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CaiF matrix and aligment

matrix-quality result

Command: 
CaiF.1nt_upstream-noorf-ovlp-2str.14.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 CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_quality_logo
; Input files
;	input	CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_quality_matrix.tf
;	prior	CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_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	2	0	4	4	0	4	0	0	0	4	4	4	2
C	0	2	4	0	0	0	0	0	0	0	0	0	0	0
G	0	0	0	0	0	0	0	0	0	4	0	0	0	2
T	0	0	0	0	0	4	0	4	4	0	0	0	0	0
//
a  0.9  0.5  0.1  0.9  0.9  0.1  0.9  0.1  0.1  0.1  0.9  0.9  0.9  0.5
c  0.0  0.4  0.8  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0
g  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.8  0.0  0.0  0.0  0.4
t  0.1  0.1  0.1  0.1  0.1  0.9  0.1  0.9  0.9  0.1  0.1  0.1  0.1  0.1
//
a  1.1  0.5 -1.6  1.1  1.1 -1.6  1.1 -1.6 -1.6 -1.6  1.1  1.1  1.1  0.5
c -1.6  0.8  1.4 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6
g -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6 -1.6  1.4 -1.6 -1.6 -1.6  0.8
t -1.6 -1.6 -1.6 -1.6 -1.6  1.1 -1.6  1.1  1.1 -1.6 -1.6 -1.6 -1.6 -1.6
//
a  0.9  0.2 -0.1  0.9  0.9 -0.1  0.9 -0.1 -0.1 -0.1  0.9  0.9  0.9  0.2
c -0.1  0.3  1.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
g -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  1.2 -0.1 -0.1 -0.1  0.3
t -0.1 -0.1 -0.1 -0.1 -0.1  0.9 -0.1  0.9  0.9 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	
;
; Matrix parameters
;	Columns                      	14
;	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                    	1
;	AC                           	1
;	id                           	1
;	name                         	1
;	description                  	AmCAATATTGAAAr
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.58562
;	information.per.column       	0.684687
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	AcCAATATTGAAAg
;	consensus.strict.rc          	CTTTCAATATTGGT
;	consensus.IUPAC              	AmCAATATTGAAAr
;	consensus.IUPAC.rc           	YTTTCAATATTGKT
;	consensus.regexp             	A[ac]CAATATTGAAA[ag]
;	consensus.regexp.rc          	[CT]TTTCAATATTG[GT]T
;	residues.content.crude.freq  	a:0.5714|c:0.1071|g:0.1071|t:0.2143
;	G+C.content.crude.freq       	0.214286
;	residues.content.corrected.freq	a:0.5153|c:0.1273|g:0.1267|t:0.2308
;	G+C.content.corrected.freq   	0.253979
;	min(P(S|M))                  	3.87933e-20
;	max(P(S|M))                  	0.0322978
;	proba_range                  	0.0322978
;	Wmin                         	-22.6
;	Wmax                         	15.2
;	Wrange                       	37.8
; logo file:CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_quality_logo_m1.png
; logo file:CaiF.1nt_upstream-noorf-ovlp-2str.14.meme_quality_logo_m1_rc.png
; Host name	compute-1-9.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.47
;	csystem	0.07
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