RegulonDB
EvgA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/EvgA/EvgA.EcolK12_1nt_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 /EvgA.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
; input /EvgA.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
; prior /EvgA.EcolK12_1nt_upstream.22.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /EvgA.EcolK12_1nt_upstream.22.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 3 3 2 3 1 0 0 0 0 7 0 6 1 1 2 0 0 8 2 0 5
C 0 1 3 0 1 0 0 8 2 0 0 7 0 1 3 0 0 0 0 0 0 2
G 5 4 2 2 0 0 0 0 0 0 0 1 2 4 1 0 8 0 0 6 7 0
T 1 0 0 4 4 7 8 0 6 8 1 0 0 2 3 6 0 8 0 0 1 1
//
A 0.3 0.4 0.4 0.3 0.4 0.1 0.0 0.0 0.0 0.0 0.8 0.0 0.7 0.1 0.1 0.3 0.0 0.0 0.9 0.3 0.0 0.6
C 0.0 0.1 0.4 0.0 0.1 0.0 0.0 0.9 0.2 0.0 0.0 0.8 0.0 0.1 0.4 0.0 0.0 0.0 0.0 0.0 0.0 0.2
G 0.6 0.5 0.2 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.1 0.2 0.5 0.1 0.0 0.9 0.0 0.0 0.7 0.8 0.0
T 0.1 0.0 0.0 0.5 0.5 0.8 0.9 0.0 0.7 0.9 0.1 0.0 0.0 0.3 0.4 0.7 0.0 0.9 0.0 0.0 0.1 0.1
//
A -0.1 0.2 0.2 -0.1 0.2 -0.7 -2.2 -2.2 -2.2 -2.2 1.0 -2.2 0.9 -0.7 -0.7 -0.1 -2.2 -2.2 1.2 -0.1 -2.2 0.7
C -2.2 -0.4 0.5 -2.2 -0.4 -2.2 -2.2 1.5 0.2 -2.2 -2.2 1.4 -2.2 -0.4 0.5 -2.2 -2.2 -2.2 -2.2 -2.2 -2.2 0.2
G 1.0 0.8 0.2 0.2 -2.2 -2.2 -2.2 -2.2 -2.2 -2.2 -2.2 -0.4 0.2 0.8 -0.4 -2.2 1.5 -2.2 -2.2 1.2 1.4 -2.2
T -0.7 -2.2 -2.2 0.5 0.5 1.0 1.1 -2.2 0.9 1.1 -0.7 -2.2 -2.2 -0.2 0.2 0.9 -2.2 1.1 -2.2 -2.2 -0.7 -0.7
//
A -0.0 0.1 0.1 -0.0 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.8 -0.1 0.6 -0.1 -0.1 -0.0 -0.1 -0.1 1.1 -0.0 -0.1 0.4
C -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 1.3 0.0 -0.1 -0.1 1.1 -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.0
G 0.6 0.4 0.0 0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 0.0 0.4 -0.1 -0.0 1.4 -0.0 -0.0 0.8 1.1 -0.0
T -0.1 -0.1 -0.1 0.2 0.2 0.8 1.0 -0.1 0.6 1.0 -0.1 -0.1 -0.1 -0.0 0.1 0.6 -0.1 1.0 -0.1 -0.1 -0.1 -0.1
//
; Sites 8
>site_0
GGAGTTTCTTACAGCTGTAGGC
>site_1
GGATTTTCTTACAGGTGTAGGC
>site_2
GGCGCTTCTTACAGTTGTAAGA
>site_3
TACAATTCTTACGCCTGTAGGA
>site_4
GCATATTCCTACAATTGTAAGA
>site_5
GGGTTATCTTACAGTTGTAGTT
>site_6
AACATTTCCTACATAAGTAGGA
>site_7
AAGTATTCTTTGGTCAGTAGGA
;
; Matrix parameters
; Number of sites 8
; Columns 22
; 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 GRVDWTTCTTACAKYTGTAGGA
; AC GRVDWTTCTTACAKYTGTAGGA
; id GRVDWTTCTTACAKYTGTAGGA
; name GRVDWTTCTTACAKYTGTAGGA
; description GrvkwTTCyTACrgytGTAGGm
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 13.0001
; information.per.column 0.590916
; max.possible.info.per.col 1.58873
; consensus.strict GgcttTTCtTACagctGTAGGa
; consensus.strict.rc TCCTACAGCTGTAAGAAAAGCC
; consensus.IUPAC GrvkwTTCyTACrgytGTAGGm
; consensus.IUPAC.rc KCCTACARCYGTARGAAWMBYC
; consensus.regexp G[ag][acg][gt][at]TTC[ct]TAC[ag]g[ct]tGTAGG[ac]
; consensus.regexp.rc [GT]CCTACA[AG]C[CT]GTA[AG]GAA[AT][AC][CGT][CT]C
; residues.content.crude.freq a:0.2614|c:0.1591|g:0.2386|t:0.3409
; G+C.content.crude.freq 0.397727
; residues.content.corrected.freq a:0.2646|c:0.1645|g:0.2348|t:0.3361
; G+C.content.corrected.freq 0.399285
; min(P(S|M)) 7.80992e-35
; max(P(S|M)) 0.000135048
; proba_range 0.000135048
; Wmin -45.4
; Wmax 21.6
; Wrange 67
; logo file:/EvgA.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/EvgA.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.58
; user 0.58
; system 0.05
; cuser 0.43
; csystem 0.05