RegulonDB
YjjQ matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/YjjQ/YjjQ.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 /YjjQ.EcolK12_2nt_upstream.18.meme_quality_logo
; Input files
; input /YjjQ.EcolK12_2nt_upstream.18.meme_quality_matrix.tf
; prior /YjjQ.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 /YjjQ.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 0 7 6 0 7 1 1 0 1 1 0 1 0 6 1 3 0 0
C 0 0 0 1 0 0 0 0 0 2 7 1 2 0 0 2 1 3
G 0 0 1 6 0 0 1 0 1 0 0 0 0 0 0 1 2 0
T 7 0 0 0 0 6 5 7 5 4 0 5 5 1 6 1 4 4
//
A 0.0 0.9 0.8 0.0 0.9 0.2 0.2 0.0 0.2 0.2 0.0 0.2 0.0 0.8 0.2 0.4 0.0 0.0
C 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.3 0.9 0.2 0.3 0.0 0.0 0.3 0.2 0.4
G 0.0 0.0 0.2 0.8 0.0 0.0 0.2 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.3 0.0
T 0.9 0.0 0.0 0.0 0.0 0.8 0.7 0.9 0.7 0.5 0.0 0.7 0.7 0.2 0.8 0.2 0.5 0.5
//
A -2.1 1.1 1.0 -2.1 1.1 -0.6 -0.6 -2.1 -0.6 -0.6 -2.1 -0.6 -2.1 1.0 -0.6 0.3 -2.1 -2.1
C -2.1 -2.1 -2.1 -0.3 -2.1 -2.1 -2.1 -2.1 -2.1 0.3 1.5 -0.3 0.3 -2.1 -2.1 0.3 -0.3 0.7
G -2.1 -2.1 -0.3 1.3 -2.1 -2.1 -0.3 -2.1 -0.3 -2.1 -2.1 -2.1 -2.1 -2.1 -2.1 -0.3 0.3 -2.1
T 1.1 -2.1 -2.1 -2.1 -2.1 1.0 0.8 1.1 0.8 0.6 -2.1 0.8 0.8 -0.6 1.0 -0.6 0.6 0.6
//
A -0.1 1.0 0.8 -0.1 1.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.8 -0.1 0.1 -0.1 -0.1
C -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.1 1.3 -0.0 0.1 -0.1 -0.1 0.1 -0.0 0.3
G -0.1 -0.1 -0.0 1.0 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.1 -0.1
T 1.0 -0.1 -0.1 -0.1 -0.1 0.8 0.5 1.0 0.5 0.3 -0.1 0.5 0.5 -0.1 0.8 -0.1 0.3 0.3
//
; Sites 7
>site_0
TAAGATATTCCTTATATC
>site_1
TAAGATTTTTCCTAAATC
>site_2
TAAGATTTTACTCATTGT
>site_3
TAAGATTTATCTTATGCT
>site_4
TAGGATTTGTCTCATCGT
>site_5
TAACAATTTCCTTATCTT
>site_6
TAAGATGTTTCATTTATC
;
; Matrix parameters
; Number of sites 7
; 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 TAAGATTTTYCTTATMKY
; AC TAAGATTTTYCTTATMKY
; id TAAGATTTTYCTTATMKY
; name TAAGATTTTYCTTATMKY
; description TAaGAttTtyCtyatmky
; statistical_basis 7 sequences
; sites 7
; nb_sites 7
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 10.1944
; information.per.column 0.566357
; max.possible.info.per.col 1.58952
; consensus.strict TAaGAttTttCttatatc
; consensus.strict.rc GATATAAGAAAAATCTTA
; consensus.IUPAC TAaGAttTtyCtyatmky
; consensus.IUPAC.rc RMKATRAGRAAAATCTTA
; consensus.regexp TAaGAttTt[ct]Ct[ct]at[ac][gt][ct]
; consensus.regexp.rc [AG][AC][GT]AT[AG]AG[AG]AAAATCTTA
; residues.content.crude.freq a:0.2778|c:0.1508|g:0.0952|t:0.4762
; G+C.content.crude.freq 0.246032
; residues.content.corrected.freq a:0.2794|c:0.1579|g:0.1088|t:0.4538
; G+C.content.corrected.freq 0.266757
; min(P(S|M)) 2.64492e-28
; max(P(S|M)) 0.00226697
; proba_range 0.00226697
; Wmin -36
; Wmax 16.7
; Wrange 52.7
; logo file:/YjjQ.EcolK12_2nt_upstream.18.meme_quality_logo_m1.png
; logo file:/YjjQ.EcolK12_2nt_upstream.18.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161128
; Job done 2019-06-03.161129
; Seconds 0.57
; user 0.57
; system 0.04
; cuser 0.4
; csystem 0.06