RegulonDB

ArcA matrix and aligment

matrix-quality result

Command: 
ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality

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 ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo
; Input files
;	input	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality_matrix.tf
;	prior	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality1nt_upstream-noorf_Escherichia_coli_K_12_substr__MG1655_uid57779-ovlp-1str.freq.gz_inclusive.tab
; Input format        	transfac
; Output files
;	output	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_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	0.29063
;		c	0.20784
;		g	0.20492
;		t	0.29662
A	8	4	7	18	62	47	12	29	52	26	28	23	14	15	24	44	33
C	0	0	2	0	3	5	18	16	3	12	12	6	7	5	7	3	20
G	13	63	0	3	9	2	6	7	4	5	12	11	34	5	10	15	1
T	56	10	68	56	3	23	41	25	18	34	25	37	22	52	36	15	23
//
a  0.1  0.1  0.1  0.2  0.8  0.6  0.2  0.4  0.7  0.3  0.4  0.3  0.2  0.2  0.3  0.6  0.4
c  0.0  0.0  0.0  0.0  0.0  0.1  0.2  0.2  0.0  0.2  0.2  0.1  0.1  0.1  0.1  0.0  0.3
g  0.2  0.8  0.0  0.0  0.1  0.0  0.1  0.1  0.1  0.1  0.2  0.1  0.4  0.1  0.1  0.2  0.0
t  0.7  0.1  0.9  0.7  0.0  0.3  0.5  0.3  0.2  0.4  0.3  0.5  0.3  0.7  0.5  0.2  0.3
//
a -1.0 -1.7 -1.1 -0.2  1.0  0.7 -0.6  0.3  0.8  0.1  0.2  0.0 -0.5 -0.4  0.1  0.7  0.4
c -4.4 -4.4 -2.0 -4.4 -1.6 -1.1  0.1 -0.0 -1.6 -0.3 -0.3 -1.0 -0.8 -1.1 -0.8 -1.6  0.2
g -0.2  1.4 -4.4 -1.6 -0.6 -2.0 -0.9 -0.8 -1.3 -1.1 -0.3 -0.4  0.8 -1.1 -0.4 -0.0 -2.6
t  0.9 -0.8  1.1  0.9 -1.9  0.0  0.6  0.1 -0.2  0.4  0.1  0.5 -0.0  0.8  0.5 -0.4  0.0
//
a -0.1 -0.1 -0.1 -0.1  0.8  0.4 -0.1  0.1  0.6  0.0  0.1  0.0 -0.1 -0.1  0.0  0.4  0.2
c -0.0 -0.0 -0.1 -0.0 -0.1 -0.1  0.0 -0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1  0.1
g -0.0  1.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1  0.3 -0.1 -0.1 -0.0 -0.0
t  0.6 -0.1  0.9  0.6 -0.1  0.0  0.3  0.0 -0.1  0.2  0.0  0.2 -0.0  0.5  0.2 -0.1  0.0
//
; Sites	77
>site_0
TGTTAACAAAAATAAAA
>site_1
GGTTAATAATAATTATA
>site_2
TATTAATCAAAATTAAC
>site_3
TGTTAACAATTTTTAAA
>site_4
TTTAAATTTTGACTAAT
>site_5
TGATAATCACCTTTCTC
>site_6
AATTAACGAAGTTTTTA
>site_7
TTTTATGTTGCTTTTTT
>site_8
TGTAATTATATTGTAAA
>site_9
TGTTTATCTATTAAAGC
>site_10
TGTTACGAATTTGATTT
>site_11
TGTTACTATTTAAAATC
>site_12
TGTTAAATAATTGTTTT
>site_13
TGTTAATTATAAAGTAA
>site_14
TGTTGTTATCGATTTGC
>site_15
GGAAATATTTAACTTGA
>site_16
AGTTAATCTTAGGTGAA
>site_17
TGTAACAACTTTGTTGA
>site_18
TGTAATGATTTTGTGAA
>site_19
TGTTAATCTGGACCTAC
>site_20
AGTTAATTATAATATAA
>site_21
AGTTAACTTATAATTAT
>site_22
AGTTAACTAAATGTTAA
>site_23
TGTTAATCATGTTTCAA
>site_24
GGTGATCAATTTATAGC
>site_25
TGTTAATAAAAACTCAA
>site_26
TGATATTTATAGCAAAA
>site_27
TGTTAGTATCTCGTCGC
>site_28
GGATAATCAAATATTTA
>site_29
GGTTAAATATCGGTAAT
>site_30
TTTTTATCGCTAAAAGA
>site_31
TGTTAATAAAGCGTAGT
>site_32
TTTAGTCCACTTTTTAC
>site_33
TTTTGTCAAAATGTGCA
>site_34
TGAAGTTGAAACGTGAT
>site_35
TGTAATAAATAAAGGGC
>site_36
TGTTAATCAAGTTTTGT
>site_37
TGTTAATTAAGAGCTAT
>site_38
TGTTAATAACCATTAAT
>site_39
TATTAACCAATTGTTAA
>site_40
TGTAATTGGCTTGTCAA
>site_41
TGTTAATGATTTGTAAT
>site_42
