RegulonDB

RcsB matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/RcsB/RcsB.EcolK12_1nt_upstream.17.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 /RcsB.EcolK12_1nt_upstream.17.meme_quality_logo
; Input files
;	input	/RcsB.EcolK12_1nt_upstream.17.meme_quality_matrix.tf
;	prior	/RcsB.EcolK12_1nt_upstream.17.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/RcsB.EcolK12_1nt_upstream.17.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	11	3	12	13	12	9	13	8	18	7	2	0	2	0	23	24	14
C	12	3	2	0	0	3	2	0	0	2	0	25	11	1	3	0	2
G	3	4	3	8	12	4	4	4	1	2	0	1	0	14	0	0	0
T	0	16	9	5	2	10	7	14	7	15	24	0	13	11	0	2	10
//
A  0.4  0.1  0.5  0.5  0.5  0.3  0.5  0.3  0.7  0.3  0.1  0.0  0.1  0.0  0.9  0.9  0.5
C  0.5  0.1  0.1  0.0  0.0  0.1  0.1  0.0  0.0  0.1  0.0  0.9  0.4  0.0  0.1  0.0  0.1
G  0.1  0.2  0.1  0.3  0.5  0.2  0.2  0.2  0.0  0.1  0.0  0.0  0.0  0.5  0.0  0.0  0.0
T  0.0  0.6  0.3  0.2  0.1  0.4  0.3  0.5  0.3  0.6  0.9  0.0  0.5  0.4  0.0  0.1  0.4
//
A  0.4 -0.9  0.4  0.5  0.4  0.2  0.5  0.1  0.8 -0.1 -1.2 -3.3 -1.2 -3.3  1.1  1.1  0.6
C  0.8 -0.6 -0.9 -3.3 -3.3 -0.6 -0.9 -3.3 -3.3 -0.9 -3.3  1.5  0.7 -1.5 -0.6 -3.3 -0.9
G -0.5 -0.3 -0.5  0.4  0.8 -0.3 -0.3 -0.3 -1.5 -0.9 -3.3 -1.5 -3.3  0.9 -3.3 -3.3 -3.3
T -3.3  0.7  0.1 -0.4 -1.3  0.2 -0.1  0.6 -0.1  0.6  1.1 -3.3  0.5  0.3 -3.3 -1.3  0.2
//
A  0.2 -0.1  0.2  0.3  0.2  0.1  0.3  0.0  0.6 -0.0 -0.1 -0.0 -0.1 -0.0  0.9  1.0  0.3
C  0.4 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1 -0.0  1.4  0.3 -0.1 -0.1 -0.0 -0.1
G -0.1 -0.0 -0.1  0.1  0.4 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.1 -0.0  0.5 -0.0 -0.0 -0.0
T -0.0  0.4  0.1 -0.1 -0.1  0.1 -0.0  0.3 -0.0  0.4  1.0 -0.0  0.2  0.1 -0.0 -0.1  0.1
//
; Sites	26
>site_0
CTAAATGTATTCTGAAA
>site_1
CTTGATATATTCTGAAT
>site_2
ATAAATATTTTCTGAAA
>site_3
CTTTATATATTCTGAAT
>site_4
CTAAGGATTATCCGAAA
>site_5
CTAAGATTTTTCCTAAA
>site_6
CTTTATAAATTCCTAAA
>site_7
CTTTATAAATTCCTAAA
>site_8
ATAAATGATTTCTGAAA
>site_9
CTTTATGTTTTCCGAAT
>site_10
AGCAGGATATTCCGAAT
>site_11
CTAAAGAAACTCCTAAA
>site_12
CGAGTCATATTCTGAAA
>site_13
GTGAGGTTAATCCTAAA
>site_14
AGAAGAAAATACTGAAT
>site_15
GTAGGATTTATCCGCAA
>site_16
AATAACAAAATCCTAAT
>site_17
CCAGGACTAATCTTAAC
>site_18
AAAGGATATTTCAGAAA
>site_19
AGGTAAATAGTCTTAAT
>site_20
GCAGTCAGATTCTTAAA
>site_21
ACCAGATGAATCTTCAA
>site_22
ATTGAATGACACTTAAT
>site_23
ATGAGACGAATCTGATC
>site_24
CATGGTTTGGTCAGCAT
>site_25
ATTAGTGAATTGCCATT
;
; Matrix parameters
;	Number of sites              	26
;	Columns                      	17
;	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                    	MTWRRWWWATTCYKAAW
;	AC                           	MTWRRWWWATTCYKAAW
;	id                           	MTWRRWWWATTCYKAAW
;	name                         	MTWRRWWWATTCYKAAW
;	description                  	mtwrrwawatTCykAAw
;	statistical_basis            	26 sequences
;	sites                        	26
;	nb_sites                     	26
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	7.5242
;	information.per.column       	0.4426
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	ctaagtatatTCcgAAa
;	consensus.strict.rc          	TTTCGGAATATACTTAG
;	consensus.IUPAC              	mtwrrwawatTCykAAw
;	consensus.IUPAC.rc           	WTTMRGAATWTWYYWAK
;	consensus.regexp             	[ac]t[at][ag][ag][at]a[at]atTC[ct][gt]AA[at]
;	consensus.regexp.rc          	[AT]TT[AC][AG]GAAT[AT]T[AT][CT][CT][AT]A[GT]
;	residues.content.crude.freq  	a:0.3869|c:0.1493|g:0.1357|t:0.3281
;	G+C.content.crude.freq       	0.285068
;	residues.content.corrected.freq	a:0.3833|c:0.1515|g:0.1383|t:0.3269
;	G+C.content.corrected.freq   	0.28976
;	min(P(S|M))                  	8.50637e-31
;	max(P(S|M))                  	9.49802e-05
;	proba_range                  	9.49802e-05
;	Wmin                         	-43.8
;	Wmax                         	13.2
;	Wrange                       	57
; logo file:/RcsB.EcolK12_1nt_upstream.17.meme_quality_logo_m1.png
; logo file:/RcsB.EcolK12_1nt_upstream.17.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.161059
; Job done	2019-06-03.161100
; Seconds	0.6
;	user	0.6
;	system	0.06
;	cuser	0.42
;	csystem	0.04
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