GadX matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/GadX/GadX.EcolK12_1nt_upstream.22.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 /GadX.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
;	input	/GadX.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
;	prior	/GadX.EcolK12_1nt_upstream.22.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/GadX.EcolK12_1nt_upstream.22.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	0.29093
;		c	0.20756
;		g	0.20418
;		t	0.29732
A	8	15	19	6	16	5	18	20	25	16	25	4	12	19	6	19	8	17	10	8	14	6
C	4	3	6	7	2	6	7	5	2	8	1	8	20	5	4	9	18	7	2	3	2	8
G	1	7	3	2	12	4	4	7	3	1	3	2	1	5	14	5	0	1	2	8	3	3
T	21	9	6	19	4	19	5	2	4	9	5	20	1	5	10	1	8	9	20	15	15	17
//
A  0.2  0.4  0.6  0.2  0.5  0.2  0.5  0.6  0.7  0.5  0.7  0.1  0.4  0.6  0.2  0.6  0.2  0.5  0.3  0.2  0.4  0.2
C  0.1  0.1  0.2  0.2  0.1  0.2  0.2  0.1  0.1  0.2  0.0  0.2  0.6  0.1  0.1  0.3  0.5  0.2  0.1  0.1  0.1  0.2
G  0.0  0.2  0.1  0.1  0.3  0.1  0.1  0.2  0.1  0.0  0.1  0.1  0.0  0.1  0.4  0.1  0.0  0.0  0.1  0.2  0.1  0.1
T  0.6  0.3  0.2  0.6  0.1  0.6  0.2  0.1  0.1  0.3  0.2  0.6  0.0  0.2  0.3  0.0  0.2  0.3  0.6  0.4  0.4  0.5
//
A -0.2  0.4  0.6 -0.5  0.5 -0.7  0.6  0.7  0.9  0.5  0.9 -0.9  0.2  0.6 -0.5  0.6 -0.2  0.5  0.0 -0.2  0.3 -0.5
C -0.5 -0.8 -0.2 -0.0 -1.2 -0.2 -0.0 -0.3 -1.2  0.1 -1.8  0.1  1.0 -0.3 -0.5  0.2  0.9 -0.0 -1.2 -0.8 -1.2  0.1
G -1.8  0.0 -0.8 -1.2  0.5 -0.5 -0.5  0.0 -0.8 -1.8 -0.8 -1.2 -1.8 -0.3  0.7 -0.3 -3.6 -1.8 -1.2  0.1 -0.8 -0.8
T  0.7 -0.1 -0.5  0.6 -0.9  0.6 -0.7 -1.5 -0.9 -0.1 -0.7  0.7 -2.1 -0.7 -0.0 -2.1 -0.2 -0.1  0.7  0.4  0.4  0.5
//
A -0.0  0.2  0.4 -0.1  0.2 -0.1  0.3  0.4  0.7  0.2  0.7 -0.1  0.1  0.4 -0.1  0.4 -0.0  0.3  0.0 -0.0  0.1 -0.1
C -0.1 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.1  0.0 -0.1  0.0  0.6 -0.0 -0.1  0.1  0.5 -0.0 -0.1 -0.1 -0.1  0.0
G -0.1  0.0 -0.1 -0.1  0.2 -0.1 -0.1  0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0  0.3 -0.0 -0.0 -0.1 -0.1  0.0 -0.1 -0.1
T  0.4 -0.0 -0.1  0.3 -0.1  0.3 -0.1 -0.1 -0.1 -0.0 -0.1  0.4 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0  0.4  0.2  0.2  0.3
//
; Sites	34
>site_0
AAATATCAAAATCAGATATTTT
>site_1
TCACGTAAAAATCAGACCTTAA
>site_2
TAATATTAAAAACAGACTTTAT
>site_3
TACGGAAAATATCAGCCATGAT
>site_4
GGATATAAACATCAGACAGGTT
>site_5
TAACGCAATCATCGCACCTTTC
>site_6
AAATATTAAAACCATAATAGAT
>site_7
TAATATAAACATTTAACATGAT
>site_8
TCATTGAAAAACAATACAATAT
>site_9
TTACGTTACTATCAGGCATATC
>site_10
TTATCGATAAATCCTACTTTTT
>site_11
TTTTATAAACATAAGCTATACG
>site_12
TGGAAATAAGATCAGCCATTTT
>site_13
AATTAGCCATTTCAAACATTAT
>site_14
TACTATCCTTATCAACAAATAT
