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TrpR matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/TrpR/TrpR.EcolK12_2nt_upstream.21.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 /TrpR.EcolK12_2nt_upstream.21.meme_quality_logo
; Input files
;	input	/TrpR.EcolK12_2nt_upstream.21.meme_quality_matrix.tf
;	prior	/TrpR.EcolK12_2nt_upstream.21.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/TrpR.EcolK12_2nt_upstream.21.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	1	1	4	0	1	0	3	6	1	0	6	0	0	2	2	4	2	0	5	0
C	0	3	2	1	1	3	0	0	0	5	1	0	0	0	0	3	0	3	0	0	0
G	1	1	0	0	3	0	5	0	0	0	1	0	6	0	1	0	2	0	1	1	6
T	1	1	3	1	2	2	1	3	0	0	4	0	0	6	3	1	0	1	5	0	0
//
A  0.6  0.2  0.2  0.6  0.0  0.2  0.0  0.5  0.9  0.2  0.0  0.9  0.0  0.0  0.3  0.3  0.6  0.3  0.0  0.8  0.0
C  0.0  0.5  0.3  0.2  0.2  0.5  0.0  0.0  0.0  0.7  0.2  0.0  0.0  0.0  0.0  0.5  0.0  0.5  0.0  0.0  0.0
G  0.2  0.2  0.0  0.0  0.5  0.0  0.7  0.0  0.0  0.0  0.2  0.0  0.9  0.0  0.2  0.0  0.3  0.0  0.2  0.2  0.9
T  0.2  0.2  0.5  0.2  0.3  0.3  0.2  0.5  0.0  0.0  0.6  0.0  0.0  0.9  0.5  0.2  0.0  0.2  0.8  0.0  0.0
//
A  0.7 -0.5 -0.5  0.7 -1.9 -0.5 -1.9  0.5  1.1 -0.5 -1.9  1.1 -1.9 -1.9  0.1  0.1  0.7  0.1 -1.9  1.0 -1.9
C -1.9  0.8  0.4 -0.2 -0.2  0.8 -1.9 -1.9 -1.9  1.3 -0.2 -1.9 -1.9 -1.9 -1.9  0.8 -1.9  0.8 -1.9 -1.9 -1.9
G -0.2 -0.2 -1.9 -1.9  0.8 -1.9  1.3 -1.9 -1.9 -1.9 -0.2 -1.9  1.5 -1.9 -0.2 -1.9  0.4 -1.9 -0.2 -0.2  1.5
T -0.5 -0.5  0.5 -0.5  0.1  0.1 -0.5  0.5 -1.9 -1.9  0.7 -1.9 -1.9  1.1  0.5 -0.5 -1.9 -0.5  0.9 -1.9 -1.9
//
A  0.5 -0.1 -0.1  0.5 -0.1 -0.1 -0.1  0.2  1.0 -0.1 -0.1  1.0 -0.1 -0.1  0.0  0.0  0.5  0.0 -0.1  0.7 -0.1
C -0.1  0.4  0.1 -0.0 -0.0  0.4 -0.1 -0.1 -0.1  0.9 -0.0 -0.1 -0.1 -0.1 -0.1  0.4 -0.1  0.4 -0.1 -0.1 -0.1
G -0.0 -0.0 -0.1 -0.1  0.4 -0.1  1.0 -0.1 -0.1 -0.1 -0.0 -0.1  1.3 -0.1 -0.0 -0.1  0.1 -0.1 -0.0 -0.0  1.3
T -0.1 -0.1  0.2 -0.1  0.0  0.0 -0.1  0.2 -0.1 -0.1  0.4 -0.1 -0.1  1.0  0.2 -0.1 -0.1 -0.1  0.7 -0.1 -0.1
//
; Sites	6
>site_0
ACTTGCGTACTAGTTAACTAG
>site_1
ATCATCGAACTAGTTAACTAG
>site_2
ACTAGAGAACTAGTGCATTAG
>site_3
TGCACTGTACCAGTACACGAG
>site_4
ACTCGCTAAAGAGTACGATAG
>site_5
GAAATTGTACTAGTTTGATGG
;
; Matrix parameters
;	Number of sites              	6
;	Columns                      	21
;	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                    	ACYAKYGWACTAGTWMRMTAG
;	AC                           	ACYAKYGWACTAGTWMRMTAG
;	id                           	ACYAKYGWACTAGTWMRMTAG
;	name                         	ACYAKYGWACTAGTWMRMTAG
;	description                  	acyakyGwACtAGTwmrmtaG
;	statistical_basis            	6 sequences
;	sites                        	6
;	nb_sites                     	6
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	10.3865
;	information.per.column       	0.494593
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	actagcGaACtAGTtcactaG
;	consensus.strict.rc          	CTAGTGAACTAGTTCGCTAGT
;	consensus.IUPAC              	acyakyGwACtAGTwmrmtaG
;	consensus.IUPAC.rc           	CTAKYKWACTAGTWCRMTRGT
;	consensus.regexp             	ac[ct]a[gt][ct]G[at]ACtAGT[at][ac][ag][ac]taG
;	consensus.regexp.rc          	CTA[GT][CT][GT][AT]ACTAGT[AT]C[AG][AC]T[AG]GT
;	residues.content.crude.freq  	a:0.3333|c:0.1746|g:0.2222|t:0.2698
;	G+C.content.crude.freq       	0.396825
;	residues.content.corrected.freq	a:0.3273|c:0.1793|g:0.2196|t:0.2737
;	G+C.content.corrected.freq   	0.39897
;	min(P(S|M))                  	7.94237e-32
;	max(P(S|M))                  	5.38569e-05
;	proba_range                  	5.38569e-05
;	Wmin                         	-39.4
;	Wmax                         	19.1
;	Wrange                       	58.5
; logo file:/TrpR.EcolK12_2nt_upstream.21.meme_quality_logo_m1.png
; logo file:/TrpR.EcolK12_2nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161114
; Job done	2019-06-03.161115
; Seconds	0.62
;	user	0.62
;	system	0.06
;	cuser	0.45
;	csystem	0.04
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