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AraC matrix and aligment

matrix-quality result

Command: 
AraC.1nt_upstream-noorf-ovlp-2str.17.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 AraC.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo
; Input files
;	input	AraC.1nt_upstream-noorf-ovlp-2str.17.cons_quality_matrix.tf
;	prior	AraC.1nt_upstream-noorf-ovlp-2str.17.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	AraC.1nt_upstream-noorf-ovlp-2str.17.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	1	12	3	1	2	10	4	3	6	5	3	3	0	3	0	0	5
C	2	2	0	0	3	1	4	0	1	1	6	6	5	0	13	4	3
G	0	1	0	13	8	1	1	3	2	1	0	2	3	11	0	0	6
T	12	0	12	1	2	3	6	9	6	8	6	4	7	1	2	11	1
//
a  0.1  0.8  0.2  0.1  0.1  0.6  0.3  0.2  0.4  0.3  0.2  0.2  0.0  0.2  0.0  0.0  0.3
c  0.1  0.1  0.0  0.0  0.2  0.1  0.3  0.0  0.1  0.1  0.4  0.4  0.3  0.0  0.8  0.3  0.2
g  0.0  0.1  0.0  0.8  0.5  0.1  0.1  0.2  0.1  0.1  0.0  0.1  0.2  0.7  0.0  0.0  0.4
t  0.8  0.0  0.8  0.1  0.1  0.2  0.4  0.6  0.4  0.5  0.4  0.3  0.5  0.1  0.1  0.7  0.1
//
a -1.3  1.0 -0.3 -1.3 -0.7  0.8 -0.1 -0.3  0.3  0.1 -0.3 -0.3 -2.8 -0.3 -2.8 -2.8  0.1
c -0.4 -0.4 -2.8 -2.8 -0.0 -1.0  0.2 -2.8 -1.0 -1.0  0.6  0.6  0.4 -2.8  1.4  0.2 -0.0
g -2.8 -1.0 -2.8  1.4  0.9 -1.0 -1.0 -0.0 -0.4 -1.0 -2.8 -0.4 -0.0  1.2 -2.8 -2.8  0.6
t  1.0 -2.8  1.0 -1.3 -0.7 -0.4  0.3  0.7  0.3  0.6  0.3 -0.1  0.4 -1.3 -0.7  0.9 -1.3
//
a -0.1  0.7 -0.1 -0.1 -0.1  0.5 -0.0 -0.1  0.1  0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1  0.0
c -0.1 -0.1 -0.0 -0.0 -0.0 -0.1  0.1 -0.0 -0.1 -0.1  0.2  0.2  0.1 -0.0  1.1  0.1 -0.0
g -0.0 -0.1 -0.0  1.1  0.5 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0 -0.1 -0.0  0.9 -0.0 -0.0  0.2
t  0.7 -0.1  0.7 -0.1 -0.1 -0.1  0.1  0.4  0.1  0.3  0.1 -0.0  0.2 -0.1 -0.1  0.6 -0.1
//
; Sites	15
>site_0
TCAGGTAGGATCCGCTA
>site_1
TATGGATAAAAATGCTA
>site_2
TGTGGACTTTTCTGCCG
>site_3
TATAGACACTTTTGTTA
>site_4
TATGGACAATTGGTTTC
>site_5
CAAGAGATAATTCGCCC
>site_6
TATTCATTATCCTGCTG
>site_7
TATGCACGTTCTCACTG
>site_8
TATGTCTTTTCCCGCTA
>site_9
TATGGATTAATCTGCTG
>site_10
CAAGGATTTCCAGGCTA
>site_11
TATGCTGTTTCCGACCT
>site_12
TATGGATTAAATTGCTG
>site_13
ACTGAAAGGGAGTGCCC
>site_14
TATGTTATTTCACACTG
;
; Matrix parameters
;	Columns                      	17
;	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                    	AraC.1nt_upstream-noorf-ovlp-2str.17.cons1
;	AC                           	AraC.1nt_upstream-noorf-ovlp-2str.17.cons1
;	id                           	AraC.1nt_upstream-noorf-ovlp-2str.17.cons1
;	name                         	AraC.1nt_upstream-noorf-ovlp-2str.17.cons1
;	description                  	tatGgaytwwycyGCyr
;	statistical_basis            	15 sequences
;	sites                        	15
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.75668
;	information.per.column       	0.397452
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	tatGgattatcccGCtg
;	consensus.strict.rc          	CAGCGGGATAATCCATA
;	consensus.IUPAC              	tatGgaytwwycyGCyr
;	consensus.IUPAC.rc           	YRGCRGRWWARTCCATA
;	consensus.regexp             	tatGga[ct]t[at][at][ct]c[ct]GC[ct][ag]
;	consensus.regexp.rc          	[CT][AG]GC[AG]G[AG][AT][AT]A[AG]TCCATA
;	residues.content.crude.freq  	a:0.2392|c:0.2000|g:0.2039|t:0.3569
;	G+C.content.crude.freq       	0.403922
;	residues.content.corrected.freq	a:0.2424|c:0.2005|g:0.2040|t:0.3531
;	G+C.content.corrected.freq   	0.404473
;	min(P(S|M))                  	1.3109e-26
;	max(P(S|M))                  	6.35174e-05
;	proba_range                  	6.35174e-05
;	Wmin                         	-34.2
;	Wmax                         	13.7
;	Wrange                       	47.9
; logo file:AraC.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1.png
; logo file:AraC.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1_rc.png
; Host name	compute-1-5.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.04
;	cuser	0.51
;	csystem	0.06
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