RegulonDB
IclR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/IclR/IclR.EcolK12_1nt_upstream.16.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 /IclR.EcolK12_1nt_upstream.16.meme_quality_logo
; Input files
; input /IclR.EcolK12_1nt_upstream.16.meme_quality_matrix.tf
; prior /IclR.EcolK12_1nt_upstream.16.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /IclR.EcolK12_1nt_upstream.16.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 4 2 1 0 6 3 0 0 1 1 2 3 3 2 2 0
C 0 0 0 4 0 3 3 0 0 5 3 0 0 0 0 3
G 1 2 2 1 1 0 0 0 1 1 1 3 1 1 2 0
T 3 4 5 3 1 2 5 8 6 1 2 2 4 5 4 5
//
A 0.5 0.3 0.1 0.0 0.7 0.4 0.0 0.0 0.1 0.1 0.3 0.4 0.4 0.3 0.3 0.0
C 0.0 0.0 0.0 0.5 0.0 0.4 0.4 0.0 0.0 0.6 0.4 0.0 0.0 0.0 0.0 0.4
G 0.1 0.2 0.2 0.1 0.1 0.0 0.0 0.0 0.1 0.1 0.1 0.4 0.1 0.1 0.2 0.0
T 0.4 0.5 0.6 0.4 0.1 0.3 0.6 0.9 0.7 0.1 0.3 0.3 0.5 0.6 0.5 0.6
//
A 0.5 -0.1 -0.7 -2.2 0.9 0.2 -2.2 -2.2 -0.7 -0.7 -0.1 0.2 0.2 -0.1 -0.1 -2.2
C -2.2 -2.2 -2.2 0.8 -2.2 0.5 0.5 -2.2 -2.2 1.0 0.5 -2.2 -2.2 -2.2 -2.2 0.5
G -0.4 0.2 0.2 -0.4 -0.4 -2.2 -2.2 -2.2 -0.4 -0.4 -0.4 0.6 -0.4 -0.4 0.2 -2.2
T 0.2 0.5 0.7 0.2 -0.7 -0.2 0.7 1.1 0.9 -0.7 -0.2 -0.2 0.5 0.7 0.5 0.7
//
A 0.2 -0.0 -0.1 -0.1 0.6 0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.1 0.1 -0.0 -0.0 -0.1
C -0.1 -0.1 -0.1 0.4 -0.1 0.2 0.2 -0.1 -0.1 0.6 0.2 -0.1 -0.1 -0.1 -0.1 0.2
G -0.1 0.0 0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 -0.1 0.2 -0.1 -0.1 0.0 -0.0
T 0.1 0.2 0.4 0.1 -0.1 -0.0 0.4 1.0 0.6 -0.1 -0.0 -0.0 0.2 0.4 0.2 0.4
//
; Sites 8
>site_0
AAACAATTTCCATTTT
>site_1
AATCATTTTCATTTTT
>site_2
AGGCACCTTCGGGTGC
>site_3
ATTCACCTGCTGAGGT
>site_4
TTTGATTTTGCATTTT
>site_5
TTTTTATTTCCGAAAC
>site_6
TTTTAATTAAAAATAC
>site_7
GGGTGCCTTTTTTATT
;
; Matrix parameters
; Number of sites 8
; Columns 16
; 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 WDTYAHYTTCHDWTDY
; AC WDTYAHYTTCHDWTDY
; id WDTYAHYTTCHDWTDY
; name WDTYAHYTTCHDWTDY
; description wkkyamyTtCcrwtky
; statistical_basis 8 sequences
; sites 8
; nb_sites 8
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.047
; information.per.column 0.315437
; max.possible.info.per.col 1.58873
; consensus.strict attcactTtCcgtttt
; consensus.strict.rc AAAACGGAAAGTGAAT
; consensus.IUPAC wkkyamyTtCcrwtky
; consensus.IUPAC.rc RMAWYGGAARKTRMMW
; consensus.regexp [at][gt][gt][ct]a[ac][ct]TtCc[ag][at]t[gt][ct]
; consensus.regexp.rc [AG][AC]A[AT][CT]GGAA[AG][GT]T[AG][AC][AC][AT]
; residues.content.crude.freq a:0.2344|c:0.1641|g:0.1328|t:0.4688
; G+C.content.crude.freq 0.296875
; residues.content.corrected.freq a:0.2407|c:0.1689|g:0.1407|t:0.4497
; G+C.content.corrected.freq 0.309638
; min(P(S|M)) 2.8294e-25
; max(P(S|M)) 3.62058e-05
; proba_range 3.62058e-05
; Wmin -32
; Wmax 11
; Wrange 43
; logo file:/IclR.EcolK12_1nt_upstream.16.meme_quality_logo_m1.png
; logo file:/IclR.EcolK12_1nt_upstream.16.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.44
; csystem 0.04