RegulonDB

Ada matrix and aligment

matrix-quality result

Command: 
Ada.1nt_upstream-noorf-ovlp-2str.19.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 Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality_logo
; Input files
;	input	Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality_matrix.tf
;	prior	Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Bernoulli model (order=0)
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29063
;		c	0.20784
;		g	0.20492
;		t	0.29662
A	3	3	2	3	3	3	0	0	3	3	3	2	1	0	0	4	2	0	3
C	1	0	0	1	1	1	0	2	1	0	0	0	2	2	4	0	0	3	0
G	0	0	1	0	0	0	2	0	0	0	0	2	0	2	0	0	2	1	1
T	0	1	1	0	0	0	2	2	0	1	1	0	1	0	0	0	0	0	0
//
a  0.7  0.7  0.5  0.7  0.7  0.7  0.1  0.1  0.7  0.7  0.7  0.5  0.3  0.1  0.1  0.9  0.5  0.1  0.7
c  0.2  0.0  0.0  0.2  0.2  0.2  0.0  0.4  0.2  0.0  0.0  0.0  0.4  0.4  0.8  0.0  0.0  0.6  0.0
g  0.0  0.0  0.2  0.0  0.0  0.0  0.4  0.0  0.0  0.0  0.0  0.4  0.0  0.4  0.0  0.0  0.4  0.2  0.2
t  0.1  0.3  0.3  0.1  0.1  0.1  0.5  0.5  0.1  0.3  0.3  0.1  0.3  0.1  0.1  0.1  0.1  0.1  0.1
//
a  0.8  0.8  0.5  0.8  0.8  0.8 -1.6 -1.6  0.8  0.8  0.8  0.5 -0.1 -1.6 -1.6  1.1  0.5 -1.6  0.8
c  0.2 -1.6 -1.6  0.2  0.2  0.2 -1.6  0.8  0.2 -1.6 -1.6 -1.6  0.8  0.8  1.4 -1.6 -1.6  1.1 -1.6
g -1.6 -1.6  0.2 -1.6 -1.6 -1.6  0.8 -1.6 -1.6 -1.6 -1.6  0.8 -1.6  0.8 -1.6 -1.6  0.8  0.2  0.2
t -1.6 -0.1 -0.1 -1.6 -1.6 -1.6  0.4  0.4 -1.6 -0.1 -0.1 -1.6 -0.1 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6
//
a  0.5  0.5  0.2  0.5  0.5  0.5 -0.1 -0.1  0.5  0.5  0.5  0.2 -0.0 -0.1 -0.1  0.9  0.2 -0.1  0.5
c  0.0 -0.1 -0.1  0.0  0.0  0.0 -0.1  0.3  0.0 -0.1 -0.1 -0.1  0.3  0.3  1.2 -0.1 -0.1  0.7 -0.1
g -0.1 -0.1  0.0 -0.1 -0.1 -0.1  0.3 -0.1 -0.1 -0.1 -0.1  0.3 -0.1  0.3 -0.1 -0.1  0.3  0.0  0.0
t -0.1 -0.0 -0.0 -0.1 -0.1 -0.1  0.2  0.2 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	19
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.2906296|c:0.2078359|g:0.2049154|t:0.2966191
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	marmmmkymaarcsCArSr
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	8.13474
;	information.per.column       	0.428144
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	aaaaaagcaaagcgCAgCa
;	consensus.strict.rc          	TGCTGCGCTTTGCTTTTTT
;	consensus.IUPAC              	marmmmkymaarcsCArSr
;	consensus.IUPAC.rc           	YSYTGSGYTTKRMKKKYTK
;	consensus.regexp             	[ac]a[ag][ac][ac][ac][gt][ct][ac]aa[ag]c[cg]CA[ag][CG][ag]
;	consensus.regexp.rc          	[CT][CG][CT]TG[CG]G[CT]TT[GT][AG][AC][GT][GT][GT][CT]T[GT]
;	residues.content.crude.freq  	a:0.5000|c:0.2368|g:0.1447|t:0.1184
;	G+C.content.crude.freq       	0.381579
;	residues.content.corrected.freq	a:0.4581|c:0.2310|g:0.1568|t:0.1541
;	G+C.content.corrected.freq   	0.387813
;	min(P(S|M))                  	9.41342e-27
;	max(P(S|M))                  	4.24472e-05
;	proba_range                  	4.24472e-05
;	Wmin                         	-30.6
;	Wmax                         	16
;	Wrange                       	46.6
; logo file:Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality_logo_m1.png
; logo file:Ada.1nt_upstream-noorf-ovlp-2str.19.meme_quality_logo_m1_rc.png
; Host name	compute-1-1.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.3
;	user	0.3
;	system	0.06
;	cuser	0.5
;	csystem	0.05
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