RegulonDB
GalR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GalR/GalR.EcolK12_2nt_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 /GalR.EcolK12_2nt_upstream.18.meme_quality_logo
; Input files
; input /GalR.EcolK12_2nt_upstream.18.meme_quality_matrix.tf
; prior /GalR.EcolK12_2nt_upstream.18.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GalR.EcolK12_2nt_upstream.18.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 5 4 0 6 3 0 0 3 7 12 4 0 3 3 0 0 8 1
C 3 1 3 1 0 1 1 1 3 0 0 9 0 0 0 0 0 11
G 4 2 5 2 6 0 10 5 0 0 6 0 8 6 0 0 1 0
T 0 5 4 3 3 11 1 3 2 0 2 3 1 3 12 12 3 0
//
A 0.4 0.3 0.0 0.5 0.3 0.0 0.0 0.3 0.6 0.9 0.3 0.0 0.3 0.3 0.0 0.0 0.6 0.1
C 0.2 0.1 0.2 0.1 0.0 0.1 0.1 0.1 0.2 0.0 0.0 0.7 0.0 0.0 0.0 0.0 0.0 0.9
G 0.3 0.2 0.4 0.2 0.5 0.0 0.8 0.4 0.0 0.0 0.5 0.0 0.6 0.5 0.0 0.0 0.1 0.0
T 0.0 0.4 0.3 0.3 0.3 0.9 0.1 0.3 0.2 0.0 0.2 0.3 0.1 0.3 0.9 0.9 0.3 0.0
//
A 0.3 0.1 -2.6 0.5 -0.1 -2.6 -2.6 -0.1 0.7 1.2 0.1 -2.6 -0.1 -0.1 -2.6 -2.6 0.8 -1.1
C 0.2 -0.8 0.2 -0.8 -2.6 -0.8 -0.8 -0.8 0.2 -2.6 -2.6 1.2 -2.6 -2.6 -2.6 -2.6 -2.6 1.4
G 0.5 -0.2 0.7 -0.2 0.8 -2.6 1.3 0.7 -2.6 -2.6 0.8 -2.6 1.1 0.8 -2.6 -2.6 -0.8 -2.6
T -2.6 0.3 0.1 -0.2 -0.2 1.1 -1.1 -0.2 -0.5 -2.6 -0.5 -0.2 -1.1 -0.2 1.2 1.2 -0.2 -2.6
//
A 0.1 0.0 -0.1 0.2 -0.0 -0.1 -0.1 -0.0 0.4 1.1 0.0 -0.1 -0.0 -0.0 -0.1 -0.1 0.5 -0.1
C 0.0 -0.1 0.0 -0.1 -0.0 -0.1 -0.1 -0.1 0.0 -0.0 -0.0 0.9 -0.0 -0.0 -0.0 -0.0 -0.0 1.2
G 0.1 -0.0 0.3 -0.0 0.4 -0.0 1.1 0.3 -0.0 -0.0 0.4 -0.0 0.7 0.4 -0.0 -0.0 -0.1 -0.0
T -0.1 0.1 0.0 -0.0 -0.0 0.9 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 -0.1 -0.0 1.1 1.1 -0.0 -0.1
//
; Sites 12
>site_0
CAGATTGAAAGCGGTTAC
>site_1
GTTAGTGTAAGCGATTAC
>site_2
AGCAATGGAAACGGTTAC
>site_3
ATTAGTGGAATCGTTTAC
>site_4
AAGAATGTAAGCGTTTAC
>site_5
CTCTGTGGCAACGGTTTC
>site_6
ACCGGTGGTAGCGGTTAC
>site_7
GTTGGTGTAATCGGTTTC
>site_8
CAGTGCGCCAGCAATTAC
>site_9
GGTTTTCACAGTTGTTAC
>site_10
AAGATTTGTAATATTTTC
>site_11
GTGCATGAAAATAATTGA
;
; Matrix parameters
; Number of sites 12
; Columns 18
; 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 VWBWDTGDAARCGDTTAC
; AC VWBWDTGDAARCGDTTAC
; id VWBWDTGDAARCGDTTAC
; name VWBWDTGDAARCGDTTAC
; description vwbagTGgmArCGgTTaC
; statistical_basis 12 sequences
; sites 12
; nb_sites 12
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.10269
; information.per.column 0.505705
; max.possible.info.per.col 1.58952
; consensus.strict gtgagTGgaAgCGgTTaC
; consensus.strict.rc GTAACCGCTTCCACTCAC
; consensus.IUPAC vwbagTGgmArCGgTTaC
; consensus.IUPAC.rc GTAACCGYTKCCACTVWB
; consensus.regexp [acg][at][cgt]agTGg[ac]A[ag]CGgTTaC
; consensus.regexp.rc GTAACCG[CT]T[GT]CCACT[ACG][AT][CGT]
; residues.content.crude.freq a:0.2731|c:0.1574|g:0.2546|t:0.3148
; G+C.content.crude.freq 0.412037
; residues.content.corrected.freq a:0.2745|c:0.1613|g:0.2507|t:0.3134
; G+C.content.corrected.freq 0.412021
; min(P(S|M)) 2.24972e-30
; max(P(S|M)) 0.000111191
; proba_range 0.000111191
; Wmin -40.9
; Wmax 16.4
; Wrange 57.3
; logo file:/GalR.EcolK12_2nt_upstream.18.meme_quality_logo_m1.png
; logo file:/GalR.EcolK12_2nt_upstream.18.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.59
; user 0.59
; system 0.05
; cuser 0.42
; csystem 0.05