OxyR matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/OxyR/OxyR.EcolK12_2nt_upstream.20.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 /OxyR.EcolK12_2nt_upstream.20.meme_quality_logo
; Input files
;	input	/OxyR.EcolK12_2nt_upstream.20.meme_quality_matrix.tf
;	prior	/OxyR.EcolK12_2nt_upstream.20.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/OxyR.EcolK12_2nt_upstream.20.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	18	13	15	6	11	9	16	16	16	26	18	3	8	34	0	4	20	11	13	9
C	5	5	7	4	8	9	5	2	6	5	14	31	1	2	0	16	0	18	4	6
G	6	2	6	27	21	4	2	6	7	6	5	0	5	6	0	5	11	6	4	15
T	13	22	14	5	2	20	19	18	13	5	5	8	28	0	42	17	11	7	21	12
//
A  0.4  0.3  0.4  0.1  0.3  0.2  0.4  0.4  0.4  0.6  0.4  0.1  0.2  0.8  0.0  0.1  0.5  0.3  0.3  0.2
C  0.1  0.1  0.2  0.1  0.2  0.2  0.1  0.1  0.1  0.1  0.3  0.7  0.0  0.1  0.0  0.4  0.0  0.4  0.1  0.1
G  0.1  0.1  0.1  0.6  0.5  0.1  0.1  0.1  0.2  0.1  0.1  0.0  0.1  0.1  0.0  0.1  0.3  0.1  0.1  0.4
T  0.3  0.5  0.3  0.1  0.1  0.5  0.4  0.4  0.3  0.1  0.1  0.2  0.7  0.0  1.0  0.4  0.3  0.2  0.5  0.3
//
A  0.4  0.1  0.2 -0.7 -0.1 -0.3  0.3  0.3  0.3  0.7  0.4 -1.3 -0.4  1.0 -3.8 -1.1  0.5 -0.1  0.1 -0.3
C -0.5 -0.5 -0.2 -0.8 -0.1  0.0 -0.5 -1.4 -0.4 -0.5  0.5  1.3 -2.0 -1.4 -3.8  0.6 -3.8  0.7 -0.8 -0.4
G -0.3 -1.4 -0.3  1.1  0.9 -0.7 -1.4 -0.3 -0.2 -0.3 -0.5 -3.8 -0.5 -0.3 -3.8 -0.5  0.2 -0.3 -0.7  0.5
T  0.0  0.6  0.1 -0.9 -1.7  0.5  0.4  0.4  0.0 -0.9 -0.9 -0.4  0.8 -3.8  1.2  0.3 -0.1 -0.6  0.5 -0.0
//
A  0.2  0.0  0.1 -0.1 -0.0 -0.1  0.1  0.1  0.1  0.5  0.2 -0.1 -0.1  0.8 -0.0 -0.1  0.2 -0.0  0.0 -0.1
C -0.1 -0.1 -0.0 -0.1 -0.0  0.0 -0.1 -0.1 -0.1 -0.1  0.2  0.9 -0.1 -0.1 -0.0  0.2 -0.0  0.3 -0.1 -0.1
G -0.0 -0.1 -0.0  0.7  0.4 -0.1 -0.1 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 -0.1  0.1 -0.0 -0.1  0.2
T  0.0  0.3  0.0 -0.1 -0.1  0.2  0.2  0.2  0.0 -0.1 -0.1 -0.1  0.5 -0.0  1.2  0.1 -0.0 -0.1  0.3 -0.0
//
; Sites	42
>site_0
AAAGGCATAACCTATCACTG
>site_1
ATCGGGTAAACCTATCGCTA
>site_2
GTAGGTTTAACCTGTTGCAT
>site_3
ATTGCTAAAAGCTATAACTG
>site_4
ATTGGCATTATCTATTAATA
>site_5
ATTGGTTATCATTATCAATG
>site_6
TAAGCTCTTACCTATGACAG
>site_7
TAAGGTAAAACTTATCGATT
>site_8
TAAGATCTCAACTATCGCAT
>site_9
ATCGATATAAACGATCGATA
>site_10
ATCGCCATGAACTATCGTGG
>site_11
ATAGAATAAAACGATCAATA
>site_12
ATGAATATAAACTATCAATA
>site_13
ATAGCCTGTGCCTATTACCC
>site_14
TCTGATTTGACCTCTCACAG
>site_15
TCTGGCTGTTCCTATCACAC
>site_16
ATTGAAAATGACTATTTAAG
>site_17
ATGTGGTTAACCAATTTCAG
>site_18
ATAGCAATGAACGATTATCC
>site_19
