RegulonDB
CytR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CytR/CytR.EcolK12_1nt_upstream.23.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 /CytR.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /CytR.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /CytR.EcolK12_1nt_upstream.23.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /CytR.EcolK12_1nt_upstream.23.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 10 11 2 4 3 3 3 4 6 3 15 7 8 9 9 4 5 5 9 5 1 4 5
C 6 4 5 5 2 7 1 4 0 14 0 0 1 1 4 4 2 5 3 1 4 2 7
G 0 1 2 1 7 3 1 0 10 0 1 3 1 3 1 2 6 1 3 3 0 7 2
T 1 1 8 7 5 4 12 9 1 0 1 7 7 4 3 7 4 6 2 8 12 4 3
//
A 0.6 0.6 0.1 0.2 0.2 0.2 0.2 0.2 0.3 0.2 0.8 0.4 0.5 0.5 0.5 0.2 0.3 0.3 0.5 0.3 0.1 0.2 0.3
C 0.3 0.2 0.3 0.3 0.1 0.4 0.1 0.2 0.0 0.8 0.0 0.0 0.1 0.1 0.2 0.2 0.1 0.3 0.2 0.1 0.2 0.1 0.4
G 0.0 0.1 0.1 0.1 0.4 0.2 0.1 0.0 0.6 0.0 0.1 0.2 0.1 0.2 0.1 0.1 0.3 0.1 0.2 0.2 0.0 0.4 0.1
T 0.1 0.1 0.5 0.4 0.3 0.2 0.7 0.5 0.1 0.0 0.1 0.4 0.4 0.2 0.2 0.4 0.2 0.3 0.1 0.5 0.7 0.2 0.2
//
A 0.7 0.8 -0.8 -0.2 -0.5 -0.5 -0.5 -0.2 0.2 -0.5 1.1 0.3 0.5 0.6 0.6 -0.2 0.0 0.0 0.6 0.0 -1.4 -0.2 0.0
C 0.5 0.1 0.3 0.3 -0.5 0.7 -1.1 0.1 -2.9 1.3 -2.9 -2.9 -1.1 -1.1 0.1 0.1 -0.5 0.3 -0.2 -1.1 0.1 -0.5 0.7
G -2.9 -1.1 -0.5 -1.1 0.7 -0.1 -1.1 -2.9 1.0 -2.9 -1.1 -0.1 -1.1 -0.1 -1.1 -0.5 0.5 -1.1 -0.1 -0.1 -2.9 0.7 -0.5
T -1.4 -1.4 0.4 0.3 -0.0 -0.2 0.8 0.6 -1.4 -2.9 -1.4 0.3 0.3 -0.2 -0.5 0.3 -0.2 0.2 -0.8 0.4 0.8 -0.2 -0.5
//
A 0.4 0.5 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 0.1 -0.1 0.9 0.1 0.2 0.3 0.3 -0.0 0.0 0.0 0.3 0.0 -0.1 -0.0 0.0
C 0.2 0.0 0.1 0.1 -0.1 0.3 -0.1 0.0 -0.0 1.1 -0.0 -0.0 -0.1 -0.1 0.0 0.0 -0.1 0.1 -0.0 -0.1 0.0 -0.1 0.3
G -0.0 -0.1 -0.1 -0.1 0.3 -0.0 -0.1 -0.0 0.6 -0.0 -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 0.2 -0.1 -0.0 -0.0 -0.0 0.3 -0.1
T -0.1 -0.1 0.2 0.1 -0.0 -0.1 0.6 0.3 -0.1 -0.0 -0.1 0.1 0.1 -0.1 -0.1 0.1 -0.1 0.1 -0.1 0.2 0.6 -0.1 -0.1
//
; Sites 17
>site_0
CATTGCTCACAAAAATATGTTTC
>site_1
AACCGATTGCAATAAAACATTTA
>site_2
ACCAGATCGCATTACAGTGATGC
>site_3
AATCGGTTGCTAAATTGCATTTT
>site_4
CCCAATTTGCAAAACGAAATTGT
>site_5
AAACGGTTACAGAATTTTCATGA
>site_6
AATTGCAAACATTCCCAATTTGC
>site_7
CATTTTATGCAACAACAAATTAT
>site_8
ACAAGCTTGCATTGAACTTGTGG
>site_9
AATGCGTTGCATAAATTTACCCA
>site_10
CATTTTTAGCAGATAGCGCGTGA
>site_11
CAGTTCTATCATTTACGTAATCG
>site_12
ATCTACTTACAAGTTTGCATCAC
>site_13
AAGCTTGTGAATAAATTACGCAC
>site_14
CATACATCAAAAATGCGCGACGC
>site_15
ACCCACCAAAAGTGATGCAAATC
>site_16
TGTTTCACGCGTTGCATAATTAA
;
; Matrix parameters
; Number of sites 17
; Columns 23
; 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 MAYHKYTTRCAWWAAHDHAWTDM
; AC MAYHKYTTRCAWWAAHDHAWTDM
; id MAYHKYTTRCAWWAAHDHAWTDM
; name MAYHKYTTRCAWWAAHDHAWTDM
; description mmyygctyRCAwwamyrhawygm
; statistical_basis 17 sequences
; sites 17
; nb_sites 17
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.67795
; information.per.column 0.246867
; max.possible.info.per.col 1.58873
; consensus.strict aatcgcttGCAaaaatgcattgc
; consensus.strict.rc GCAATGCATTTTTGCAAGCGATT
; consensus.IUPAC mmyygctyRCAwwamyrhawygm
; consensus.IUPAC.rc KCRWTDYRKTWWTGYRAGCRRKK
; consensus.regexp [ac][ac][ct][ct]gct[ct][AG]CA[at][at]a[ac][ct][ag][act]a[at][ct]g[ac]
; consensus.regexp.rc [GT]C[AG][AT]T[AGT][CT][AG][GT]T[AT][AT]TG[CT][AG]AGC[AG][AG][GT][GT]
; residues.content.crude.freq a:0.3453|c:0.2097|g:0.1483|t:0.2967
; G+C.content.crude.freq 0.358056
; residues.content.corrected.freq a:0.3422|c:0.2096|g:0.1514|t:0.2967
; G+C.content.corrected.freq 0.361039
; min(P(S|M)) 7.88244e-31
; max(P(S|M)) 9.12773e-08
; proba_range 9.12773e-08
; Wmin -34.3
; Wmax 14.7
; Wrange 49
; logo file:/CytR.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/CytR.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.44
; csystem 0.06