RegulonDB

ArgP matrix and aligment

matrix-quality result

Command: 
ArgP.1nt_upstream-noorf-ovlp-2str.18.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 ArgP.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo
; Input files
;	input	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons_quality_matrix.tf
;	prior	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	ArgP.1nt_upstream-noorf-ovlp-2str.18.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	7	5	3	9	3	2	5	0	0	5	6	4	0	8	3	6	6	4
C	8	1	0	1	2	0	0	3	7	2	9	0	0	0	3	4	0	8
G	1	0	4	0	0	3	8	0	7	4	1	3	5	6	3	0	6	1
T	0	10	9	6	11	11	3	13	2	5	0	9	11	2	7	6	4	3
//
a  0.4  0.3  0.2  0.5  0.2  0.1  0.3  0.0  0.0  0.3  0.4  0.3  0.0  0.5  0.2  0.4  0.4  0.3
c  0.5  0.1  0.0  0.1  0.1  0.0  0.0  0.2  0.4  0.1  0.5  0.0  0.0  0.0  0.2  0.2  0.0  0.5
g  0.1  0.0  0.2  0.0  0.0  0.2  0.5  0.0  0.4  0.2  0.1  0.2  0.3  0.4  0.2  0.0  0.4  0.1
t  0.0  0.6  0.5  0.4  0.7  0.7  0.2  0.8  0.1  0.3  0.0  0.5  0.7  0.1  0.4  0.4  0.3  0.2
//
a  0.4  0.1 -0.4  0.6 -0.4 -0.8  0.1 -2.8 -2.8  0.1  0.2 -0.1 -2.8  0.5 -0.4  0.2  0.2 -0.1
c  0.8 -1.1 -2.8 -1.1 -0.5 -2.8 -2.8 -0.1  0.7 -0.5  1.0 -2.8 -2.8 -2.8 -0.1  0.2 -2.8  0.8
g -1.1 -2.8  0.2 -2.8 -2.8 -0.1  0.9 -2.8  0.7  0.2 -1.1 -0.1  0.4  0.6 -0.1 -2.8  0.6 -1.1
t -2.8  0.7  0.6  0.2  0.8  0.8 -0.4  1.0 -0.8  0.0 -2.8  0.6  0.8 -0.8  0.4  0.2 -0.2 -0.4
//
a  0.2  0.0 -0.1  0.3 -0.1 -0.1  0.0 -0.0 -0.0  0.0  0.1 -0.0 -0.0  0.3 -0.1  0.1  0.1 -0.0
c  0.4 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0  0.3 -0.1  0.5 -0.0 -0.0 -0.0 -0.0  0.0 -0.0  0.4
g -0.1 -0.0  0.0 -0.0 -0.0 -0.0  0.4 -0.0  0.3  0.0 -0.1 -0.0  0.1  0.2 -0.0 -0.0  0.2 -0.1
t -0.0  0.4  0.3  0.1  0.5  0.5 -0.1  0.8 -0.1  0.0 -0.0  0.3  0.5 -0.1  0.2  0.1 -0.0 -0.1
//
; Sites	16
>site_0
ATGCCTTTCACTGATATC
>site_1
ATGAAGGTGTCTTATAAC
>site_2
CTTATAATCCCTGGGCGA
>site_3
GTTATTGTTAAATGCTAA
>site_4
CTTACATTCGCTTATATA
>site_5
CAGATTATGTGATGACTC
>site_6
CTTTTTGCTAATGATTGC
>site_7
ATATAGATGGCTTATTAA
>site_8
CCTATTATGCCGTTCAAG
>site_9
AATTTTGTGTCAGGTTGC
>site_10
AAAATTGTGTCATAGTGC
>site_11
AATATTATCAATTTCCGC
>site_12
CTGATTGCCAATTAATAT
>site_13
CTTTTGTTCGAGTGGAGT
>site_14
CAATATGCGGCGTAAATC
>site_15
ATTTTTGTCTATGGTCAT
;
; Matrix parameters
;	Columns                      	18
;	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                    	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons1
;	AC                           	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons1
;	id                           	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons1
;	name                         	ArgP.1nt_upstream-noorf-ovlp-2str.18.cons1
;	description                  	mwkwttrtsdmtkrthrc
;	statistical_basis            	16 sequences
;	sites                        	16
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.86991
;	information.per.column       	0.326106
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	cttattgtggcttgtagc
;	consensus.strict.rc          	GCTACAAGCCACAATAAG
;	consensus.IUPAC              	mwkwttrtsdmtkrthrc
;	consensus.IUPAC.rc           	GYDAYMAKHSAYAAWMWK
;	consensus.regexp             	[ac][at][gt][at]tt[ag]t[cg][agt][ac]t[gt][ag]t[act][ag]c
;	consensus.regexp.rc          	G[CT][AGT]A[CT][AC]A[GT][ACT][CG]A[CT]AA[AT][AC][AT][GT]
;	residues.content.crude.freq  	a:0.2639|c:0.1667|g:0.1806|t:0.3889
;	G+C.content.crude.freq       	0.347222
;	residues.content.corrected.freq	a:0.2655|c:0.1691|g:0.1820|t:0.3835
;	G+C.content.corrected.freq   	0.351077
;	min(P(S|M))                  	9.38241e-32
;	max(P(S|M))                  	5.24686e-06
;	proba_range                  	5.24686e-06
;	Wmin                         	-44.5
;	Wmax                         	12.2
;	Wrange                       	56.7
; logo file:ArgP.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo_m1.png
; logo file:ArgP.1nt_upstream-noorf-ovlp-2str.18.cons_quality_logo_m1_rc.png
; Host name	compute-1-9.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.51
;	csystem	0.05
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