RegulonDB

GadW matrix and aligment

matrix-quality result

Command: 
GadW.1nt_upstream-noorf-ovlp-2str.20.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 GadW.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo
; Input files
;	input	GadW.1nt_upstream-noorf-ovlp-2str.20.cons_quality_matrix.tf
;	prior	GadW.1nt_upstream-noorf-ovlp-2str.20.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	GadW.1nt_upstream-noorf-ovlp-2str.20.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	6	3	5	14	0	6	0	4	9	9	0	8	3	3	9	4	9	11	7	5
C	11	1	1	0	1	1	2	0	0	0	7	3	1	3	1	0	4	6	0	0
G	0	3	9	0	0	3	4	0	4	0	0	5	2	2	1	3	0	0	2	8
T	0	10	2	3	16	7	11	13	4	8	10	1	11	9	6	10	4	0	8	4
//
a  0.3  0.2  0.3  0.8  0.0  0.3  0.0  0.2  0.5  0.5  0.0  0.5  0.2  0.2  0.5  0.2  0.5  0.6  0.4  0.3
c  0.6  0.1  0.1  0.0  0.1  0.1  0.1  0.0  0.0  0.0  0.4  0.2  0.1  0.2  0.1  0.0  0.2  0.3  0.0  0.0
g  0.0  0.2  0.5  0.0  0.0  0.2  0.2  0.0  0.2  0.0  0.0  0.3  0.1  0.1  0.1  0.2  0.0  0.0  0.1  0.5
t  0.0  0.6  0.1  0.2  0.9  0.4  0.6  0.7  0.2  0.5  0.6  0.1  0.6  0.5  0.3  0.6  0.2  0.0  0.5  0.2
//
a  0.2 -0.5  0.0  1.0 -2.9  0.2 -2.9 -0.2  0.6  0.6 -2.9  0.5 -0.5 -0.5  0.6 -0.2  0.6  0.8  0.3  0.0
c  1.1 -1.1 -1.1 -2.9 -1.1 -1.1 -0.5 -2.9 -2.9 -2.9  0.7 -0.2 -1.1 -0.2 -1.1 -2.9  0.1  0.5 -2.9 -2.9
g -2.9 -0.1  0.9 -2.9 -2.9 -0.1  0.1 -2.9  0.1 -2.9 -2.9  0.3 -0.5 -0.5 -1.1 -0.1 -2.9 -2.9 -0.5  0.8
t -2.9  0.7 -0.8 -0.5  1.1  0.3  0.7  0.9 -0.2  0.4  0.7 -1.4  0.7  0.6  0.2  0.7 -0.2 -2.9  0.4 -0.2
//
a  0.1 -0.1  0.0  0.8 -0.0  0.1 -0.0 -0.0  0.3  0.3 -0.0  0.2 -0.1 -0.1  0.3 -0.0  0.3  0.5  0.1  0.0
c  0.7 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 -0.0 -0.0  0.3 -0.0 -0.1 -0.0 -0.1 -0.0  0.0  0.2 -0.0 -0.0
g -0.0 -0.0  0.5 -0.0 -0.0 -0.0  0.0 -0.0  0.0 -0.0 -0.0  0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.0 -0.1  0.4
t -0.0  0.4 -0.1 -0.1  1.0  0.1  0.5  0.7 -0.1  0.2  0.4 -0.1  0.5  0.3  0.1  0.4 -0.1 -0.0  0.2 -0.1
//
; Sites	17
>site_0
AAAATATTATTCGCGTAATA
>site_1
CATATTGTATTGTTTTTCAA
>site_2
CTGATTTTTACGTGATAATT
>site_3
CTAATAGTGATATTTTAAGG
>site_4
AGGATATAAACATCAGACAG
>site_5
CTGATAGTAACGTAAACCTG
>site_6
CTGATTTTGATATTTTCCAT
>site_7
CTCATTGTATTGAAATAAAA
>site_8
AGAATGCAGTCGATTTAATA
>site_9
CCATTTCAAACATTATCATG
>site_10
CTGATATTTTCCGTAGTCAG
>site_11
CTTATGTTTATAAAAAAATG
>site_12
CTGATCTTATTTCCAGTAAA
>site_13
AGGATTTTGTTATTTAAATT
>site_14
AAGTCGTTTTTCTGCTTAGG
>site_15
ATAATATAAACATTTAACAT
>site_16
CTGTTTTTAATATTATCATG
;
; Matrix parameters
;	Columns                      	20
;	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                    	GadW.1nt_upstream-noorf-ovlp-2str.20.cons1
;	AC                           	GadW.1nt_upstream-noorf-ovlp-2str.20.cons1
;	id                           	GadW.1nt_upstream-noorf-ovlp-2str.20.cons1
;	name                         	GadW.1nt_upstream-noorf-ovlp-2str.20.cons1
;	description                  	MtrATwktrwyrttwtmmwr
;	statistical_basis            	17 sequences
;	sites                        	17
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.2702
;	information.per.column       	0.36351
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	CtgATtttaatattataatg
;	consensus.strict.rc          	CATTATAATATTAAAATCAG
;	consensus.IUPAC              	MtrATwktrwyrttwtmmwr
;	consensus.IUPAC.rc           	YWKKAWAAYRWYAMWATYAK
;	consensus.regexp             	[AC]t[ag]AT[at][gt]t[ag][at][ct][ag]tt[at]t[ac][ac][at][ag]
;	consensus.regexp.rc          	[CT][AT][GT][GT]A[AT]AA[CT][AG][AT][CT]A[AC][AT]AT[CT]A[GT]
;	residues.content.crude.freq  	a:0.3382|c:0.1235|g:0.1353|t:0.4029
;	G+C.content.crude.freq       	0.258824
;	residues.content.corrected.freq	a:0.3356|c:0.1282|g:0.1392|t:0.3970
;	G+C.content.corrected.freq   	0.267375
;	min(P(S|M))                  	9.6953e-34
;	max(P(S|M))                  	1.12427e-05
;	proba_range                  	1.12427e-05
;	Wmin                         	-45.2
;	Wmax                         	14.2
;	Wrange                       	59.4
; logo file:GadW.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo_m1.png
; logo file:GadW.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo_m1_rc.png
; Host name	compute-1-5.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.32
;	user	0.32
;	system	0.03
;	cuser	0.52
;	csystem	0.07
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