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Dan matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/Dan/Dan.EcolK12_1nt_upstream.11.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 /Dan.EcolK12_1nt_upstream.11.meme_quality_logo
; Input files
;	input	/Dan.EcolK12_1nt_upstream.11.meme_quality_matrix.tf
;	prior	/Dan.EcolK12_1nt_upstream.11.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/Dan.EcolK12_1nt_upstream.11.meme_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	0.29093
;		c	0.20756
;		g	0.20418
;		t	0.29732
A	1	3	1	1	1	0	0	2	5	0	0
C	3	1	2	2	0	0	0	1	0	0	0
G	0	1	1	0	4	0	1	1	0	0	0
T	1	0	1	2	0	5	4	1	0	5	5
//
A  0.2  0.5  0.2  0.2  0.2  0.0  0.0  0.4  0.9  0.0  0.0
C  0.5  0.2  0.4  0.4  0.0  0.0  0.0  0.2  0.0  0.0  0.0
G  0.0  0.2  0.2  0.0  0.7  0.0  0.2  0.2  0.0  0.0  0.0
T  0.2  0.0  0.2  0.4  0.0  0.9  0.7  0.2  0.0  0.9  0.9
//
A -0.3  0.6 -0.3 -0.3 -0.3 -1.8 -1.8  0.3  1.1 -1.8 -1.8
C  0.9 -0.0  0.6  0.6 -1.8 -1.8 -1.8 -0.0 -1.8 -1.8 -1.8
G -1.8 -0.0 -0.0 -1.8  1.2 -1.8 -0.0 -0.0 -1.8 -1.8 -1.8
T -0.3 -1.8 -0.3  0.3 -1.8  1.1  0.9 -0.3 -1.8  1.1  1.1
//
A -0.1  0.3 -0.1 -0.1 -0.1 -0.1 -0.1  0.1  1.0 -0.1 -0.1
C  0.5 -0.0  0.2  0.2 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1
G -0.1 -0.0 -0.0 -0.1  0.9 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1
T -0.1 -0.1 -0.1  0.1 -0.1  1.0  0.6 -0.1 -0.1  1.0  1.0
//
; Sites	5
>site_0
CATCGTTAATT
>site_1
AACTGTTAATT
>site_2
TCGCGTTGATT
>site_3
CGCAGTGTATT
>site_4
CAATATTCATT
;
; Matrix parameters
;	Number of sites              	5
;	Columns                      	11
;	Rows                         	4
;	Alphabet                     	A|C|G|T
;	Prior                        	A:0.290929484294843|C:0.207560750607506|G:0.204184816848168|T:0.297324948249482|a:0.290929484294843|c:0.207560750607506|g:0.204184816848168|t:0.297324948249482
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	CANHGTTNATT
;	AC                           	CANHGTTNATT
;	id                           	CANHGTTNATT
;	name                         	CANHGTTNATT
;	description                  	cacyGTtaATT
;	statistical_basis            	5 sequences
;	sites                        	5
;	nb_sites                     	5
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.98555
;	information.per.column       	0.453232
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	caccGTtaATT
;	consensus.strict.rc          	AATTAACGGTG
;	consensus.IUPAC              	cacyGTtaATT
;	consensus.IUPAC.rc           	AATTAACRGTG
;	consensus.regexp             	cac[ct]GTtaATT
;	consensus.regexp.rc          	AATTAAC[AG]GTG
;	residues.content.crude.freq  	a:0.2545|c:0.1636|g:0.1455|t:0.4364
;	G+C.content.crude.freq       	0.309091
;	residues.content.corrected.freq	a:0.2606|c:0.1710|g:0.1552|t:0.4132
;	G+C.content.corrected.freq   	0.3262
;	min(P(S|M))                  	3.71009e-15
;	max(P(S|M))                  	0.00480351
;	proba_range                  	0.00480351
;	Wmin                         	-16.8
;	Wmax                         	9.5
;	Wrange                       	26.3
; logo file:/Dan.EcolK12_1nt_upstream.11.meme_quality_logo_m1.png
; logo file:/Dan.EcolK12_1nt_upstream.11.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.160931
; Job done	2019-06-03.160931
; Seconds	0.58
;	user	0.58
;	system	0.07
;	cuser	0.4
;	csystem	0.05
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