GCTTGTTACCACTATTAGTG
>site_20
ATTAGCAATCATTATCATTT
>site_21
ATAGACCAGGATTATGACTA
>site_22
ATGCGTTTCCATTATCAAAT
>site_23
TTCGGCATGAATAATTTGCG
>site_24
CACTTTTTTACCTATCTCTT
>site_25
GACTATCATACCTATTGAAT
>site_26
CATGATTTCATCTCTTTCAT
>site_27
ATGGATTGTGGTGATTTCTC
>site_28
TTCGGGTTGACATGTCTTAC
>site_29
GTGGATTAATTCAATTATAA
>site_30
TTAGCAATAACAGGTTGATT
>site_31
CAGGCATAAATCTATGAGGA
>site_32
TCTGGAGGAAACTGTTTTGG
>site_33
GGAAGAAGAACTAATTGCTG
>site_34
AATCGTAATGAATATGAGAA
>site_35
TGAGGAATATACAGTAACCG
>site_36
GTTCCAGACAACAATCTGTT
>site_37
CAAAGTTATTTCCATTTCTG
>site_38
TAACGGTAACACTGTAGAGG
>site_39
CAAATTTGTAGCAATTATTT
>site_40
TATAGCACCGGCTATGTGTT
>site_41
TCTTGTCCGTGCAATAGCTC
;
; Matrix parameters
;	Number of sites              	42
;	Columns                      	20
;	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                    	WWWGRTWWWAMCTATYDMWD
;	AC                           	WWWGRTWWWAMCTATYDMWD
;	id                           	WWWGRTWWWAMCTATYDMWD
;	name                         	WWWGRTWWWAMCTATYDMWD
;	description                  	wwwGgywwwamCtATyrcwg
;	statistical_basis            	42 sequences
;	sites                        	42
;	nb_sites                     	42
;	min.prior                    	0.204024
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.29412
;	information.per.column       	0.264706
;	max.possible.info.per.col    	1.58952
;	consensus.strict             	ataGgtttaacCtATcactg
;	consensus.strict.rc          	CAGTGATAGGTTAAACCTAT
;	consensus.IUPAC              	wwwGgywwwamCtATyrcwg
;	consensus.IUPAC.rc           	CWGYRATAGKTWWWRCCWWW
;	consensus.regexp             	[at][at][at]Gg[ct][at][at][at]a[ac]CtAT[ct][ag]c[at]g
;	consensus.regexp.rc          	C[AT]G[CT][AG]ATAG[GT]T[AT][AT][AT][AG]CC[AT][AT][AT]
;	residues.content.crude.freq  	a:0.3167|c:0.1762|g:0.1714|t:0.3357
;	G+C.content.crude.freq       	0.347619
;	residues.content.corrected.freq	a:0.3161|c:0.1769|g:0.1722|t:0.3348
;	G+C.content.corrected.freq   	0.349112
;	min(P(S|M))                  	1.09355e-26
;	max(P(S|M))                  	1.1461e-06
;	proba_range                  	1.1461e-06
;	Wmin                         	-30.3
;	Wmax                         	13
;	Wrange                       	43.3
; logo file:/OxyR.EcolK12_2nt_upstream.20.meme_quality_logo_m1.png
; logo file:/OxyR.EcolK12_2nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161059
; Job done	2019-06-03.161100
; Seconds	0.55
;	user	0.55
;	system	0.05
;	cuser	0.45
;	csystem	0.05