DnaA matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/DnaA/DnaA.EcolK12_1nt_upstream.10.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 /DnaA.EcolK12_1nt_upstream.10.meme_quality_logo
; Input files
;	input	/DnaA.EcolK12_1nt_upstream.10.meme_quality_matrix.tf
;	prior	/DnaA.EcolK12_1nt_upstream.10.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/DnaA.EcolK12_1nt_upstream.10.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	2	16	0	4	2	20	0	19	11
C	2	0	0	2	13	20	2	20	0	0
G	0	0	1	0	2	0	0	3	0	6
T	20	21	6	21	4	1	1	0	4	6
//
A  0.1  0.1  0.7  0.0  0.2  0.1  0.8  0.0  0.8  0.5
C  0.1  0.0  0.0  0.1  0.6  0.8  0.1  0.8  0.0  0.0
G  0.0  0.0  0.1  0.0  0.1  0.0  0.0  0.1  0.0  0.3
T  0.8  0.9  0.3  0.9  0.2  0.1  0.1  0.0  0.2  0.3
//
A -1.7 -1.1  0.8 -3.2 -0.5 -1.1  1.1 -3.2  1.0  0.5
C -0.8 -3.2 -3.2 -0.8  1.0  1.4 -0.8  1.4 -3.2 -3.2
G -3.2 -3.2 -1.4 -3.2 -0.8 -3.2 -3.2 -0.4 -3.2  0.2
T  1.0  1.1 -0.1  1.1 -0.5 -1.7 -1.7 -3.2 -0.5 -0.1
//
A -0.1 -0.1  0.6 -0.0 -0.1 -0.1  0.9 -0.0  0.8  0.2
C -0.1 -0.0 -0.0 -0.1  0.5  1.2 -0.1  1.2 -0.0 -0.0
G -0.0 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0  0.1
T  0.9  1.0 -0.0  1.0 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0
//
; Sites	23
>site_0
TTATCCACAA
>site_1
TTATCCACAA
>site_2
TTATCCACAA
>site_3
TTATCCACAG
>site_4
TTATCCACAG
>site_5
TTATCCACAG
>site_6
TTATCCACAT
>site_7
TTATCCACTA
>site_8
TTATTCACAA
>site_9
TTATCCCCAA
>site_10
ATATCCACAG
>site_11
TTATCCAGTA
>site_12
TTATGCACTT
>site_13
TAATACACAT
>site_14
TTTCTCACAG
>site_15
CTTTCCAGAA
>site_16
TTATATACAG
>site_17
TTTTCCCGAT
>site_18
TTTTTAACAT
>site_19
CTGTACACAA
>site_20
TTTCACACTA
>site_21
TTTTGCTCAT
>site_22
TAATTAACAA
;
; Matrix parameters
;	Number of sites              	23
;	Columns                      	10
;	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                    	TTATCCACAD
;	AC                           	TTATCCACAD
;	id                           	TTATCCACAD
;	name                         	TTATCCACAD
;	description                  	TTaTcCACAr
;	statistical_basis            	23 sequences
;	sites                        	23
;	nb_sites                     	23
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.6646
;	information.per.column       	0.66646
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	TTaTcCACAa
;	consensus.strict.rc          	TTGTGGATAA
;	consensus.IUPAC              	TTaTcCACAr
;	consensus.IUPAC.rc           	YTGTGGATAA
;	consensus.regexp             	TTaTcCACA[ag]
;	consensus.regexp.rc          	[CT]TGTGGATAA
;	residues.content.crude.freq  	a:0.3261|c:0.2565|g:0.0522|t:0.3652
;	G+C.content.crude.freq       	0.308696
;	residues.content.corrected.freq	a:0.3246|c:0.2545|g:0.0585|t:0.3624
;	G+C.content.corrected.freq   	0.312989
;	min(P(S|M))                  	3.15758e-20
;	max(P(S|M))                  	0.0563842
;	proba_range                  	0.0563842
;	Wmin                         	-29.5
;	Wmax                         	10.5
;	Wrange                       	40
; logo file:/DnaA.EcolK12_1nt_upstream.10.meme_quality_logo_m1.png
; logo file:/DnaA.EcolK12_1nt_upstream.10.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.160931
; Job done	2019-06-03.160931
; Seconds	0.57
;	user	0.57
;	system	0.04
;	cuser	0.41
;	csystem	0.04