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AcrR matrix and aligment

matrix-quality result

Command: 
AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_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 AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_quality_logo
; Input files
;	input	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_quality_matrix.tf
;	prior	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_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	1	3	0	1	1	4	0	0	0	0
C	3	0	0	0	3	0	1	0	0	1
G	0	1	0	0	0	0	0	0	0	3
T	0	0	4	3	0	0	3	4	4	0
//
a  0.3  0.7  0.1  0.3  0.3  0.9  0.1  0.1  0.1  0.1
c  0.6  0.0  0.0  0.0  0.6  0.0  0.2  0.0  0.0  0.2
g  0.0  0.2  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.6
t  0.1  0.1  0.9  0.7  0.1  0.1  0.7  0.9  0.9  0.1
//
a -0.1  0.8 -1.6 -0.1 -0.1  1.1 -1.6 -1.6 -1.6 -1.6
c  1.1 -1.6 -1.6 -1.6  1.1 -1.6  0.2 -1.6 -1.6  0.2
g -1.6  0.2 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6  1.1
t -1.6 -1.6  1.1  0.8 -1.6 -1.6  0.8  1.1  1.1 -1.6
//
a -0.0  0.5 -0.1 -0.0 -0.0  0.9 -0.1 -0.1 -0.1 -0.1
c  0.7 -0.1 -0.1 -0.1  0.7 -0.1  0.0 -0.1 -0.1  0.0
g -0.1  0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.7
t -0.1 -0.1  0.9  0.5 -0.1 -0.1  0.5  0.9  0.9 -0.1
//
; Sites	4
>site_0
CATACATTTG
>site_1
CATTCATTTG
>site_2
CATTCATTTC
>site_3
AGTTAACTTG
;
; Matrix parameters
;	Columns                      	10
;	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                    	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons1
;	AC                           	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons1
;	id                           	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons1
;	name                         	AcrR.1nt_upstream-noorf-ovlp-2str.10.cons1
;	description                  	CrTtCAyTTS
;	statistical_basis            	4 sequences
;	sites                        	4
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.58544
;	information.per.column       	0.558544
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	CaTtCAtTTG
;	consensus.strict.rc          	CAAATGAATG
;	consensus.IUPAC              	CrTtCAyTTS
;	consensus.IUPAC.rc           	SAARTGAAYG
;	consensus.regexp             	C[ag]TtCA[ct]TT[CG]
;	consensus.regexp.rc          	[CG]AA[AG]TGAA[CT]G
;	residues.content.crude.freq  	a:0.2500|c:0.2000|g:0.1000|t:0.4500
;	G+C.content.crude.freq       	0.3
;	residues.content.corrected.freq	a:0.2581|c:0.2016|g:0.1210|t:0.4193
;	G+C.content.corrected.freq   	0.32255
;	min(P(S|M))                  	1.9229e-14
;	max(P(S|M))                  	0.0411016
;	proba_range                  	0.0411016
;	Wmin                         	-16.1
;	Wmax                         	10.1
;	Wrange                       	26.2
; logo file:AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_quality_logo_m1.png
; logo file:AcrR.1nt_upstream-noorf-ovlp-2str.10.cons_quality_logo_m1_rc.png
; Host name	compute-1-2.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.48
;	csystem	0.05
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