RegulonDB
GlrR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GlrR/GlrR.EcolK12_1nt_upstream.23.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 /GlrR.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /GlrR.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /GlrR.EcolK12_1nt_upstream.23.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GlrR.EcolK12_1nt_upstream.23.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 2 0 1 1 1 0 1 0 3 3 6 3 2 1 3 1 6 0 5 5 1 1 1
C 0 1 0 0 3 0 2 1 0 1 0 0 2 1 2 1 0 5 0 1 2 0 2
G 4 0 5 1 1 2 3 1 0 1 0 1 1 3 1 4 0 1 0 0 1 3 1
T 0 5 0 4 1 4 0 4 3 1 0 2 1 1 0 0 0 0 1 0 2 2 2
//
A 0.3 0.0 0.2 0.2 0.2 0.0 0.2 0.0 0.5 0.5 0.9 0.5 0.3 0.2 0.5 0.2 0.9 0.0 0.8 0.8 0.2 0.2 0.2
C 0.0 0.2 0.0 0.0 0.5 0.0 0.3 0.2 0.0 0.2 0.0 0.0 0.3 0.2 0.3 0.2 0.0 0.7 0.0 0.2 0.3 0.0 0.3
G 0.6 0.0 0.7 0.2 0.2 0.3 0.5 0.2 0.0 0.2 0.0 0.2 0.2 0.5 0.2 0.6 0.0 0.2 0.0 0.0 0.2 0.5 0.2
T 0.0 0.8 0.0 0.6 0.2 0.6 0.0 0.6 0.5 0.2 0.0 0.3 0.2 0.2 0.0 0.0 0.0 0.0 0.2 0.0 0.3 0.3 0.3
//
A 0.1 -1.9 -0.5 -0.5 -0.5 -1.9 -0.5 -1.9 0.5 0.5 1.1 0.5 0.1 -0.5 0.5 -0.5 1.1 -1.9 1.0 1.0 -0.5 -0.5 -0.5
C -1.9 -0.2 -1.9 -1.9 0.8 -1.9 0.4 -0.2 -1.9 -0.2 -1.9 -1.9 0.4 -0.2 0.4 -0.2 -1.9 1.3 -1.9 -0.2 0.4 -1.9 0.4
G 1.1 -1.9 1.3 -0.2 -0.2 0.4 0.8 -0.2 -1.9 -0.2 -1.9 -0.2 -0.2 0.8 -0.2 1.1 -1.9 -0.2 -1.9 -1.9 -0.2 0.8 -0.2
T -1.9 0.9 -1.9 0.7 -0.5 0.7 -1.9 0.7 0.5 -0.5 -1.9 0.1 -0.5 -0.5 -1.9 -1.9 -1.9 -1.9 -0.5 -1.9 0.1 0.1 0.1
//
A 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 0.2 1.0 0.2 0.0 -0.1 0.2 -0.1 1.0 -0.1 0.7 0.7 -0.1 -0.1 -0.1
C -0.1 -0.0 -0.1 -0.1 0.4 -0.1 0.1 -0.0 -0.1 -0.0 -0.1 -0.1 0.1 -0.0 0.1 -0.0 -0.1 0.9 -0.1 -0.0 0.1 -0.1 0.1
G 0.6 -0.1 1.0 -0.0 -0.0 0.1 0.4 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 0.4 -0.0 0.6 -0.1 -0.0 -0.1 -0.1 -0.0 0.4 -0.0
T -0.1 0.7 -0.1 0.4 -0.1 0.4 -0.1 0.4 0.2 -0.1 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0 0.0 0.0
//
; Sites 6
>site_0
GTGTCGCTAAAAAGAGACAACTT
>site_1
GTGTCTGTAAATCACGACAATGG
>site_2
GTGTCGCCAGAAAGCGACACGGC
>site_3
ATGAATGTTCAGGGAGAGTATTC
>site_4
ATGTTTAGTAAATTAAACAAAGA
>site_5
GCAGGTGTTTATCCGCACAACAT
;
; Matrix parameters
; Number of sites 6
; Columns 23
; 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 RTGTCKSTWAAWNGMGACAANKN
; AC RTGTCKSTWAAWNGMGACAANKN
; id RTGTCKSTWAAWNGMGACAANKN
; name RTGTCKSTWAAWNGMGACAANKN
; description RtGtckstwaAwmgmGACaayky
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.64676
; information.per.column 0.375946
; max.possible.info.per.col 1.58873
; consensus.strict GtGtctgtaaAacgaGACaacgc
; consensus.strict.rc GCGTTGTCTCGTTTTACAGACAC
; consensus.IUPAC RtGtckstwaAwmgmGACaayky
; consensus.IUPAC.rc RMRTTGTCKCKWTTWASMGACAY
; consensus.regexp [AG]tGtc[gt][cg]t[at]aA[at][ac]g[ac]GACaa[ct][gt][ct]
; consensus.regexp.rc [AG][AC][AG]TTGTC[GT]C[GT][AT]TT[AT]A[CG][AC]GACA[CT]
; residues.content.crude.freq a:0.3406|c:0.1739|g:0.2464|t:0.2391
; G+C.content.crude.freq 0.42029
; residues.content.corrected.freq a:0.3335|c:0.1787|g:0.2403|t:0.2474
; G+C.content.corrected.freq 0.419069
; min(P(S|M)) 1.44013e-30
; max(P(S|M)) 1.2222e-06
; proba_range 1.2222e-06
; Wmin -35.9
; Wmax 18.4
; Wrange 54.3
; logo file:/GlrR.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/GlrR.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.06
; cuser 0.43
; csystem 0.05