RegulonDB
GadE matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GadE/GadE.EcolK12_2nt_upstream.22.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 /GadE.EcolK12_2nt_upstream.22.meme_quality_logo
; Input files
; input /GadE.EcolK12_2nt_upstream.22.meme_quality_matrix.tf
; prior /GadE.EcolK12_2nt_upstream.22.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GadE.EcolK12_2nt_upstream.22.meme_quality_matrix_info.txt
; Output format tab
; pseudo-weight 1
; Background model
; Strand undef
; Background pseudo-frequency 0.01
; Residue probabilities
; a 0.29114
; c 0.20781
; g 0.20402
; t 0.29702
A 2 1 2 6 6 7 1 10 7 3 6 9 6 6 1 1 1 1 8 5 3 2
C 1 1 0 2 0 1 0 0 0 3 2 0 2 2 1 8 7 0 0 2 0 5
G 0 3 1 0 1 0 1 0 2 0 0 0 0 0 1 0 0 2 0 2 2 1
T 7 5 7 2 3 2 8 0 1 4 2 1 2 2 7 1 2 7 2 1 5 2
//
A 0.2 0.1 0.2 0.6 0.6 0.7 0.1 0.9 0.7 0.3 0.6 0.8 0.6 0.6 0.1 0.1 0.1 0.1 0.8 0.5 0.3 0.2
C 0.1 0.1 0.0 0.2 0.0 0.1 0.0 0.0 0.0 0.3 0.2 0.0 0.2 0.2 0.1 0.7 0.7 0.0 0.0 0.2 0.0 0.5
G 0.0 0.3 0.1 0.0 0.1 0.0 0.1 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.2 0.0 0.2 0.2 0.1
T 0.7 0.5 0.7 0.2 0.3 0.2 0.8 0.0 0.1 0.4 0.2 0.1 0.2 0.2 0.7 0.1 0.2 0.7 0.2 0.1 0.5 0.2
//
A -0.3 -0.9 -0.3 0.7 0.7 0.8 -0.9 1.2 0.8 0.0 0.7 1.1 0.7 0.7 -0.9 -0.9 -0.9 -0.9 1.0 0.5 0.0 -0.3
C -0.6 -0.6 -2.4 -0.0 -2.4 -0.6 -2.4 -2.4 -2.4 0.3 -0.0 -2.4 -0.0 -0.0 -0.6 1.3 1.1 -2.4 -2.4 -0.0 -2.4 0.8
G -2.4 0.4 -0.6 -2.4 -0.6 -2.4 -0.6 -2.4 -0.0 -2.4 -2.4 -2.4 -2.4 -2.4 -0.6 -2.4 -2.4 -0.0 -2.4 -0.0 -0.0 -0.6
T 0.8 0.5 0.8 -0.4 0.0 -0.4 0.9 -2.4 -0.9 0.3 -0.4 -0.9 -0.4 -0.4 0.8 -0.9 -0.4 0.8 -0.4 -0.9 0.5 -0.4
//
A -0.1 -0.1 -0.1 0.4 0.4 0.5 -0.1 1.1 0.5 0.0 0.4 0.9 0.4 0.4 -0.1 -0.1 -0.1 -0.1 0.7 0.2 0.0 -0.1
C -0.1 -0.1 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 0.1 -0.0 -0.0 -0.0 -0.0 -0.1 1.0 0.8 -0.0 -0.0 -0.0 -0.0 0.4
G -0.0 0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1
T 0.5 0.2 0.5 -0.1 0.0 -0.1 0.7 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.5 -0.1 -0.1 0.5 -0.1 -0.1 0.2 -0.1
//
; Sites 10
>site_0
TTTAAATAACAAAATCCTAAGC
>site_1
TTTAAATAACAAAATCCTAATG
>site_2
ATTTAATAAAAATTTCCTAATT
>site_3
TTTCATTATTTACATCCTTGTC
>site_4
AGGAGATAAAAAAATCTGACAC
>site_5
TTTTTTTAATCACACCTTTATC
>site_6
TCAATATAGTAAACGCCTATAA
>site_7
CGTCACGAATCAATTTCGACAC
>site_8
TAAATAAAAATTTATCCTAAGA
>site_9
TGTAAATAGCAAACAAAAAGTT
;
; Matrix parameters
; Number of sites 10
; Columns 22
; Rows 4
; Alphabet A|C|G|T
; Prior A:0.291144263562772|C:0.207810681831126|G:0.204024081631615|T:0.297020972974487|a:0.291144263562772|c:0.207810681831126|g:0.204024081631615|t:0.297020972974487
; program transfac
; matrix.nb 1
; accession TKTAWATAAHAAAATCCTAAWC
; AC TKTAWATAAHAAAATCCTAAWC
; id TKTAWATAAHAAAATCCTAAWC
; name TKTAWATAAHAAAATCCTAAWC
; description tktawatAahaAaatCCtaawc
; statistical_basis 10 sequences
; sites 10
; nb_sites 10
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 8.14687
; information.per.column 0.370312
; max.possible.info.per.col 1.58952
; consensus.strict tttaaatAacaAaatCCtaatc
; consensus.strict.rc GATTAGGATTTTGTTATTTAAA
; consensus.IUPAC tktawatAahaAaatCCtaawc
; consensus.IUPAC.rc GWTTAGGATTTTDTTATWTAMA
; consensus.regexp t[gt]ta[at]atAa[act]aAaatCCtaa[at]c
; consensus.regexp.rc G[AT]TTAGGATTTT[AGT]TTAT[AT]TA[AC]A
; residues.content.crude.freq a:0.4273|c:0.1682|g:0.0727|t:0.3318
; G+C.content.crude.freq 0.240909
; residues.content.corrected.freq a:0.4149|c:0.1718|g:0.0847|t:0.3287
; G+C.content.corrected.freq 0.256448
; min(P(S|M)) 1.16886e-35
; max(P(S|M)) 2.35895e-05
; proba_range 2.35895e-05
; Wmin -46.6
; Wmax 17.5
; Wrange 64.1
; logo file:/GadE.EcolK12_2nt_upstream.22.meme_quality_logo_m1.png
; logo file:/GadE.EcolK12_2nt_upstream.22.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 0.45
; csystem 0.05