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NanR matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/NanR/NanR.EcolK12_2nt_upstream.7.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 /NanR.EcolK12_2nt_upstream.7.meme_quality_logo
; Input files
;	input	/NanR.EcolK12_2nt_upstream.7.meme_quality_matrix.tf
;	prior	/NanR.EcolK12_2nt_upstream.7.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/NanR.EcolK12_2nt_upstream.7.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	0	8	0	9	0	0	3
C	0	0	1	0	9	9	0
G	0	1	0	0	0	0	0
T	9	0	8	0	0	0	6
//
A  0.0  0.8  0.0  0.9  0.0  0.0  0.3
C  0.0  0.0  0.1  0.0  0.9  0.9  0.0
G  0.0  0.1  0.0  0.0  0.0  0.0  0.0
T  0.9  0.0  0.8  0.0  0.0  0.0  0.6
//
A -2.3  1.0 -2.3  1.2 -2.3 -2.3  0.1
C -2.3 -2.3 -0.5 -2.3  1.5  1.5 -2.3
G -2.3 -0.5 -2.3 -2.3 -2.3 -2.3 -2.3
T  1.1 -2.3  1.0 -2.3 -2.3 -2.3  0.8
//
A -0.1  0.9 -0.1  1.1 -0.1 -0.1  0.0
C -0.0 -0.0 -0.1 -0.0  1.4  1.4 -0.0
G -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0
T  1.1 -0.1  0.9 -0.1 -0.1 -0.1  0.5
//
; Sites	9
>site_0
TATACCT
>site_1
TATACCT
>site_2
TATACCT
>site_3
TATACCT
>site_4
TATACCT
>site_5
TATACCA
>site_6
TATACCA
>site_7
TATACCA
>site_8
TGCACCT
;
; Matrix parameters
;	Number of sites              	9
;	Columns                      	7
;	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                    	TATACCW
;	AC                           	TATACCW
;	id                           	TATACCW
;	name                         	TATACCW
;	description                  	TATACCw
;	statistical_basis            	9 sequences
;	sites                        	9
;	nb_sites                     	9
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.96987
;	information.per.column       	0.852838
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	TATACCt
;	consensus.strict.rc          	AGGTATA
;	consensus.IUPAC              	TATACCw
;	consensus.IUPAC.rc           	WGGTATA
;	consensus.regexp             	TATACC[at]
;	consensus.regexp.rc          	[AT]GGTATA
;	residues.content.crude.freq  	a:0.3175|c:0.3016|g:0.0159|t:0.3651
;	G+C.content.crude.freq       	0.31746
;	residues.content.corrected.freq	a:0.3148|c:0.2922|g:0.0347|t:0.3583
;	G+C.content.corrected.freq   	0.326898
;	min(P(S|M))                  	1.49884e-12
;	max(P(S|M))                  	0.317247
;	proba_range                  	0.317247
;	Wmin                         	-16.2
;	Wmax                         	8.2
;	Wrange                       	24.4
; logo file:/NanR.EcolK12_2nt_upstream.7.meme_quality_logo_m1.png
; logo file:/NanR.EcolK12_2nt_upstream.7.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161029
; Job done	2019-06-03.161030
; Seconds	0.6
;	user	0.6
;	system	0.05
;	cuser	0.41
;	csystem	0.04
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