RegulonDB

MalT matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/MalT/MalT.EcolK12_2nt_upstream.9.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 /MalT.EcolK12_2nt_upstream.9.meme_quality_logo
; Input files
;	input	/MalT.EcolK12_2nt_upstream.9.meme_quality_matrix.tf
;	prior	/MalT.EcolK12_2nt_upstream.9.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/MalT.EcolK12_2nt_upstream.9.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	4	6	0	0	10	0	0	15	0
C	2	0	0	0	2	0	0	0	0
G	9	8	14	15	1	7	14	0	13
T	0	1	1	0	2	8	1	0	2
//
A  0.3  0.4  0.0  0.0  0.6  0.0  0.0  1.0  0.0
C  0.1  0.0  0.0  0.0  0.1  0.0  0.0  0.0  0.0
G  0.6  0.5  0.9  1.0  0.1  0.5  0.9  0.0  0.8
T  0.0  0.1  0.1  0.0  0.1  0.5  0.1  0.0  0.1
//
A -0.1  0.3 -2.8 -2.8  0.8 -2.8 -2.8  1.2 -2.8
C -0.4 -2.8 -2.8 -2.8 -0.4 -2.8 -2.8 -2.8 -2.8
G  1.0  0.9  1.5  1.5 -1.0  0.8  1.5 -2.8  1.4
T -2.8 -1.3 -1.3 -2.8 -0.7  0.6 -1.3 -2.8 -0.7
//
A -0.0  0.1 -0.1 -0.1  0.5 -0.1 -0.1  1.1 -0.1
C -0.1 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0
G  0.6  0.5  1.3  1.5 -0.1  0.4  1.3 -0.0  1.2
T -0.1 -0.1 -0.1 -0.1 -0.1  0.3 -0.1 -0.1 -0.1
//
; Sites	15
>site_0
GGGGAGGAG
>site_1
GGGGAGGAG
>site_2
GGGGATGAG
>site_3
GAGGATGAG
>site_4
AGGGAGGAG
>site_5
AGGGATGAG
>site_6
GGGGTGGAG
>site_7
CAGGATGAG
>site_8
CAGGATGAG
>site_9
GGGGCGGAT
>site_10
GATGATGAG
>site_11
AAGGGTGAG
>site_12
AAGGAGGAT
>site_13
GGGGCGTAG
>site_14
GTGGTTGAG
;
; Matrix parameters
;	Number of sites              	15
;	Columns                      	9
;	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                    	GRGGAKGAG
;	AC                           	GRGGAKGAG
;	id                           	GRGGAKGAG
;	name                         	GRGGAKGAG
;	description                  	GrGGakGAG
;	statistical_basis            	15 sequences
;	sites                        	15
;	nb_sites                     	15
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.2754
;	information.per.column       	0.808378
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	GgGGagGAG
;	consensus.strict.rc          	CTCCTCCCC
;	consensus.IUPAC              	GrGGakGAG
;	consensus.IUPAC.rc           	CTCMTCCYC
;	consensus.regexp             	G[ag]GGa[gt]GAG
;	consensus.regexp.rc          	CTC[AC]TCC[CT]C
;	residues.content.crude.freq  	a:0.2593|c:0.0296|g:0.6000|t:0.1111
;	G+C.content.crude.freq       	0.62963
;	residues.content.corrected.freq	a:0.2613|c:0.0408|g:0.5753|t:0.1227
;	G+C.content.corrected.freq   	0.616017
;	min(P(S|M))                  	8.55128e-17
;	max(P(S|M))                  	0.0581083
;	proba_range                  	0.0581083
;	Wmin                         	-23.2
;	Wmax                         	10.7
;	Wrange                       	33.9
; logo file:/MalT.EcolK12_2nt_upstream.9.meme_quality_logo_m1.png
; logo file:/MalT.EcolK12_2nt_upstream.9.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161014
; Job done	2019-06-03.161015
; Seconds	0.59
;	user	0.59
;	system	0.06
;	cuser	0.41
;	csystem	0.04
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