>site_15
CTAAGCAGAAAAACGACTTTTT
>site_16
ATTTATAAAATTATTACATAAA
>site_17
CAATAAAAAAGTAGGATTTATC
>site_18
TATTACGCGAATAATATTTTTT
>site_19
TGCAGTCGATTTAATAAAAATT
>site_20
CGCAATGGAAGCAAGGCATTAC
>site_21
TTTTAGCTAAATCTGCTATCTC
>site_22
TTATTTCAATACAATGAGTTAC
>site_23
CAGGGCAGAAAGCATCCAATAA
>site_24
TAATTTAAATAACAAAATCCTA
>site_25
TTATGCACTTGCATAACCTGTT
>site_26
TCAAGTACTAATAGTGATATTT
>site_27
AGATGATGACTTCCCACCGAAT
>site_28
AGACACAGAATGCGCATAAAAA
>site_29
TATCTTAGATACCCCTCCAAGC
>site_30
TACTGAGAGCACAAAGTTTCCC
>site_31
TAAAGTAAGCAAGTGCAAAGGA
>site_32
ATGCCTGAAAATCGGCACCGGG
>site_33
AGCCATCACCCCCCTCTCAGTG
;
; Matrix parameters
;	Number of sites              	34
;	Columns                      	22
;	Rows                         	4
;	Alphabet                     	A|C|G|T
;	Prior                        	A:0.290929484294843|C:0.207560750607506|G:0.204184816848168|T:0.297324948249482|a:0.290929484294843|c:0.207560750607506|g:0.204184816848168|t:0.297324948249482
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	TWATRTAAAHATMAKACWWDWT
;	AC                           	TWATRTAAAHATMAKACWWDWT
;	id                           	TWATRTAAAHATMAKACWWDWT
;	name                         	TWATRTAAAHATMAKACWWDWT
;	description                  	tratrtaramayMagmcawkwy
;	statistical_basis            	34 sequences
;	sites                        	34
;	nb_sites                     	34
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	4.85368
;	information.per.column       	0.220622
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	taatgtaaaaatCagacatttt
;	consensus.strict.rc          	AAAATGTCTGATTTTTACATTA
;	consensus.IUPAC              	tratrtaramayMagmcawkwy
;	consensus.IUPAC.rc           	RWMWTGKCTKRTKTYTAYATYA
;	consensus.regexp             	t[ag]at[ag]ta[ag]a[ac]a[ct][AC]ag[ac]ca[at][gt][at][ct]
;	consensus.regexp.rc          	[AG][AT][AC][AT]TG[GT]CT[GT][AG]T[GT]T[CT]TA[CT]AT[CT]A
;	residues.content.crude.freq  	a:0.3957|c:0.1832|g:0.1217|t:0.2995
;	G+C.content.crude.freq       	0.304813
;	residues.content.corrected.freq	a:0.3927|c:0.1839|g:0.1240|t:0.2994
;	G+C.content.corrected.freq   	0.307868
;	min(P(S|M))                  	7.80716e-28
;	max(P(S|M))                  	8.86671e-07
;	proba_range                  	8.86671e-07
;	Wmin                         	-29.3
;	Wmax                         	14.2
;	Wrange                       	43.5
; logo file:/GadX.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/GadX.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.160930
; Job done	2019-06-03.160931
; Seconds	0.62
;	user	0.62
;	system	0.05
;	cuser	0.47
;	csystem	0.05