NsrR matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/NsrR/NsrR.EcolK12_1nt_upstream.15.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 /NsrR.EcolK12_1nt_upstream.15.meme_quality_logo
; Input files
;	input	/NsrR.EcolK12_1nt_upstream.15.meme_quality_matrix.tf
;	prior	/NsrR.EcolK12_1nt_upstream.15.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/NsrR.EcolK12_1nt_upstream.15.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	14	32	39	11	36	0	1	6	25	9	11	9	8	19	13
C	3	0	0	9	0	0	0	22	1	3	3	1	9	7	10
G	6	0	0	15	1	1	38	4	3	7	0	1	7	4	9
T	16	7	0	4	2	38	0	7	10	20	25	28	15	9	7
//
A  0.4  0.8  1.0  0.3  0.9  0.0  0.0  0.2  0.6  0.2  0.3  0.2  0.2  0.5  0.3
C  0.1  0.0  0.0  0.2  0.0  0.0  0.0  0.6  0.0  0.1  0.1  0.0  0.2  0.2  0.3
G  0.2  0.0  0.0  0.4  0.0  0.0  1.0  0.1  0.1  0.2  0.0  0.0  0.2  0.1  0.2
T  0.4  0.2  0.0  0.1  0.1  1.0  0.0  0.2  0.3  0.5  0.6  0.7  0.4  0.2  0.2
//
A  0.2  1.0  1.2 -0.0  1.1 -3.7 -2.2 -0.6  0.8 -0.2 -0.0 -0.2 -0.3  0.5  0.1
C -1.0 -3.7 -3.7  0.1 -3.7 -3.7 -3.7  1.0 -1.9 -1.0 -1.0 -1.9  0.1 -0.1  0.2
G -0.3 -3.7 -3.7  0.6 -1.9 -1.9  1.5 -0.7 -0.9 -0.1 -3.7 -1.9 -0.1 -0.7  0.1
T  0.3 -0.5 -3.7 -1.0 -1.6  1.2 -3.7 -0.5 -0.1  0.5  0.8  0.9  0.3 -0.2 -0.5
//
A  0.1  0.8  1.2 -0.0  1.0 -0.0 -0.1 -0.1  0.5 -0.1 -0.0 -0.1 -0.1  0.2  0.0
C -0.1 -0.0 -0.0  0.0 -0.0 -0.0 -0.0  0.5 -0.1 -0.1 -0.1 -0.1  0.0 -0.0  0.1
G -0.0 -0.0 -0.0  0.2 -0.1 -0.1  1.5 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1  0.0
T  0.1 -0.1 -0.0 -0.1 -0.1  1.1 -0.0 -0.1 -0.0  0.3  0.5  0.6  0.1 -0.1 -0.1
//
; Sites	39
>site_0
TAAGATGCATTTGAG
>site_1
AAAGATGCATTTAAA
>site_2
AAAGATGCATTTCCC
>site_3
TAAAATGCATTTCAA
>site_4
TAAAATGCAATTTAG
>site_5
AAAGATGCATTATCA
>site_6
TAACATGCATTACAA
>site_7
AAAGATGCTGTTTTG
>site_8
AAACATGCTTTTTGC
>site_9
TAAGATGTATTTATA
>site_10
TAAAATGCAAATTAT
>site_11
AAACATGTATATTAA
>site_12
GAACATGCAGTTATG
>site_13
TAAGATGCAAAAAAA
>site_14
TAACATGCTGTTATA
>site_15
AAAGATGAATTTCGT
>site_16
AAACATGGTATTTAC
>site_17
AAAGATGAGTTTTTC
>site_18
AAAGATGAACTTACC
>site_19
TTAGATGTAAATCAC
>site_20
TAAATTGCAATTCAA
>site_21
AAAGAGGCATATTAT
>site_22
TTACATGCACTTACA
>site_23
AAAAATACATTTCAC
>site_24
GAAAATGTTATTTTC
>site_25
AAAAATGCAGCAGTG
>site_26
TTACATGATTATGAG
>site_27
GAAGATGTTGTAAAT
>site_28
TAAAATGCAGAGGAT
>site_29
GAACGTGCATTTTGT
>site_30
AAATATGTAAAATCC
>site_31
GAAAATGTTCTTCGC
>site_32
CAATTTGCATATCAA
>site_33
TAATATGCCGATGAT
>site_34
TTAGATGGAACATTG
>site_35
CAAAATGAGTAAGAA
>site_36
GTAAATGGTTCTTTG
>site_37
TTATATGAGTTATCG
>site_38
CTAGATGGTTTCGCA
;
; Matrix parameters
;	Number of sites              	39
;	Columns                      	15
;	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                    	WAAVATGCATTTHAN
;	AC                           	WAAVATGCATTTHAN
;	id                           	WAAVATGCATTTHAN
;	name                         	WAAVATGCATTTHAN
;	description                  	wAAsATGcatttyav
;	statistical_basis            	39 sequences
;	sites                        	39
;	nb_sites                     	39
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.98811
;	information.per.column       	0.465874
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	tAAgATGcattttac
;	consensus.strict.rc          	GTAAAATGCATCTTA
;	consensus.IUPAC              	wAAsATGcatttyav
;	consensus.IUPAC.rc           	BTRAAATGCATSTTW
;	consensus.regexp             	[at]AA[cg]ATGcattt[ct]a[acg]
;	consensus.regexp.rc          	[CGT]T[AG]AAATGCAT[CG]TT[AT]
;	residues.content.crude.freq  	a:0.3983|c:0.1162|g:0.1641|t:0.3214
;	G+C.content.crude.freq       	0.280342
;	residues.content.corrected.freq	a:0.3956|c:0.1185|g:0.1651|t:0.3208
;	G+C.content.corrected.freq   	0.283627
;	min(P(S|M))                  	4.23515e-24
;	max(P(S|M))                  	0.000497598
;	proba_range                  	0.000497598
;	Wmin                         	-31.1
;	Wmax                         	12
;	Wrange                       	43.1
; logo file:/NsrR.EcolK12_1nt_upstream.15.meme_quality_logo_m1.png
; logo file:/NsrR.EcolK12_1nt_upstream.15.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161045
; Job done	2019-06-03.161046
; Seconds	0.59
;	user	0.59
;	system	0.06
;	cuser	0.44
;	csystem	0.04