RegulonDB

CRP matrix and aligment

matrix-quality result

Command: 
CRP.2nt_upstream-noorf-ovlp-2str.22.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 CRP.2nt_upstream-noorf-ovlp-2str.22.meme_quality_logo
; Input files
;	input	CRP.2nt_upstream-noorf-ovlp-2str.22.meme_quality_matrix.tf
;	prior	CRP.2nt_upstream-noorf-ovlp-2str.22.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	CRP.2nt_upstream-noorf-ovlp-2str.22.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	110	37	37	26	34	192	63	67	52	112	50	129	18	25	231	22	190	86	90	71	51	57
C	43	39	16	48	5	32	47	83	71	32	77	37	15	221	2	224	13	60	19	22	34	41
G	27	23	146	18	195	18	45	41	47	57	79	41	15	12	15	6	41	20	0	20	16	50
T	80	161	61	168	26	18	105	69	90	59	54	53	212	2	12	8	16	94	151	147	159	112
//
a  0.4  0.1  0.1  0.1  0.1  0.7  0.2  0.3  0.2  0.4  0.2  0.5  0.1  0.1  0.9  0.1  0.7  0.3  0.3  0.3  0.2  0.2
c  0.2  0.2  0.1  0.2  0.0  0.1  0.2  0.3  0.3  0.1  0.3  0.1  0.1  0.8  0.0  0.9  0.1  0.2  0.1  0.1  0.1  0.2
g  0.1  0.1  0.6  0.1  0.7  0.1  0.2  0.2  0.2  0.2  0.3  0.2  0.1  0.0  0.1  0.0  0.2  0.1  0.0  0.1  0.1  0.2
t  0.3  0.6  0.2  0.6  0.1  0.1  0.4  0.3  0.3  0.2  0.2  0.2  0.8  0.0  0.0  0.0  0.1  0.4  0.6  0.6  0.6  0.4
//
a  0.4 -0.7 -0.7 -1.1 -0.8  0.9 -0.2 -0.1 -0.4  0.4 -0.4  0.5 -1.4 -1.1  1.1 -1.2  0.9  0.1  0.2 -0.1 -0.4 -0.3
c -0.2 -0.3 -1.2 -0.1 -2.3 -0.5 -0.1  0.4  0.3 -0.5  0.4 -0.4 -1.3  1.4 -3.2  1.4 -1.4  0.1 -1.0 -0.9 -0.5 -0.3
g -0.7 -0.8  1.0 -1.1  1.3 -1.1 -0.2 -0.3 -0.1  0.1  0.4 -0.3 -1.3 -1.5 -1.3 -2.2 -0.3 -1.0 -5.6 -1.0 -1.2 -0.1
t  0.0  0.7 -0.2  0.8 -1.1 -1.4  0.3 -0.1  0.2 -0.3 -0.4 -0.4  1.0 -3.5 -1.8 -2.2 -1.6  0.2  0.7  0.6  0.7  0.4
//
a  0.2 -0.1 -0.1 -0.1 -0.1  0.7 -0.0 -0.0 -0.1  0.2 -0.1  0.3 -0.1 -0.1  1.0 -0.1  0.7  0.0  0.1 -0.0 -0.1 -0.1
c -0.0 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0  0.1  0.1 -0.1  0.1 -0.1 -0.1  1.2 -0.0  1.2 -0.1  0.0 -0.1 -0.1 -0.1 -0.0
g -0.1 -0.1  0.6 -0.1  1.0 -0.1 -0.0 -0.0 -0.0  0.0  0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0
t  0.0  0.5 -0.1  0.5 -0.1 -0.1  0.1 -0.0  0.1 -0.1 -0.1 -0.1  0.8 -0.0 -0.1 -0.1 -0.1  0.1  0.4  0.4  0.4  0.2
//
; Sites	
;
; Matrix parameters
;	Columns                      	22
;	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                  	wtGtGatcyrsaTCACahwttt
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.0948
;	information.per.column       	0.322491
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	atGtGatccagaTCACattttt
;	consensus.strict.rc          	AAAAATGTGATCTGGATCACAT
;	consensus.IUPAC              	wtGtGatcyrsaTCACahwttt
;	consensus.IUPAC.rc           	AAAWDTGTGATSYRGATCACAW
;	consensus.regexp             	[at]tGtGatc[ct][ag][cg]aTCACa[act][at]ttt
;	consensus.regexp.rc          	AAA[AT][AGT]TGTGAT[CG][CT][AG]GATCACA[AT]
;	residues.content.crude.freq  	a:0.3059|c:0.2065|g:0.1629|t:0.3247
;	G+C.content.crude.freq       	0.369406
;	residues.content.corrected.freq	a:0.3059|c:0.2065|g:0.1631|t:0.3245
;	G+C.content.corrected.freq   	0.369572
;	min(P(S|M))                  	2.25156e-28
;	max(P(S|M))                  	1.77634e-06
;	proba_range                  	1.77634e-06
;	Wmin                         	-30.7
;	Wmax                         	16
;	Wrange                       	46.7
; logo file:CRP.2nt_upstream-noorf-ovlp-2str.22.meme_quality_logo_m1.png
; logo file:CRP.2nt_upstream-noorf-ovlp-2str.22.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	0.33
;	user	0.33
;	system	0.04
;	cuser	0.56
;	csystem	0.07
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