RegulonDB

Fur matrix and aligment

matrix-quality result

Command: 
Fur.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 Fur.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo
; Input files
;	input	Fur.2nt_upstream-noorf-ovlp-2str.18.meme_quality_matrix.tf
;	prior	Fur.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	Fur.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	44	38	2	8	41	7	39	37	3	4	42	2	8	28	2	5	36	13
C	1	2	5	2	2	0	0	5	9	13	1	6	1	4	10	28	3	9
G	3	3	0	34	1	15	1	0	8	22	5	1	0	3	7	0	5	0
T	0	5	41	4	4	26	8	6	28	9	0	39	39	13	29	15	4	26
//
a  0.9  0.8  0.0  0.2  0.8  0.1  0.8  0.8  0.1  0.1  0.9  0.0  0.2  0.6  0.0  0.1  0.7  0.3
c  0.0  0.0  0.1  0.0  0.0  0.0  0.0  0.1  0.2  0.3  0.0  0.1  0.0  0.1  0.2  0.6  0.1  0.2
g  0.1  0.1  0.0  0.7  0.0  0.3  0.0  0.0  0.2  0.5  0.1  0.0  0.0  0.1  0.1  0.0  0.1  0.0
t  0.0  0.1  0.8  0.1  0.1  0.5  0.2  0.1  0.6  0.2  0.0  0.8  0.8  0.3  0.6  0.3  0.1  0.5
//
a  1.1  1.0 -1.8 -0.5  1.1 -0.7  1.0  1.0 -1.5 -1.2  1.1 -1.8 -0.5  0.7 -1.8 -1.0  0.9 -0.1
c -2.1 -1.5 -0.7 -1.5 -1.5 -3.9 -3.9 -0.7 -0.1  0.3 -2.1 -0.5 -2.1 -0.9  0.0  1.0 -1.2 -0.1
g -1.1 -1.1 -3.9  1.2 -2.1  0.4 -2.1 -3.9 -0.2  0.8 -0.7 -2.1 -3.9 -1.1 -0.3 -3.9 -0.7 -3.9
t -3.9 -1.0  1.0 -1.2 -1.2  0.6 -0.6 -0.8  0.7 -0.4 -3.9  1.0  1.0 -0.1  0.7  0.1 -1.2  0.6
//
a  1.0  0.8 -0.1 -0.1  0.9 -0.1  0.8  0.7 -0.1 -0.1  0.9 -0.1 -0.1  0.4 -0.1 -0.1  0.7 -0.0
c -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0  0.1 -0.1 -0.1 -0.1 -0.1  0.0  0.6 -0.1 -0.0
g -0.1 -0.1 -0.0  0.9 -0.1  0.1 -0.1 -0.0 -0.0  0.4 -0.1 -0.1 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0
t -0.0 -0.1  0.9 -0.1 -0.1  0.3 -0.1 -0.1  0.4 -0.1 -0.0  0.8  0.8 -0.0  0.4  0.0 -0.1  0.3
//
; 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                  	AaTGAkAatsAttayYat
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.07096
;	information.per.column       	0.503942
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	AaTGAtAatgAttatCat
;	consensus.strict.rc          	ATGATAATCATTATCATT
;	consensus.IUPAC              	AaTGAkAatsAttayYat
;	consensus.IUPAC.rc           	ATRRTAATSATTMTCATT
;	consensus.regexp             	AaTGA[gt]Aat[cg]Atta[ct][CT]at
;	consensus.regexp.rc          	AT[AG][AG]TAAT[CG]ATT[AC]TCATT
;	residues.content.crude.freq  	a:0.4155|c:0.1169|g:0.1250|t:0.3426
;	G+C.content.crude.freq       	0.241898
;	residues.content.corrected.freq	a:0.4130|c:0.1188|g:0.1266|t:0.3416
;	G+C.content.corrected.freq   	0.245387
;	min(P(S|M))                  	1.21437e-33
;	max(P(S|M))                  	0.00131574
;	proba_range                  	0.00131574
;	Wmin                         	-49.2
;	Wmax                         	16.6
;	Wrange                       	65.8
; logo file:Fur.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1.png
; logo file:Fur.2nt_upstream-noorf-ovlp-2str.18.meme_quality_logo_m1_rc.png
; Host name	compute-1-6.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.53
;	csystem	0.06
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