RegulonDB
GalS matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GalS/GalS.EcolK12_1nt_upstream.19.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 /GalS.EcolK12_1nt_upstream.19.meme_quality_logo
; Input files
; input /GalS.EcolK12_1nt_upstream.19.meme_quality_matrix.tf
; prior /GalS.EcolK12_1nt_upstream.19.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GalS.EcolK12_1nt_upstream.19.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 5 0 7 3 0 0 2 7 12 3 0 3 2 0 0 8 0 10 0
C 1 3 0 0 2 1 2 3 0 0 9 0 0 0 0 0 12 2 5
G 2 4 2 6 0 9 5 0 0 6 0 8 6 0 0 0 0 0 2
T 4 5 3 3 10 2 3 2 0 3 3 1 4 12 12 4 0 0 5
//
A 0.4 0.0 0.6 0.3 0.0 0.0 0.2 0.6 0.9 0.3 0.0 0.3 0.2 0.0 0.0 0.6 0.0 0.8 0.0
C 0.1 0.2 0.0 0.0 0.2 0.1 0.2 0.2 0.0 0.0 0.7 0.0 0.0 0.0 0.0 0.0 0.9 0.2 0.4
G 0.2 0.3 0.2 0.5 0.0 0.7 0.4 0.0 0.0 0.5 0.0 0.6 0.5 0.0 0.0 0.0 0.0 0.0 0.2
T 0.3 0.4 0.3 0.3 0.8 0.2 0.3 0.2 0.0 0.3 0.3 0.1 0.3 0.9 0.9 0.3 0.0 0.0 0.4
//
A 0.3 -2.6 0.7 -0.1 -2.6 -2.6 -0.5 0.7 1.2 -0.1 -2.6 -0.1 -0.5 -2.6 -2.6 0.8 -2.6 1.0 -2.6
C -0.8 0.2 -2.6 -2.6 -0.2 -0.8 -0.2 0.2 -2.6 -2.6 1.2 -2.6 -2.6 -2.6 -2.6 -2.6 1.5 -0.2 0.7
G -0.2 0.5 -0.2 0.8 -2.6 1.2 0.7 -2.6 -2.6 0.8 -2.6 1.1 0.8 -2.6 -2.6 -2.6 -2.6 -2.6 -0.2
T 0.1 0.3 -0.2 -0.2 1.0 -0.5 -0.2 -0.5 -2.6 -0.2 -0.2 -1.1 0.1 1.2 1.2 0.1 -2.6 -2.6 0.3
//
A 0.1 -0.1 0.4 -0.0 -0.1 -0.1 -0.1 0.4 1.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 0.5 -0.1 0.8 -0.1
C -0.1 0.0 -0.0 -0.0 -0.0 -0.1 -0.0 0.0 -0.0 -0.0 0.9 -0.0 -0.0 -0.0 -0.0 -0.0 1.4 -0.0 0.3
G -0.0 0.1 -0.0 0.4 -0.0 0.9 0.3 -0.0 -0.0 0.4 -0.0 0.7 0.4 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0
T 0.0 0.1 -0.0 -0.0 0.8 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.1 0.0 1.1 1.1 0.0 -0.1 -0.1 0.1
//
; Sites 12
>site_0
TTAGTGGAATCGTTTACAC
>site_1
TTAGTGTAAGCGATTACAC
>site_2
AGATTGAAAGCGGTTACAT
>site_3
GCAATGGAAACGGTTACAG
>site_4
AGAATGTAAGCGTTTACCC
>site_5
CCGGTGGTAGCGGTTACAT
>site_6
TTGGTGTAATCGGTTTCAG
>site_7
TCTGTGGCAACGGTTTCCC
>site_8
AGTGCGCCAGCAATTACAC
>site_9
AGATTTGTAATATTTTCAT
>site_10
ATAACTCAATTATTTTCAT
>site_11
GTTTTCACAGTTGTTACAT
;
; Matrix parameters
; Number of sites 12
; Columns 19
; 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 WBADTGKAADCGKTTWCAY
; AC WBADTGKAADCGKTTWCAY
; id WBADTGKAADCGKTTWCAY
; name WBADTGKAADCGKTTWCAY
; description wbagtGgmAgCGkTTwCAy
; statistical_basis 12 sequences
; sites 12
; nb_sites 12
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 9.98039
; information.per.column 0.525284
; max.possible.info.per.col 1.58873
; consensus.strict agagtGgaAgCGgTTaCAc
; consensus.strict.rc GTGTAACCGCTTCCACTCT
; consensus.IUPAC wbagtGgmAgCGkTTwCAy
; consensus.IUPAC.rc RTGWAAMCGCTKCCACTVW
; consensus.regexp [at][cgt]agtGg[ac]AgCG[gt]TT[at]CA[ct]
; consensus.regexp.rc [AG]TG[AT]AA[AC]CGCT[GT]CCACT[ACG][AT]
; residues.content.crude.freq a:0.2719|c:0.1754|g:0.2193|t:0.3333
; G+C.content.crude.freq 0.394737
; residues.content.corrected.freq a:0.2734|c:0.1779|g:0.2181|t:0.3306
; G+C.content.corrected.freq 0.396045
; min(P(S|M)) 1.06708e-32
; max(P(S|M)) 9.29987e-05
; proba_range 9.29987e-05
; Wmin -45
; Wmax 17.4
; Wrange 62.4
; logo file:/GalS.EcolK12_1nt_upstream.19.meme_quality_logo_m1.png
; logo file:/GalS.EcolK12_1nt_upstream.19.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.58
; user 0.58
; system 0.07
; cuser 0.42
; csystem 0.05