RegulonDB

ArgR matrix and aligment

matrix-quality result

Command: 
ArgR.2nt_upstream-noorf-ovlp-2str.18.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 ArgR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo
; Input files
;	input	ArgR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix.tf
;	prior	ArgR.2nt_upstream-noorf-ovlp-2str.18.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	ArgR.2nt_upstream-noorf-ovlp-2str.18.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	19	8	5	3	19	23	3	11	8	5	4	27	6	1	0	28	10	16
C	2	6	5	3	4	3	1	0	2	0	8	0	2	3	28	0	5	0
G	2	8	1	23	3	1	1	1	0	1	0	1	0	14	0	0	3	1
T	6	7	18	0	3	2	24	17	19	23	17	1	21	11	1	1	11	12
//
a  0.6  0.3  0.2  0.1  0.6  0.8  0.1  0.4  0.3  0.2  0.1  0.9  0.2  0.0  0.0  0.9  0.3  0.5
c  0.1  0.2  0.2  0.1  0.1  0.1  0.0  0.0  0.1  0.0  0.3  0.0  0.1  0.1  0.9  0.0  0.2  0.0
g  0.1  0.3  0.0  0.8  0.1  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.5  0.0  0.0  0.1  0.0
t  0.2  0.2  0.6  0.0  0.1  0.1  0.8  0.6  0.6  0.8  0.6  0.0  0.7  0.4  0.0  0.0  0.4  0.4
//
a  0.8 -0.1 -0.5 -1.0  0.8  1.0 -1.0  0.3 -0.1 -0.5 -0.7  1.1 -0.3 -1.9 -3.4  1.2  0.2  0.6
c -1.0 -0.0 -0.2 -0.7 -0.4 -0.7 -1.6 -3.4 -1.0 -3.4  0.3 -3.4 -1.0 -0.7  1.5 -3.4 -0.2 -3.4
g -1.0  0.3 -1.6  1.3 -0.7 -1.6 -1.6 -1.6 -3.4 -1.6 -3.4 -1.6 -3.4  0.8 -3.4 -3.4 -0.7 -1.6
t -0.3 -0.2  0.7 -3.4 -1.0 -1.4  1.0  0.7  0.8  1.0  0.7 -1.9  0.9  0.2 -1.9 -1.9  0.2  0.3
//
a  0.5 -0.0 -0.1 -0.1  0.5  0.8 -0.1  0.1 -0.0 -0.1 -0.1  1.0 -0.1 -0.1 -0.0  1.1  0.1  0.3
c -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0  0.1 -0.0 -0.1 -0.1  1.4 -0.0 -0.0 -0.0
g -0.1  0.1 -0.1  1.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.0  0.4 -0.0 -0.0 -0.1 -0.1
t -0.1 -0.0  0.4 -0.0 -0.1 -0.1  0.8  0.4  0.5  0.7  0.4 -0.1  0.6  0.1 -0.1 -0.1  0.1  0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	18
;	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                  	agtGaaTwttyAtkCAww
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	8.76658
;	information.per.column       	0.487032
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	agtGaaTttttAtgCAta
;	consensus.strict.rc          	TATGCATAAAAATTCACT
;	consensus.IUPAC              	agtGaaTwttyAtkCAww
;	consensus.IUPAC.rc           	WWTGMATRAAWATTCACT
;	consensus.regexp             	agtGaaT[at]tt[ct]At[gt]CA[at][at]
;	consensus.regexp.rc          	[AT][AT]TG[AC]AT[AG]AA[AT]ATTCACT
;	residues.content.crude.freq  	a:0.3755|c:0.1379|g:0.1149|t:0.3716
;	G+C.content.crude.freq       	0.252874
;	residues.content.corrected.freq	a:0.3727|c:0.1403|g:0.1179|t:0.3691
;	G+C.content.corrected.freq   	0.258206
;	min(P(S|M))                  	1.63773e-31
;	max(P(S|M))                  	0.000311966
;	proba_range                  	0.000311966
;	Wmin                         	-43.8
;	Wmax                         	15.4
;	Wrange                       	59.2
; logo file:ArgR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1.png
; logo file:ArgR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1_rc.png
; Host name	compute-1-5.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.3
;	user	0.3
;	system	0.05
;	cuser	0.51
;	csystem	0.06
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