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GalR matrix and aligment

matrix-quality result

Command: 
GalR.2nt_upstream-noorf-ovlp-2str.15.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 GalR.2nt_upstream-noorf-ovlp-2str.15.meme_quality_logo
; Input files
;	input	GalR.2nt_upstream-noorf-ovlp-2str.15.meme_quality_matrix.tf
;	prior	GalR.2nt_upstream-noorf-ovlp-2str.15.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	GalR.2nt_upstream-noorf-ovlp-2str.15.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	4	12	12	4	1	3	3	0	2	3	2	10	3	3
C	0	0	0	0	6	8	0	6	0	0	5	9	0	6	2
G	12	0	0	0	0	0	9	0	0	3	2	1	2	0	0
T	0	8	0	0	2	3	0	3	12	7	2	0	0	3	7
//
a  0.0  0.3  0.9  0.9  0.3  0.1  0.3  0.3  0.0  0.2  0.3  0.2  0.8  0.3  0.3
c  0.0  0.0  0.0  0.0  0.5  0.6  0.0  0.5  0.0  0.0  0.4  0.7  0.0  0.5  0.2
g  0.9  0.0  0.0  0.0  0.0  0.0  0.7  0.0  0.0  0.2  0.2  0.1  0.2  0.0  0.0
t  0.0  0.6  0.0  0.0  0.2  0.3  0.0  0.3  0.9  0.6  0.2  0.0  0.0  0.3  0.6
//
a -2.6  0.1  1.2  1.2  0.1 -1.1 -0.1 -0.1 -2.6 -0.5 -0.1 -0.5  1.0 -0.1 -0.1
c -2.6 -2.6 -2.6 -2.6  0.8  1.1 -2.6  0.8 -2.6 -2.6  0.7  1.2 -2.6  0.8 -0.2
g  1.5 -2.6 -2.6 -2.6 -2.6 -2.6  1.2 -2.6 -2.6  0.2 -0.2 -0.8 -0.2 -2.6 -2.6
t -2.6  0.8 -2.6 -2.6 -0.5 -0.2 -2.6 -0.2  1.2  0.6 -0.5 -2.6 -2.6 -0.2  0.6
//
a -0.1  0.0  1.1  1.1  0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1  0.8 -0.0 -0.0
c -0.0 -0.0 -0.0 -0.0  0.4  0.7 -0.0  0.4 -0.0 -0.0  0.3  0.9 -0.0  0.4 -0.0
g  1.4 -0.0 -0.0 -0.0 -0.0 -0.0  0.9 -0.0 -0.0  0.0 -0.0 -0.1 -0.0 -0.0 -0.0
t -0.1  0.5 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0  1.1  0.4 -0.1 -0.1 -0.1 -0.0  0.4
//
; Sites	
;
; Matrix parameters
;	Columns                      	15
;	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                  	GwAAmCGcTkcCAct
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	8.69482
;	information.per.column       	0.579655
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	GtAAcCGcTtcCAct
;	consensus.strict.rc          	AGTGGAAGCGGTTAC
;	consensus.IUPAC              	GwAAmCGcTkcCAct
;	consensus.IUPAC.rc           	AGTGGMAGCGKTTWC
;	consensus.regexp             	G[at]AA[ac]CGcT[gt]cCAct
;	consensus.regexp.rc          	AGTGG[AC]AGCG[GT]TT[AT]C
;	residues.content.crude.freq  	a:0.3444|c:0.2333|g:0.1611|t:0.2611
;	G+C.content.crude.freq       	0.394444
;	residues.content.corrected.freq	a:0.3403|c:0.2314|g:0.1645|t:0.2638
;	G+C.content.corrected.freq   	0.39586
;	min(P(S|M))                  	1.51396e-26
;	max(P(S|M))                  	0.00174516
;	proba_range                  	0.00174516
;	Wmin                         	-36.5
;	Wmax                         	14.9
;	Wrange                       	51.4
; logo file:GalR.2nt_upstream-noorf-ovlp-2str.15.meme_quality_logo_m1.png
; logo file:GalR.2nt_upstream-noorf-ovlp-2str.15.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	0.31
;	user	0.31
;	system	0.04
;	cuser	0.5
;	csystem	0.06
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