RegulonDB

AgaR matrix and aligment

matrix-quality result

Command: 
AgaR.1nt_upstream-noorf-ovlp-2str.20.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 AgaR.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo
; Input files
;	input	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons_quality_matrix.tf
;	prior	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	AgaR.1nt_upstream-noorf-ovlp-2str.20.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	2	2	0	0	3	2	0	0	1	0	4	0	0	0	1	3	3	0	3	1
C	7	0	0	1	7	0	3	0	1	6	2	0	0	1	7	0	2	0	1	0
G	0	0	0	0	0	8	0	1	0	0	3	0	0	0	0	3	1	0	0	5
T	2	9	11	10	1	1	8	10	9	5	2	11	11	10	3	5	5	11	7	5
//
a  0.2  0.2  0.0  0.0  0.3  0.2  0.0  0.0  0.1  0.0  0.4  0.0  0.0  0.0  0.1  0.3  0.3  0.0  0.3  0.1
c  0.6  0.0  0.0  0.1  0.6  0.0  0.3  0.0  0.1  0.5  0.2  0.0  0.0  0.1  0.6  0.0  0.2  0.0  0.1  0.0
g  0.0  0.0  0.0  0.0  0.0  0.7  0.0  0.1  0.0  0.0  0.3  0.0  0.0  0.0  0.0  0.3  0.1  0.0  0.0  0.4
t  0.2  0.8  0.9  0.9  0.1  0.1  0.7  0.9  0.8  0.4  0.2  0.9  0.9  0.9  0.3  0.4  0.4  0.9  0.6  0.4
//
a -0.4 -0.4 -2.5 -2.5 -0.1 -0.4 -2.5 -2.5 -1.0 -2.5  0.2 -2.5 -2.5 -2.5 -1.0 -0.1 -0.1 -2.5 -0.1 -1.0
c  1.1 -2.5 -2.5 -0.7  1.1 -2.5  0.3 -2.5 -0.7  0.9 -0.1 -2.5 -2.5 -0.7  1.1 -2.5 -0.1 -2.5 -0.7 -2.5
g -2.5 -2.5 -2.5 -2.5 -2.5  1.2 -2.5 -0.7 -2.5 -2.5  0.3 -2.5 -2.5 -2.5 -2.5  0.3 -0.7 -2.5 -2.5  0.7
t -0.4  1.0  1.2  1.1 -1.0 -1.0  0.8  1.1  1.0  0.4 -0.4  1.2  1.2  1.1 -0.1  0.4  0.4  1.2  0.7  0.4
//
a -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1  0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1
c  0.6 -0.0 -0.0 -0.1  0.6 -0.0  0.1 -0.0 -0.1  0.5 -0.0 -0.0 -0.0 -0.1  0.6 -0.0 -0.0 -0.0 -0.1 -0.0
g -0.0 -0.0 -0.0 -0.0 -0.0  0.8 -0.0 -0.1 -0.0 -0.0  0.1 -0.0 -0.0 -0.0 -0.0  0.1 -0.1 -0.0 -0.0  0.3
t -0.1  0.7  1.1  0.9 -0.1 -0.1  0.6  0.9  0.7  0.2 -0.1  1.1  1.1  0.9 -0.0  0.2  0.2  1.1  0.4  0.2
//
; Sites	11
>site_0
CTTTCGTTTCATTTCGTTTT
>site_1
TATTAACGCCTTTCTATTAA
>site_2
CTTTCATTATGTTTCTTTTG
>site_3
CTTTCGTTTTATTTTTATCT
>site_4
CTTTCGTTTTGTTTCAGTTG
>site_5
AATTAGCTTCGTTTTGATAG
>site_6
CTTTCTTTTTCTTTCGTTTT
>site_7
CTTTTGCTTCCTTTATCTTT
>site_8
ATTTCGTTTTATTTCTTTTT
>site_9
TTTCAGTTTCTTTTCTATAG
>site_10
CTTTCGTTTCATTTCACTTG
;
; Matrix parameters
;	Columns                      	20
;	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                    	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons1
;	AC                           	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons1
;	id                           	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons1
;	name                         	AgaR.1nt_upstream-noorf-ovlp-2str.20.cons1
;	description                  	CtTTCGyTtyrTTTCktTtk
;	statistical_basis            	11 sequences
;	sites                        	11
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	11.0748
;	information.per.column       	0.553741
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	CtTTCGtTtcgTTTCttTtg
;	consensus.strict.rc          	CAAAAGAAACGAAACGAAAG
;	consensus.IUPAC              	CtTTCGyTtyrTTTCktTtk
;	consensus.IUPAC.rc           	MAAAMGAAAYRAARCGAAAG
;	consensus.regexp             	CtTTCG[ct]Tt[ct][ag]TTTC[gt]tTt[gt]
;	consensus.regexp.rc          	[AC]AAA[AC]GAAA[CT][AG]AA[AG]CGAAAG
;	residues.content.crude.freq  	a:0.1136|c:0.1727|g:0.0955|t:0.6182
;	G+C.content.crude.freq       	0.268182
;	residues.content.corrected.freq	a:0.1284|c:0.1757|g:0.1046|t:0.5914
;	G+C.content.corrected.freq   	0.280229
;	min(P(S|M))                  	2.98006e-34
;	max(P(S|M))                  	0.000295034
;	proba_range                  	0.000295034
;	Wmin                         	-45.9
;	Wmax                         	18.5
;	Wrange                       	64.4
; logo file:AgaR.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo_m1.png
; logo file:AgaR.1nt_upstream-noorf-ovlp-2str.20.cons_quality_logo_m1_rc.png
; Host name	compute-1-7.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.52
;	csystem	0.05
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