RegulonDB
GcvA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GcvA/GcvA.EcolK12_1nt_upstream.18.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 /GcvA.EcolK12_1nt_upstream.18.meme_quality_logo
; Input files
; input /GcvA.EcolK12_1nt_upstream.18.meme_quality_matrix.tf
; prior /GcvA.EcolK12_1nt_upstream.18.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GcvA.EcolK12_1nt_upstream.18.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 0 1 6 2 5 2 2 4 2 1 0 4 6 0 1 0 0 2
C 1 1 0 2 0 0 0 0 1 5 0 0 0 0 0 1 3 0
G 1 2 0 0 0 0 0 0 1 0 0 0 0 0 4 4 1 0
T 4 2 0 2 1 4 4 2 2 0 6 2 0 6 1 1 2 4
//
A 0.0 0.2 0.9 0.3 0.8 0.3 0.3 0.6 0.3 0.2 0.0 0.6 0.9 0.0 0.2 0.0 0.0 0.3
C 0.2 0.2 0.0 0.3 0.0 0.0 0.0 0.0 0.2 0.7 0.0 0.0 0.0 0.0 0.0 0.2 0.5 0.0
G 0.2 0.3 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.6 0.6 0.2 0.0
T 0.6 0.3 0.0 0.3 0.2 0.6 0.6 0.3 0.3 0.0 0.9 0.3 0.0 0.9 0.2 0.2 0.3 0.6
//
A -1.9 -0.5 1.1 0.1 1.0 0.1 0.1 0.7 0.1 -0.5 -1.9 0.7 1.1 -1.9 -0.5 -1.9 -1.9 0.1
C -0.2 -0.2 -1.9 0.4 -1.9 -1.9 -1.9 -1.9 -0.2 1.3 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 0.8 -1.9
G -0.2 0.4 -1.9 -1.9 -1.9 -1.9 -1.9 -1.9 -0.2 -1.9 -1.9 -1.9 -1.9 -1.9 1.1 1.1 -0.2 -1.9
T 0.7 0.1 -1.9 0.1 -0.5 0.7 0.7 0.1 0.1 -1.9 1.1 0.1 -1.9 1.1 -0.5 -0.5 0.1 0.7
//
A -0.1 -0.1 1.0 0.0 0.7 0.0 0.0 0.5 0.0 -0.1 -0.1 0.5 1.0 -0.1 -0.1 -0.1 -0.1 0.0
C -0.0 -0.0 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.9 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.4 -0.1
G -0.0 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.6 0.6 -0.0 -0.1
T 0.4 0.0 -0.1 0.0 -0.1 0.4 0.4 0.0 0.0 -0.1 1.0 0.0 -0.1 1.0 -0.1 -0.1 0.0 0.4
//
; Sites 6
>site_0
TCACATTAGCTTATGGTT
>site_1
TTATATTTTCTAATGCCA
>site_2
GGACAATTTATAATGGCT
>site_3
TTAAAAAAACTAATAGGT
>site_4
TGAAATAAACTAATTTCA
>site_5
CAATTTTACCTTATGGTT
;
; Matrix parameters
; Number of sites 6
; Columns 18
; 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 TNAHAWWWNCTWATGGYW
; AC TNAHAWWWNCTWATGGYW
; id TNAHAWWWNCTWATGGYW
; name TNAHAWWWNCTWATGGYW
; description tkAhawwwwCTwATGGyw
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 7.99964
; information.per.column 0.444425
; max.possible.info.per.col 1.58873
; consensus.strict tgAcattaaCTaATGGct
; consensus.strict.rc AGCCATTAGTTAATGTCA
; consensus.IUPAC tkAhawwwwCTwATGGyw
; consensus.IUPAC.rc WRCCATWAGWWWWTDTMA
; consensus.regexp t[gt]A[act]a[at][at][at][at]CT[at]ATGG[ct][at]
; consensus.regexp.rc [AT][AG]CCAT[AT]AG[AT][AT][AT][AT]T[AGT]T[AC]A
; residues.content.crude.freq a:0.3519|c:0.1296|g:0.1204|t:0.3981
; G+C.content.crude.freq 0.25
; residues.content.corrected.freq a:0.3431|c:0.1408|g:0.1323|t:0.3837
; G+C.content.corrected.freq 0.273107
; min(P(S|M)) 2.39677e-26
; max(P(S|M)) 0.000114616
; proba_range 0.000114616
; Wmin -31.8
; Wmax 15.1
; Wrange 46.9
; logo file:/GcvA.EcolK12_1nt_upstream.18.meme_quality_logo_m1.png
; logo file:/GcvA.EcolK12_1nt_upstream.18.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 0.4
; csystem 0.04