RegulonDB
SoxR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/SoxR/SoxR.EcolK12_2nt_upstream.20.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 /SoxR.EcolK12_2nt_upstream.20.meme_quality_logo
; Input files
; input /SoxR.EcolK12_2nt_upstream.20.meme_quality_matrix.tf
; prior /SoxR.EcolK12_2nt_upstream.20.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /SoxR.EcolK12_2nt_upstream.20.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 1 4 0 0 0 0 4 2 1 1 1 4 2 0 1 0 1 2 0 1
C 0 0 3 1 1 4 0 2 1 1 1 1 1 4 1 0 0 0 0 1
G 1 0 0 5 1 0 1 0 3 0 0 0 2 1 0 3 1 2 4 4
T 4 2 3 0 4 2 1 2 1 4 4 1 1 1 4 3 4 2 2 0
//
A 0.2 0.6 0.0 0.0 0.0 0.0 0.6 0.3 0.2 0.2 0.2 0.6 0.3 0.0 0.2 0.0 0.2 0.3 0.0 0.2
C 0.0 0.0 0.5 0.2 0.2 0.6 0.0 0.3 0.2 0.2 0.2 0.2 0.2 0.6 0.2 0.0 0.0 0.0 0.0 0.2
G 0.2 0.0 0.0 0.7 0.2 0.0 0.2 0.0 0.5 0.0 0.0 0.0 0.3 0.2 0.0 0.5 0.2 0.3 0.6 0.6
T 0.6 0.3 0.5 0.0 0.6 0.3 0.2 0.3 0.2 0.6 0.6 0.2 0.2 0.2 0.6 0.5 0.6 0.3 0.3 0.0
//
A -0.5 0.7 -1.9 -1.9 -1.9 -1.9 0.7 0.1 -0.5 -0.5 -0.5 0.7 0.1 -1.9 -0.5 -1.9 -0.5 0.1 -1.9 -0.5
C -1.9 -1.9 0.8 -0.2 -0.2 1.1 -1.9 0.4 -0.2 -0.2 -0.2 -0.2 -0.2 1.1 -0.2 -1.9 -1.9 -1.9 -1.9 -0.2
G -0.2 -1.9 -1.9 1.3 -0.2 -1.9 -0.2 -1.9 0.8 -1.9 -1.9 -1.9 0.4 -0.2 -1.9 0.8 -0.2 0.4 1.1 1.1
T 0.7 0.1 0.5 -1.9 0.7 0.1 -0.5 0.1 -0.5 0.7 0.7 -0.5 -0.5 -0.5 0.7 0.5 0.7 0.1 0.1 -1.9
//
A -0.1 0.5 -0.1 -0.1 -0.1 -0.1 0.5 0.0 -0.1 -0.1 -0.1 0.5 0.0 -0.1 -0.1 -0.1 -0.1 0.0 -0.1 -0.1
C -0.1 -0.1 0.4 -0.0 -0.0 0.6 -0.1 0.1 -0.0 -0.0 -0.0 -0.0 -0.0 0.6 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0
G -0.0 -0.1 -0.1 1.0 -0.0 -0.1 -0.0 -0.1 0.4 -0.1 -0.1 -0.1 0.1 -0.0 -0.1 0.4 -0.0 0.1 0.6 0.6
T 0.4 0.0 0.2 -0.1 0.4 0.0 -0.1 0.0 -0.1 0.4 0.4 -0.1 -0.1 -0.1 0.4 0.2 0.4 0.0 0.0 -0.1
//
; Sites 6
>site_0
TACCTCAAGTTAACTTGAGG
>site_1
TTCGTTAATTCATCTGTTGG
>site_2
TACGTCATCCTCGCTGAGGA
>site_3
AATGCCGCGTAAGCAGTTGG
>site_4
TTTGTTTCATTAATTTTGTG
>site_5
GATGGCATGATTCGCTTATC
;
; Matrix parameters
; Number of sites 6
; Columns 20
; 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 TWYGTYAHGTTANCTKTDKG
; AC TWYGTYAHGTTANCTKTDKG
; id TWYGTYAHGTTANCTKTDKG
; name TWYGTYAHGTTANCTKTDKG
; description twyGtYahgttarCtktdKG
; statistical_basis 6 sequences
; sites 6
; nb_sites 6
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.74601
; information.per.column 0.337301
; max.possible.info.per.col 1.58952
; consensus.strict tacGtCacgttagCtgtgGG
; consensus.strict.rc CCCACAGCTAACGTGACGTA
; consensus.IUPAC twyGtYahgttarCtktdKG
; consensus.IUPAC.rc CMHAMAGYTAACDTRACRWA
; consensus.regexp t[at][ct]Gt[CT]a[act]gtta[ag]Ct[gt]t[agt][GT]G
; consensus.regexp.rc C[AC][ACT]A[AC]AG[CT]TAAC[AGT]T[AG]AC[AG][AT]A
; residues.content.crude.freq a:0.2083|c:0.1833|g:0.2333|t:0.3750
; G+C.content.crude.freq 0.416667
; residues.content.corrected.freq a:0.2202|c:0.1868|g:0.2291|t:0.3639
; G+C.content.corrected.freq 0.415976
; min(P(S|M)) 3.24047e-29
; max(P(S|M)) 4.27432e-06
; proba_range 4.27432e-06
; Wmin -36
; Wmax 15.9
; Wrange 51.9
; logo file:/SoxR.EcolK12_2nt_upstream.20.meme_quality_logo_m1.png
; logo file:/SoxR.EcolK12_2nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161114
; Job done 2019-06-03.161115
; Seconds 0.56
; user 0.56
; system 0.05
; cuser 0.44
; csystem 0.04