MraZ matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/MraZ/MraZ.EcolK12_2nt_upstream.8.meme 

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 /MraZ.EcolK12_2nt_upstream.8.meme_quality_logo
; Input files
;	input	/MraZ.EcolK12_2nt_upstream.8.meme_quality_matrix.tf
;	prior	/MraZ.EcolK12_2nt_upstream.8.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/MraZ.EcolK12_2nt_upstream.8.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29114
;		c	0.20781
;		g	0.20402
;		t	0.29702
A	2	1	0	0	0	1	5	3
C	0	0	0	0	0	0	0	1
G	1	4	0	6	6	5	1	0
T	3	1	6	0	0	0	0	2
//
A  0.3  0.2  0.0  0.0  0.0  0.2  0.8  0.5
C  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.2
G  0.2  0.6  0.0  0.9  0.9  0.7  0.2  0.0
T  0.5  0.2  0.9  0.0  0.0  0.0  0.0  0.3
//
A  0.1 -0.5 -1.9 -1.9 -1.9 -0.5  1.0  0.5
C -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2
G -0.2  1.1 -1.9  1.5  1.5  1.3 -0.2 -1.9
T  0.5 -0.5  1.1 -1.9 -1.9 -1.9 -1.9  0.1
//
A  0.0 -0.1 -0.1 -0.1 -0.1 -0.1  0.7  0.2
C -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0
G -0.0  0.6 -0.1  1.3  1.3  1.0 -0.0 -0.1
T  0.2 -0.1  1.0 -0.1 -0.1 -0.1 -0.1  0.0
//
; Sites	6
>site_0
AGTGGGAA
>site_1
AGTGGGAA
>site_2
TGTGGGGC
>site_3
TGTGGAAA
>site_4
TATGGGAT
>site_5
GTTGGGAT
;
; Matrix parameters
;	Number of sites              	6
;	Columns                      	8
;	Rows                         	4
;	Alphabet                     	A|C|G|T
;	Prior                        	A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	WGTGGGAW
;	AC                           	WGTGGGAW
;	id                           	WGTGGGAW
;	name                         	WGTGGGAW
;	description                  	wGTGGGaw
;	statistical_basis            	6 sequences
;	sites                        	6
;	nb_sites                     	6
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.00725
;	information.per.column       	0.625906
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	tGTGGGaa
;	consensus.strict.rc          	TTCCCACA
;	consensus.IUPAC              	wGTGGGaw
;	consensus.IUPAC.rc           	WTCCCACW
;	consensus.regexp             	[at]GTGGGa[at]
;	consensus.regexp.rc          	[AT]TCCCAC[AT]
;	residues.content.crude.freq  	a:0.2500|c:0.0208|g:0.4792|t:0.2500
;	G+C.content.crude.freq       	0.5
;	residues.content.corrected.freq	a:0.2559|c:0.0475|g:0.4399|t:0.2567
;	G+C.content.corrected.freq   	0.487405
;	min(P(S|M))                  	5.81548e-13
;	max(P(S|M))                  	0.0528105
;	proba_range                  	0.0528105
;	Wmin                         	-15.6
;	Wmax                         	8.4
;	Wrange                       	24
; logo file:/MraZ.EcolK12_2nt_upstream.8.meme_quality_logo_m1.png
; logo file:/MraZ.EcolK12_2nt_upstream.8.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161029
; Job done	2019-06-03.161030
; Seconds	0.59
;	user	0.59
;	system	0.06
;	cuser	0.37
;	csystem	0.05