SoxS matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/SoxS/SoxS.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 /SoxS.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
;	input	/SoxS.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
;	prior	/SoxS.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	/SoxS.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	10	7	13	8	2	2	13	12	1	12	10	9	6	8	6	4	0	0	4	13	3	8
C	3	9	1	2	1	0	3	5	17	10	2	1	3	7	1	1	1	25	18	1	7	8
G	9	7	8	1	4	3	11	10	4	6	8	3	1	0	20	2	31	2	4	12	0	4
T	10	9	10	21	25	27	5	5	10	4	12	19	22	17	5	25	0	5	6	6	22	12
//
A  0.3  0.2  0.4  0.3  0.1  0.1  0.4  0.4  0.0  0.4  0.3  0.3  0.2  0.3  0.2  0.1  0.0  0.0  0.1  0.4  0.1  0.3
C  0.1  0.3  0.0  0.1  0.0  0.0  0.1  0.2  0.5  0.3  0.1  0.0  0.1  0.2  0.0  0.0  0.0  0.8  0.6  0.0  0.2  0.2
G  0.3  0.2  0.2  0.0  0.1  0.1  0.3  0.3  0.1  0.2  0.2  0.1  0.0  0.0  0.6  0.1  0.9  0.1  0.1  0.4  0.0  0.1
T  0.3  0.3  0.3  0.6  0.8  0.8  0.2  0.2  0.3  0.1  0.4  0.6  0.7  0.5  0.2  0.8  0.0  0.2  0.2  0.2  0.7  0.4
//
A  0.1 -0.3  0.3 -0.1 -1.4 -1.4  0.3  0.2 -2.0  0.2  0.1 -0.0 -0.4 -0.1 -0.4 -0.8 -3.5 -3.5 -0.8  0.3 -1.1 -0.1
C -0.8  0.3 -1.7 -1.1 -1.7 -3.5 -0.8 -0.3  0.9  0.4 -1.1 -1.7 -0.8  0.1 -1.7 -1.7 -1.7  1.3  1.0 -1.7  0.1  0.2
G  0.3  0.1  0.2 -1.7 -0.5 -0.7  0.5  0.4 -0.5 -0.1  0.2 -0.7 -1.7 -3.5  1.1 -1.1  1.5 -1.1 -0.5  0.6 -3.5 -0.5
T  0.0 -0.1  0.0  0.8  0.9  1.0 -0.6 -0.6  0.0 -0.8  0.2  0.7  0.8  0.6 -0.6  0.9 -3.5 -0.6 -0.4 -0.4  0.8  0.2
//
A  0.0 -0.1  0.1 -0.0 -0.1 -0.1  0.1  0.1 -0.1  0.1  0.0 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1  0.1 -0.1 -0.0
C -0.1  0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0  0.5  0.1 -0.1 -0.1 -0.1  0.0 -0.1 -0.1 -0.1  1.0  0.5 -0.1  0.0  0.0
G  0.1  0.0  0.0 -0.1 -0.1 -0.1  0.2  0.1 -0.1 -0.0  0.0 -0.1 -0.1 -0.0  0.7 -0.1  1.4 -0.1 -0.1  0.2 -0.0 -0.1
T  0.0 -0.0  0.0  0.5  0.7  0.8 -0.1 -0.1  0.0 -0.1  0.1  0.4  0.6  0.3 -0.1  0.7 -0.0 -0.1 -0.1 -0.1  0.6  0.1
//
; Sites	32
>site_0
GAATTTGTCATTTTGTGCCGTG
>site_1
ATGTTTGGTCTTTCGTGCCATG
>site_2
TTGTTTGGTTTTTCGTGCCATA
>site_3
CTATTTAACCGTTAGTGCCTCC
>site_4
TAAATTGCCCATTTGTGCCACG
>site_5
TGTTTTGACATTCAGTGCTGTC
>site_6
TGATTTGATCGATTGAGCCTTC
>site_7
GCTTTTAGCAATTAATGCAACA
>site_8
TCATTTGATCCATTATGCCTTA
>site_9
AAGGTTGGCGTTACGTGCCATA
>site_10
GCGTTTTACAGTTTCTGCTTTT
>site_11
CGATTTAGCAAAACGTGGCATC
>site_12
TGTTTTGTCAAAATGTGCAACT
>site_13
AGATGTAGTGGTTTATGCGATG
>site_14
AAATTGACAGATTTGTGCCATT
>site_15
TCTTTTATCAATTTGGGTTGTT
>site_16
GTGTTTAACAGTTATAGCTTTT
>site_17
GATAATAGCATTTTTTGCTGTT
>site_18
GCATTTTCGCTTTTGTGTCCCC
>site_19
ATTTTTAACGTAACGAGCGACT
>site_20
TCATGTAGCACAGTGTGCAGTC
>site_21
CGTATTAATAGATAATGCCAAT
>site_22
ATGTGATGGTTTTAGTGCCGTT
>site_23
AGCACTCCCCTTTTGTGCGGTC
>site_24
AATCTTAATGAAACGTGTCGTA
>site_25
ACGCTTATCCACCCGTGCGATT
>site_26
GAAAATGATTATCAATGCCGTA
>site_27
TTAATTCATCTGTTGGGGAGTA
>site_28
GTTAGGTGCTTATTTCGCCATT
>site_29
ATGTTTCAGGGGAAAAGCCGAC
>site_30
TCTATAGCGCATTTTTCTCGCT
>site_31
GCATTGTTTAGGTTTTGTTTAA
;
; Matrix parameters
;	Number of sites              	32
;	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                    	DNDTTTRRYVDTTTGTGCCRTH
;	AC                           	DNDTTTRRYVDTTTGTGCCRTH
;	id                           	DNDTTTRRYVDTTTGTGCCRTH
;	name                         	DNDTTTRRYVDTTTGTGCCRTH
;	description                  	dsdttTrrymdttyGtGCcryy
;	statistical_basis            	32 sequences
;	sites                        	32
;	nb_sites                     	32
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.24732
;	information.per.column       	0.329424
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	gcattTggccttttGtGCcgtt
;	consensus.strict.rc          	AACGGCACAAAAGGCCAAATGC
;	consensus.IUPAC              	dsdttTrrymdttyGtGCcryy
;	consensus.IUPAC.rc           	RRYGGCACRAAHKRYYAAAHSH
;	consensus.regexp             	[agt][cg][agt]ttT[ag][ag][ct][ac][agt]tt[ct]GtGCc[ag][ct][ct]
;	consensus.regexp.rc          	[AG][AG][CT]GGCAC[AG]AA[ACT][GT][AG][CT][CT]AAA[ACT][CG][ACT]
;	residues.content.crude.freq  	a:0.2145|c:0.1790|g:0.2131|t:0.3935
;	G+C.content.crude.freq       	0.392045
;	residues.content.corrected.freq	a:0.2168|c:0.1798|g:0.2128|t:0.3906
;	G+C.content.corrected.freq   	0.392642
;	min(P(S|M))                  	1.07708e-31
;	max(P(S|M))                  	6.17966e-07
;	proba_range                  	6.17966e-07
;	Wmin                         	-39
;	Wmax                         	15.8
;	Wrange                       	54.8
; logo file:/SoxS.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/SoxS.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161114
; Job done	2019-06-03.161115
; Seconds	0.56
;	user	0.56
;	system	0.04
;	cuser	0.45
;	csystem	0.05