0	0	0	0	3	0	0	0	0	0	0
//
a  0.1  0.1  0.1  0.1  0.7  0.1  0.9  0.1  0.1  0.1  0.3  0.5  0.3  0.9  0.7  0.7
c  0.0  0.2  0.2  0.6  0.0  0.8  0.0  0.4  0.8  0.0  0.0  0.4  0.6  0.0  0.0  0.0
g  0.2  0.6  0.2  0.0  0.2  0.0  0.0  0.4  0.0  0.2  0.6  0.0  0.0  0.0  0.2  0.2
t  0.7  0.1  0.5  0.3  0.1  0.1  0.1  0.1  0.1  0.7  0.1  0.1  0.1  0.1  0.1  0.1
//
a -1.6 -1.6 -1.6 -1.6  0.8 -1.6  1.1 -1.6 -1.6 -1.6 -0.1  0.5 -0.1  1.1  0.8  0.8
c -1.6  0.1  0.1  1.1 -1.6  1.4 -1.6  0.8  1.4 -1.6 -1.6  0.8  1.1 -1.6 -1.6 -1.6
g  0.2  1.1  0.2 -1.6  0.2 -1.6 -1.6  0.8 -1.6  0.2  1.1 -1.6 -1.6 -1.6  0.2  0.2
t  0.8 -1.6  0.4 -0.1 -1.6 -1.6 -1.6 -1.6 -1.6  0.8 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6
//
a -0.1 -0.1 -0.1 -0.1  0.5 -0.1  0.9 -0.1 -0.1 -0.1 -0.0  0.2 -0.0  0.9  0.5  0.5
c -0.1  0.0  0.0  0.7 -0.1  1.2 -0.1  0.3  1.2 -0.1 -0.1  0.3  0.7 -0.1 -0.1 -0.1
g  0.0  0.7  0.0 -0.1  0.0 -0.1 -0.1  0.3 -0.1  0.0  0.7 -0.1 -0.1 -0.1  0.0  0.0
t  0.5 -0.1  0.2 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1  0.5 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	16
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.29085999082|c:0.208089935287|g:0.204758708047|t:0.296291365846
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	kSbCrCAsCkGmCArr
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	8.5168
;	information.per.column       	0.5323
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	tGtCaCAgCtGcCAaa
;	consensus.strict.rc          	TTTGGCAGCTGTGACA
;	consensus.IUPAC              	kSbCrCAsCkGmCArr
;	consensus.IUPAC.rc           	YYTGKCMGSTGYGVSM
;	consensus.regexp             	[gt][CG][cgt]C[ag]CA[cg]C[gt]G[ac]CA[ag][ag]
;	consensus.regexp.rc          	[CT][CT]TG[GT]C[AC]G[CG]TG[CT]G[ACG][CG][AC]
;	residues.content.crude.freq  	a:0.3281|c:0.3125|g:0.2188|t:0.1406
;	G+C.content.crude.freq       	0.53125
;	residues.content.corrected.freq	a:0.3207|c:0.2916|g:0.2160|t:0.1718
;	G+C.content.corrected.freq   	0.50757
;	min(P(S|M))                  	1.97576e-22
;	max(P(S|M))                  	0.00101588
;	proba_range                  	0.00101588
;	Wmin                         	-25.8
;	Wmax                         	15.6
;	Wrange                       	41.4
; logo file:FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality_logo_m1.png
; logo file:FeaR.2nt_upstream-noorf-ovlp-2str.16.meme_quality_logo_m1_rc.png
; Host name	compute-1-2.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.33
;	user	0.33
;	system	0.04
;	cuser	0.49
;	csystem	0.06
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