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FhlA matrix and aligment

matrix-quality result

Command: 
FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_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 FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_quality_logo
; Input files
;	input	FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_quality_matrix.tf
;	prior	FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_quality2nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29086
;		c	0.20809
;		g	0.20476
;		t	0.29629
A	4	0	0	0	0	2	6	4	7	2	1	1	3	1	4
C	1	5	1	0	7	0	0	2	0	4	0	0	3	4	1
G	1	0	5	2	0	5	0	1	0	0	3	6	1	1	2
T	1	2	1	5	0	0	1	0	0	1	3	0	0	1	0
//
a  0.5  0.0  0.0  0.0  0.0  0.3  0.8  0.5  0.9  0.3  0.2  0.2  0.4  0.2  0.5
c  0.2  0.7  0.2  0.0  0.9  0.0  0.0  0.3  0.0  0.5  0.0  0.0  0.4  0.5  0.2
g  0.2  0.0  0.7  0.3  0.0  0.7  0.0  0.2  0.0  0.0  0.4  0.8  0.2  0.2  0.3
t  0.2  0.3  0.2  0.7  0.0  0.0  0.2  0.0  0.0  0.2  0.4  0.0  0.0  0.2  0.0
//
a  0.6 -2.1 -2.1 -2.1 -2.1 -0.0  1.0  0.6  1.1 -0.0 -0.6 -0.6  0.3 -0.6  0.6
c -0.3  1.1 -0.3 -2.1  1.5 -2.1 -2.1  0.3 -2.1  0.9 -2.1 -2.1  0.7  0.9 -0.3
g -0.3 -2.1  1.2  0.3 -2.1  1.2 -2.1 -0.3 -2.1 -2.1  0.7  1.3 -0.3 -0.3  0.3
t -0.6 -0.0 -0.6  0.8 -2.1 -2.1 -0.6 -2.1 -2.1 -0.6  0.3 -2.1 -2.1 -0.6 -2.1
//
a  0.3 -0.1 -0.1 -0.1 -0.1 -0.0  0.8  0.3  1.0 -0.0 -0.1 -0.1  0.1 -0.1  0.3
c -0.0  0.7 -0.0 -0.1  1.3 -0.1 -0.1  0.1 -0.1  0.5 -0.1 -0.1  0.3  0.5 -0.0
g -0.0 -0.1  0.8  0.1 -0.1  0.8 -0.1 -0.0 -0.1 -0.1  0.3  1.0 -0.0 -0.0  0.1
t -0.1 -0.0 -0.1  0.5 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	15
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.29085999082|c:0.208089935287|g:0.204758708047|t:0.296291365846
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	aCGkCGamAckGmcr
;	min.prior                    	0.204759
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.41304
;	information.per.column       	0.494203
;	max.possible.info.per.col    	1.58592
;	consensus.strict             	aCGtCGaaAcgGcca
;	consensus.strict.rc          	TGGCCGTTTCGACGT
;	consensus.IUPAC              	aCGkCGamAckGmcr
;	consensus.IUPAC.rc           	YGKCMGTKTCGMCGT
;	consensus.regexp             	aCG[gt]CGa[ac]Ac[gt]G[ac]c[ag]
;	consensus.regexp.rc          	[CT]G[GT]C[AC]GT[GT]TCG[AC]CGT
;	residues.content.crude.freq  	a:0.3333|c:0.2667|g:0.2571|t:0.1429
;	G+C.content.crude.freq       	0.52381
;	residues.content.corrected.freq	a:0.3280|c:0.2593|g:0.2506|t:0.1620
;	G+C.content.corrected.freq   	0.509939
;	min(P(S|M))                  	2.10624e-22
;	max(P(S|M))                  	0.00066111
;	proba_range                  	0.00066111
;	Wmin                         	-28.3
;	Wmax                         	14.3
;	Wrange                       	42.6
; logo file:FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_quality_logo_m1.png
; logo file:FhlA.2nt_upstream-noorf-ovlp-2str.15.meme_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	0.49
;	csystem	0.06
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