RegulonDB

GadX matrix and aligment

matrix-quality result

Command: 
GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality

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 GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality_logo
; Input files
;	input	GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality_matrix.tf
;	prior	GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	GadX.1nt_upstream-noorf-ovlp-2str.21.cons_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	0.29063
;		c	0.20784
;		g	0.20492
;		t	0.29662
A	4	4	0	8	4	4	18	6	6	0	0	7	12	0	12	6	5	16	1	3	13
C	4	5	0	7	0	0	1	3	4	4	7	3	6	5	3	5	6	3	0	4	6
G	3	12	10	0	2	11	2	0	6	3	3	6	0	0	1	3	3	0	6	5	1
T	13	3	14	9	18	9	3	15	8	17	14	8	6	19	8	10	10	5	17	12	4
//
a  0.2  0.2  0.0  0.3  0.2  0.2  0.7  0.3  0.3  0.0  0.0  0.3  0.5  0.0  0.5  0.3  0.2  0.7  0.1  0.1  0.5
c  0.2  0.2  0.0  0.3  0.0  0.0  0.0  0.1  0.2  0.2  0.3  0.1  0.2  0.2  0.1  0.2  0.2  0.1  0.0  0.2  0.2
g  0.1  0.5  0.4  0.0  0.1  0.4  0.1  0.0  0.2  0.1  0.1  0.2  0.0  0.0  0.0  0.1  0.1  0.0  0.2  0.2  0.0
t  0.5  0.1  0.6  0.4  0.7  0.4  0.1  0.6  0.3  0.7  0.6  0.3  0.3  0.8  0.3  0.4  0.4  0.2  0.7  0.5  0.2
//
a -0.5 -0.5 -3.2  0.1 -0.5 -0.5  0.9 -0.1 -0.1 -3.2 -3.2  0.0  0.5 -3.2  0.5 -0.1 -0.3  0.8 -1.7 -0.8  0.6
c -0.2  0.0 -3.2  0.3 -3.2 -3.2 -1.5 -0.5 -0.2 -0.2  0.3 -0.5  0.2  0.0 -0.5  0.0  0.2 -0.5 -3.2 -0.2  0.2
g -0.5  0.9  0.7 -3.2 -0.8  0.8 -0.8 -3.2  0.2 -0.5 -0.5  0.2 -3.2 -3.2 -1.4 -0.5 -0.5 -3.2  0.2  0.0 -1.4
t  0.6 -0.8  0.7  0.2  0.9  0.2 -0.8  0.7  0.1  0.8  0.7  0.1 -0.2  1.0  0.1  0.3  0.3 -0.3  0.8  0.5 -0.5
//
a -0.1 -0.1 -0.0  0.0 -0.1 -0.1  0.7 -0.0 -0.0 -0.0 -0.0  0.0  0.3 -0.0  0.3 -0.0 -0.1  0.5 -0.1 -0.1  0.3
c -0.0  0.0 -0.0  0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0  0.1 -0.1  0.0  0.0 -0.1  0.0  0.0 -0.1 -0.0 -0.0  0.0
g -0.1  0.4  0.3 -0.0 -0.1  0.4 -0.1 -0.0  0.0 -0.1 -0.1  0.0 -0.0 -0.0 -0.1 -0.1 -0.1 -0.0  0.0  0.0 -0.1
t  0.3 -0.1  0.4  0.1  0.7  0.1 -0.1  0.4  0.0  0.6  0.4  0.0 -0.0  0.7  0.0  0.1  0.1 -0.1  0.6  0.2 -0.1
//
; Sites	24
>site_0
TCGATAAATCCTACTTTTTTA
>site_1
CCTTTGCACTTGCTTACTTTA
>site_2
GATATTACGCGAATAATATTT
>site_3
TATTGTATTGTTTTTCAATGA
>site_4
GGTCTGATTTTTACGTGATAA
>site_5
CTTAAAATATCACTATTAGTA
>site_6
TGTCTGATGTTTATATCCTTT
>site_7
AGGTTTACGTTACTATCAGGC
>site_8
TATCTGATTTTGATATTTTCC
>site_9
ATTTTTATTTCAATACAATGA
>site_10
TTTATTAAATCGACTGCATTC
>site_11
TGTTTGAAATGGCTAATTTGC
>site_12
TGGCTGATATTTTCCGTAGTC
>site_13
TAGCTTATGTTTATAAAAAAA
>site_14
TGGCTGATCTTATTTCCAGTA
>site_15
CGGATAAATCCTACTTTTTTA
>site_16
TGTAATGCCTTGCTTCCATTG
>site_17
AGGATTTTGTTATTTAAATTA
>site_18
TCGTTTTTCTGCTTAGGATTT
>site_19
TGTTAAATGTTTATATTATAA
>site_20
AGTCTGTTTTTAATATTATCA
>site_21
GCGATGATTGCGTTATGCGGA
>site_22
CGGTGGGAAGTCATCATCTCT
>site_23
TCTTAGATACCCCTCCAAGCC
;
; Matrix parameters
;	Columns                      	21
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.2906296|c:0.2078359|g:0.2049154|t:0.2966191
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	GadX.1nt_upstream-noorf-ovlp-2str.21.cons1
;	AC                           	GadX.1nt_upstream-noorf-ovlp-2str.21.cons1
;	id                           	GadX.1nt_upstream-noorf-ovlp-2str.21.cons1
;	name                         	GadX.1nt_upstream-noorf-ovlp-2str.21.cons1
;	description                  	tskhtkatktydmywyyakkm
;	statistical_basis            	24 sequences
;	sites                        	24
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.89485
;	information.per.column       	0.280707
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	tggctgatgttgatattatta
;	consensus.strict.rc          	TAATAATATCAACATCAGCCA
;	consensus.IUPAC              	tskhtkatktydmywyyakkm
;	consensus.IUPAC.rc           	KMMTRRWRKHRAMATMADMSA
;	consensus.regexp             	t[cg][gt][act]t[gt]at[gt]t[ct][agt][ac][ct][at][ct][ct]a[gt][gt][ac]
;	consensus.regexp.rc          	[GT][AC][AC]T[AG][AG][AT][AG][GT][ACT][AG]A[AC]AT[AC]A[AGT][AC][CG]A
;	residues.content.crude.freq  	a:0.2560|c:0.1508|g:0.1528|t:0.4405
;	G+C.content.crude.freq       	0.303571
;	residues.content.corrected.freq	a:0.2573|c:0.1531|g:0.1549|t:0.4347
;	G+C.content.corrected.freq   	0.307939
;	min(P(S|M))                  	2.11682e-33
;	max(P(S|M))                  	1.31809e-06
;	proba_range                  	1.31809e-06
;	Wmin                         	-43.6
;	Wmax                         	13.2
;	Wrange                       	56.8
; logo file:GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality_logo_m1.png
; logo file:GadX.1nt_upstream-noorf-ovlp-2str.21.cons_quality_logo_m1_rc.png
; Host name	compute-1-1.local
; Job started	2015-08-06.164357
; Job done	2015-08-06.164359
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.53
;	csystem	0.05
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