TTTTAATTAATTTATTT
>site_43
TTTTAATTACAGGATGT
>site_44
TGTTATCAAATCGTTAC
>site_45
TGTTCATTATATTTTCC
>site_46
TGTTATTGACAGTTAGC
>site_47
GGCAATTTTTAACGTAA
>site_48
TGTGAACCACTTGTTTG
>site_49
TGTTAATTAACAATGTA
>site_50
TGTTTGTTTTCGGTGAA
>site_51
GGTTAATGATGTGAATA
>site_52
AGTTAATATTATGTTAA
>site_53
TGTTGATATTATGTAAA
>site_54
TGTAAAAAAATGGTTAA
>site_55
TGTTGCAAGTATGTTTC
>site_56
TAAAATCCATTTGCGAC
>site_57
TTTACATCAACTTATGC
>site_58
TGCTAACAAAATGTTGC
>site_59
TGTGATCAAGCCTGCAC
>site_60
ATTTAACATTGAGTTAA
>site_61
TGTAATTAATTAAAGCA
>site_62
TGTAAAATAATTGTTAT
>site_63
TGTAACAAATCATTTAA
>site_64
GTTTATCAATATAATAA
>site_65
GGTTAACTAAATGTTAT
>site_66
TGTTGTGTAGGGATAAT
>site_67
TGTTAAAAATATGCAAA
>site_68
TGATAATCATTTTCAAT
>site_69
AGTTAATTAAATGATAT
>site_70
GGTTCATTATAGTTAAT
>site_71
GGTTAATTATGACACAA
>site_72
TGTTGTGTAACAATGTC
>site_73
TGTTGTGACCTCGGTTC
>site_74
TGTAAACGCGCGATTGT
>site_75
GGTTAAATTTATGTAAT
>site_76
GGTAATACGCCGTTAAT
;
; Matrix parameters
;	Columns                      	17
;	Rows                         	4
;	Alphabet                     	a|c|g|t
;	Prior                        	a:0.2906296|c:0.2078359|g:0.2049154|t:0.2966191
;	program                      	transfac
;	matrix.nb                    	1
;	accession                    	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons1
;	AC                           	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons1
;	id                           	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons1
;	name                         	ArcA.1nt_upstream-noorf-ovlp-2str.17.cons1
;	description                  	tGTtAwywawwwgtwah
;	statistical_basis            	77 sequences
;	sites                        	77
;	min.prior                    	0.204915
;	alphabet.size                	4
;	max.bits                     	2
;	total.information            	5.39373
;	information.per.column       	0.317278
;	max.possible.info.per.col    	1.58516
;	consensus.strict             	tGTtAataatatgttaa
;	consensus.strict.rc          	TTAACATATTATTAACA
;	consensus.IUPAC              	tGTtAwywawwwgtwah
;	consensus.IUPAC.rc           	DTWACWWWTWRWTAACA
;	consensus.regexp             	tGTtA[at][ct][at]a[at][at][at]gt[at]a[act]
;	consensus.regexp.rc          	[AGT]T[AT]AC[AT][AT][AT]T[AT][AG][AT]TAACA
;	residues.content.crude.freq  	a:0.3407|c:0.0909|g:0.1528|t:0.4156
;	G+C.content.crude.freq       	0.243697
;	residues.content.corrected.freq	a:0.3401|c:0.0924|g:0.1535|t:0.4141
;	G+C.content.corrected.freq   	0.245865
;	min(P(S|M))                  	5.25279e-27
;	max(P(S|M))                  	6.03111e-05
;	proba_range                  	6.03111e-05
;	Wmin                         	-34.1
;	Wmax                         	11.9
;	Wrange                       	46
; logo file:ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1.png
; logo file:ArcA.1nt_upstream-noorf-ovlp-2str.17.cons_quality_logo_m1_rc.png
; Host name	compute-1-10.local
; Job started	2015-08-06.164341
; Job done	2015-08-06.164342
; Seconds	0.31
;	user	0.31
;	system	0.05
;	cuser	0.53
;	csystem	0.05
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