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TorR matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/TorR/TorR.EcolK12_2nt_upstream.13.meme 

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 /TorR.EcolK12_2nt_upstream.13.meme_quality_logo
; Input files
;	input	/TorR.EcolK12_2nt_upstream.13.meme_quality_matrix.tf
;	prior	/TorR.EcolK12_2nt_upstream.13.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/TorR.EcolK12_2nt_upstream.13.meme_quality_matrix_info.txt
; Output format       	tab
; pseudo-weight       	1
; Background model
;	Strand        	undef
;	Background pseudo-frequency	0.01
;	Residue probabilities
;		a	0.29114
;		c	0.20781
;		g	0.20402
;		t	0.29702
A	4	8	7	0	7	2	3	8	9	1	7	1	8
C	1	0	0	3	1	0	0	0	0	7	2	0	2
G	1	2	1	1	2	0	6	0	0	0	1	9	0
T	4	0	2	6	0	8	1	2	1	2	0	0	0
//
A  0.4  0.8  0.7  0.0  0.7  0.2  0.3  0.8  0.8  0.1  0.7  0.1  0.8
C  0.1  0.0  0.0  0.3  0.1  0.0  0.0  0.0  0.0  0.7  0.2  0.0  0.2
G  0.1  0.2  0.1  0.1  0.2  0.0  0.6  0.0  0.0  0.0  0.1  0.8  0.0
T  0.4  0.0  0.2  0.6  0.0  0.8  0.1  0.2  0.1  0.2  0.0  0.0  0.0
//
A  0.3  1.0  0.8 -2.4  0.8 -0.3  0.0  1.0  1.1 -0.9  0.8 -0.9  1.0
C -0.6 -2.4 -2.4  0.3 -0.6 -2.4 -2.4 -2.4 -2.4  1.1 -0.0 -2.4 -0.0
G -0.6 -0.0 -0.6 -0.6 -0.0 -2.4  1.0 -2.4 -2.4 -2.4 -0.6  1.4 -2.4
T  0.3 -2.4 -0.4  0.7 -2.4  0.9 -0.9 -0.4 -0.9 -0.4 -2.4 -2.4 -2.4
//
A  0.1  0.7  0.5 -0.1  0.5 -0.1  0.0  0.7  0.9 -0.1  0.5 -0.1  0.7
C -0.1 -0.0 -0.0  0.1 -0.1 -0.0 -0.0 -0.0 -0.0  0.8 -0.0 -0.0 -0.0
G -0.1 -0.0 -0.1 -0.1 -0.0 -0.0  0.6 -0.0 -0.0 -0.0 -0.1  1.2 -0.0
T  0.1 -0.1 -0.1  0.4 -0.1  0.7 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1
//
; Sites	10
>site_0
AAATATGAACAGC
>site_1
GAATATGAACAGA
>site_2
AGATATGAACAGA
>site_3
AAATGTGAATCGA
>site_4
TATTAAAAACAGA
>site_5
AAACGTGAATCGA
>site_6
TGACATATACAGA
>site_7
TATCAAAATCAGA
>site_8
CAGGATGAACGGC
>site_9
TAATCTTTAAAAA
;
; Matrix parameters
;	Number of sites              	10
;	Columns                      	13
;	Rows                         	4
;	Alphabet                     	A|C|G|T
;	Prior                        	A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	WAAYATRAACAGA
;	AC                           	WAAYATRAACAGA
;	id                           	WAAYATRAACAGA
;	name                         	WAAYATRAACAGA
;	description                  	waayatRaACaGa
;	statistical_basis            	10 sequences
;	sites                        	10
;	nb_sites                     	10
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	6.5178
;	information.per.column       	0.50137
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	aaatatGaACaGa
;	consensus.strict.rc          	TCTGTTCATATTT
;	consensus.IUPAC              	waayatRaACaGa
;	consensus.IUPAC.rc           	TCTGTTYATRTTW
;	consensus.regexp             	[at]aa[ct]at[AG]aACaGa
;	consensus.regexp.rc          	TCTGTT[CT]AT[AG]TT[AT]
;	residues.content.crude.freq  	a:0.5000|c:0.1231|g:0.1769|t:0.2000
;	G+C.content.crude.freq       	0.3
;	residues.content.corrected.freq	a:0.4810|c:0.1308|g:0.1794|t:0.2088
;	G+C.content.corrected.freq   	0.310167
;	min(P(S|M))                  	5.90597e-22
;	max(P(S|M))                  	0.00549382
;	proba_range                  	0.00549382
;	Wmin                         	-29.5
;	Wmax                         	11.9
;	Wrange                       	41.4
; logo file:/TorR.EcolK12_2nt_upstream.13.meme_quality_logo_m1.png
; logo file:/TorR.EcolK12_2nt_upstream.13.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161114
; Job done	2019-06-03.161114
; Seconds	0.5
;	user	0.5
;	system	0.04
;	cuser	0.41
;	csystem	0.04
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