RegulonDB

FadR matrix and aligment

matrix-quality result

Command: 
FadR.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 FadR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo
; Input files
;	input	FadR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix.tf
;	prior	FadR.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	FadR.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	5	1	2	0	3	0	4	1	0	13	1	1	7	1	3	3	4	9
C	1	12	0	0	0	1	12	4	0	1	8	6	0	5	0	2	8	0
G	7	3	0	16	12	0	0	4	15	1	1	5	0	9	1	3	2	3
T	3	0	14	0	1	15	0	7	1	1	6	4	9	1	12	8	2	4
//
a  0.3  0.1  0.1  0.0  0.2  0.0  0.3  0.1  0.0  0.8  0.1  0.1  0.4  0.1  0.2  0.2  0.3  0.5
c  0.1  0.7  0.0  0.0  0.0  0.1  0.7  0.2  0.0  0.1  0.5  0.4  0.0  0.3  0.0  0.1  0.5  0.0
g  0.4  0.2  0.0  1.0  0.7  0.0  0.0  0.2  0.9  0.1  0.1  0.3  0.0  0.5  0.1  0.2  0.1  0.2
t  0.2  0.0  0.8  0.0  0.1  0.9  0.0  0.4  0.1  0.1  0.4  0.3  0.5  0.1  0.7  0.5  0.1  0.3
//
a  0.1 -1.3 -0.8 -2.8 -0.4 -2.8 -0.1 -1.3 -2.8  1.0 -1.3 -1.3  0.4 -1.3 -0.4 -0.4 -0.1  0.6
c -1.1  1.2 -2.8 -2.8 -2.8 -1.1  1.2  0.2 -2.8 -1.1  0.8  0.6 -2.8  0.4 -2.8 -0.5  0.8 -2.8
g  0.7 -0.1 -2.8  1.5  1.3 -2.8 -2.8  0.2  1.5 -1.1 -1.1  0.4 -2.8  1.0 -1.1 -0.1 -0.5 -0.1
t -0.4 -2.8  1.0 -2.8 -1.4  1.1 -2.8  0.4 -1.4 -1.4  0.2 -0.2  0.6 -1.4  0.9  0.5 -0.8 -0.2
//
a  0.0 -0.1 -0.1 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0  0.8 -0.1 -0.1  0.2 -0.1 -0.1 -0.1 -0.0  0.3
c -0.1  0.9 -0.0 -0.0 -0.0 -0.1  0.9  0.0 -0.0 -0.1  0.4  0.2 -0.0  0.1 -0.0 -0.1  0.4 -0.0
g  0.3 -0.0 -0.0  1.5  0.9 -0.0 -0.0  0.0  1.3 -0.1 -0.1  0.1 -0.0  0.5 -0.1 -0.0 -0.1 -0.0
t -0.1 -0.0  0.9 -0.0 -0.1  1.0 -0.0  0.2 -0.1 -0.1  0.1 -0.0  0.3 -0.1  0.6  0.2 -0.1 -0.0
//
; 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                  	rCTGGTCbGayswsttca
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.39783
;	information.per.column       	0.522101
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	gCTGGTCtGacctgttca
;	consensus.strict.rc          	TGAACAGGTCAGACCAGC
;	consensus.IUPAC              	rCTGGTCbGayswsttca
;	consensus.IUPAC.rc           	TGAASWSRTCVGACCAGY
;	consensus.regexp             	[ag]CTGGTC[cgt]Ga[ct][cg][at][cg]ttca
;	consensus.regexp.rc          	TGAA[CG][AT][CG][AG]TC[ACG]GACCAG[CT]
;	residues.content.crude.freq  	a:0.2014|c:0.2083|g:0.2847|t:0.3056
;	G+C.content.crude.freq       	0.493056
;	residues.content.corrected.freq	a:0.2067|c:0.2083|g:0.2800|t:0.3050
;	G+C.content.corrected.freq   	0.488338
;	min(P(S|M))                  	2.65325e-28
;	max(P(S|M))                  	0.000165169
;	proba_range                  	0.000165169
;	Wmin                         	-37.5
;	Wmax                         	16.9
;	Wrange                       	54.4
; logo file:FadR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1.png
; logo file:FadR.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1_rc.png
; Host name	compute-1-7.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.32
;	user	0.32
;	system	0.04
;	cuser	0.5
;	csystem	0.06
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