Cra matrix and aligment

matrix-quality result

Command: matrix-quality  -v 1 -ms ./data/Matrices_NR/Cra/Cra.EcolK12_1nt_upstream.21.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 /Cra.EcolK12_1nt_upstream.21.meme_quality_logo
; Input files
;	input	/Cra.EcolK12_1nt_upstream.21.meme_quality_matrix.tf
;	prior	/Cra.EcolK12_1nt_upstream.21.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	/Cra.EcolK12_1nt_upstream.21.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	10	17	4	3	6	9	41	40	11	0	3	13	2	9	13	29	18	2	20	15
C	10	9	4	0	31	0	0	0	0	0	34	3	7	0	5	24	2	5	12	6	7
G	12	10	3	34	6	3	31	1	0	2	2	35	6	6	0	0	5	14	6	6	10
T	10	13	18	4	2	33	2	0	2	29	6	1	16	34	28	5	6	5	22	10	10
//
A  0.2  0.2  0.4  0.1  0.1  0.1  0.2  1.0  0.9  0.3  0.0  0.1  0.3  0.1  0.2  0.3  0.7  0.4  0.1  0.5  0.4
C  0.2  0.2  0.1  0.0  0.7  0.0  0.0  0.0  0.0  0.0  0.8  0.1  0.2  0.0  0.1  0.6  0.1  0.1  0.3  0.1  0.2
G  0.3  0.2  0.1  0.8  0.1  0.1  0.7  0.0  0.0  0.1  0.1  0.8  0.1  0.1  0.0  0.0  0.1  0.3  0.1  0.1  0.2
T  0.2  0.3  0.4  0.1  0.1  0.8  0.1  0.0  0.1  0.7  0.1  0.0  0.4  0.8  0.7  0.1  0.1  0.1  0.5  0.2  0.2
//
A -0.2 -0.2  0.3 -1.1 -1.3 -0.7 -0.3  1.2  1.2 -0.1 -3.8 -1.3  0.1 -1.7 -0.3  0.1  0.9  0.4 -1.7  0.5  0.2
C  0.1  0.0 -0.8 -3.8  1.3 -3.8 -3.8 -3.8 -3.8 -3.8  1.3 -1.0 -0.2 -3.8 -0.5  1.0 -1.4 -0.5  0.3 -0.4 -0.2
G  0.3  0.2 -1.0  1.4 -0.3 -1.0  1.3 -2.0 -3.8 -1.4 -1.4  1.4 -0.3 -0.3 -3.8 -3.8 -0.5  0.5 -0.3 -0.3  0.2
T -0.2  0.0  0.4 -1.1 -1.7  1.0 -1.7 -3.8 -1.7  0.8 -0.7 -2.3  0.2  1.0  0.8 -0.9 -0.7 -0.9  0.6 -0.2 -0.2
//
A -0.0 -0.0  0.1 -0.1 -0.1 -0.1 -0.1  1.1  1.1 -0.0 -0.0 -0.1  0.0 -0.1 -0.1  0.0  0.6  0.2 -0.1  0.2  0.1
C  0.0  0.0 -0.1 -0.0  0.9 -0.0 -0.0 -0.0 -0.0 -0.0  1.1 -0.1 -0.0 -0.0 -0.1  0.6 -0.1 -0.1  0.1 -0.1 -0.0
G  0.1  0.0 -0.1  1.1 -0.1 -0.1  0.9 -0.1 -0.0 -0.1 -0.1  1.1 -0.1 -0.1 -0.0 -0.0 -0.1  0.2 -0.1 -0.1  0.0
T -0.1  0.0  0.2 -0.1 -0.1  0.7 -0.1 -0.0 -0.1  0.6 -0.1 -0.1  0.1  0.8  0.5 -0.1 -0.1 -0.1  0.3 -0.1 -0.1
//
; Sites	42
>site_0
GAGGCTGAATCGTTTCAATTC
>site_1
ACAGCTGAATCGATAAAATAG
>site_2
CTAGCTGAAGCGTTTCAGTCG
>site_3
GGTGCTGAAACGATAAAGTAA
>site_4
CGCGCTGAAACGTTTCAAGAA
>site_5
CGAGCTGAATCGCTTAACCTG
>site_6
GTTGCTGAATCGTTAAGGTAG
>site_7
GGTGCTGAATCGCTTAACGAT
>site_8
GCTGCGAAATCGCTTCAGCAA
>site_9
CCAGCTTAATCGGTTCAACAG
>site_10
CCTGCTGAATTGATTCAGGTC
>site_11
TTTGCTGAATGGATTCAGTCT
>site_12
CAAGCGGAATCGTGTCAATCA
>site_13
TTTGCTAAATCGGTTCAAGTT
>site_14
GTTGCTGAATCGTTTTTTCAA
>site_15
AGTGCTGAAACCATTCAAGAG
>site_16
TTAGCTGAATCGTGTAAGAAA
>site_17
TCAGGTGAATCGCGCCAGCAA
>site_18
AAAGCTGAATCGATTTTATGA
>site_19
TTATCTGAATCGATTCGATTG
>site_20
GTAAGTGAATCGGTTCAATTC
>site_21
AACGGTGAATCGTTCAAGCAA
>site_22
CGTGGTGAATCGATACTTTAC
>site_23
TCTGATGAATCGAGCCAACAG
>site_24
CATGCTGAAGCGAGACACCAG
>site_25
GATGCTGAAAGGTGTCAGCTT
>site_26
AATGATGAAACGGTTCATCAA
>site_27
TAAGCTGAATCGTTTACAAAT
>site_28
AGGGCAAAAACGTTTCAGTCA
>site_29
GGCACTGAATCGGTTAACTGT
>site_30
GCCGCAAAATCCTTACAATAA
>site_31
GGAGCAGGATCGTATCGATCA
>site_32
CAAGTTGAAATGATTTAATTT
>site_33
AATGCAAATTTGCTTCAACAA
>site_34
TCTTGTGAATCGATCAGTTTG
>site_35
TTAACTGAAACGCATATTTGC
>site_36
AGGGCTGATTTATTACTACAC
>site_37
TCATGTAAAACGTTCTTGTTT
>site_38
ATTGTTAAATTCATATAATGC
>site_39
GTAACATAATCACTTACGTGA
>site_40
CTTGCGAAAACTGTAAACGCT
>site_41
ATATAAAAAATATTTCGGTGT
;
; Matrix parameters
;	Number of sites              	42
;	Columns                      	21
;	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                    	NNWGCTGAATCGWTTMARYWD
;	AC                           	NNWGCTGAATCGWTTMARYWD
;	id                           	NNWGCTGAATCGWTTMARYWD
;	name                         	NNWGCTGAATCGWTTMARYWD
;	description                  	sbwGCtGAAtCGwttmaryar
;	statistical_basis            	42 sequences
;	sites                        	42
;	nb_sites                     	42
;	min.prior                    	0.204185
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	9.49687
;	information.per.column       	0.452232
;	max.possible.info.per.col    	1.58873
;	consensus.strict             	ggtGCtGAAtCGtttcagtaa
;	consensus.strict.rc          	TTACTGAAACGATTCAGCACC
;	consensus.IUPAC              	sbwGCtGAAtCGwttmaryar
;	consensus.IUPAC.rc           	YTRYTKAAWCGATTCAGCWVS
;	consensus.regexp             	[cg][cgt][at]GCtGAAtCG[at]tt[ac]a[ag][ct]a[ag]
;	consensus.regexp.rc          	[CT]T[AG][CT]T[GT]AA[AT]CGATTCAGC[AT][ACG][CG]
;	residues.content.crude.freq  	a:0.3118|c:0.1803|g:0.2177|t:0.2902
;	G+C.content.crude.freq       	0.397959
;	residues.content.corrected.freq	a:0.3113|c:0.1809|g:0.2174|t:0.2904
;	G+C.content.corrected.freq   	0.39828
;	min(P(S|M))                  	6.46642e-35
;	max(P(S|M))                  	1.36591e-05
;	proba_range                  	1.36591e-05
;	Wmin                         	-48
;	Wmax                         	17.2
;	Wrange                       	65.2
; logo file:/Cra.EcolK12_1nt_upstream.21.meme_quality_logo_m1.png
; logo file:/Cra.EcolK12_1nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name	sinik
; Job started	2019-06-03.160931
; Job done	2019-06-03.160931
; Seconds	0.59
;	user	0.59
;	system	0.06
;	cuser	0.44
;	csystem	0.04