RegulonDB
AgaR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/AgaR/AgaR.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 /AgaR.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /AgaR.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /AgaR.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 /AgaR.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 5 5 1 0 0 0 0 3 2 0 1 2 5 0 0 1 2 3 1 1 0 2 2
C 2 4 9 0 0 0 10 0 1 0 0 3 3 1 1 0 7 1 2 0 2 0 1
G 4 0 1 1 1 0 0 6 1 0 0 0 3 1 0 0 0 3 1 1 0 3 5
T 0 2 0 10 10 11 1 2 7 11 10 6 0 9 10 10 2 4 7 9 9 6 3
//
A 0.4 0.4 0.1 0.0 0.0 0.0 0.0 0.3 0.2 0.0 0.1 0.2 0.4 0.0 0.0 0.1 0.2 0.3 0.1 0.1 0.0 0.2 0.2
C 0.2 0.4 0.8 0.0 0.0 0.0 0.9 0.0 0.1 0.0 0.0 0.3 0.3 0.1 0.1 0.0 0.6 0.1 0.2 0.0 0.2 0.0 0.1
G 0.4 0.0 0.1 0.1 0.1 0.0 0.0 0.5 0.1 0.0 0.0 0.0 0.3 0.1 0.0 0.0 0.0 0.3 0.1 0.1 0.0 0.3 0.4
T 0.0 0.2 0.0 0.9 0.9 0.9 0.1 0.2 0.6 0.9 0.9 0.5 0.0 0.8 0.9 0.9 0.2 0.4 0.6 0.8 0.8 0.5 0.3
//
A 0.4 0.4 -1.0 -2.5 -2.5 -2.5 -2.5 -0.1 -0.4 -2.5 -1.0 -0.4 0.4 -2.5 -2.5 -1.0 -0.4 -0.1 -1.0 -1.0 -2.5 -0.4 -0.4
C -0.1 0.5 1.3 -2.5 -2.5 -2.5 1.4 -2.5 -0.7 -2.5 -2.5 0.3 0.3 -0.7 -0.7 -2.5 1.1 -0.7 -0.1 -2.5 -0.1 -2.5 -0.7
G 0.5 -2.5 -0.7 -0.7 -0.7 -2.5 -2.5 0.9 -0.7 -2.5 -2.5 -2.5 0.3 -0.7 -2.5 -2.5 -2.5 0.3 -0.7 -0.7 -2.5 0.3 0.8
T -2.5 -0.4 -2.5 1.1 1.1 1.2 -1.0 -0.4 0.7 1.2 1.1 0.6 -2.5 1.0 1.1 1.1 -0.4 0.2 0.7 1.0 1.0 0.6 -0.1
//
A 0.2 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1
C -0.0 0.2 1.0 -0.0 -0.0 -0.0 1.2 -0.0 -0.1 -0.0 -0.0 0.1 0.1 -0.1 -0.1 -0.0 0.6 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1
G 0.2 -0.0 -0.1 -0.1 -0.1 -0.0 -0.0 0.5 -0.1 -0.0 -0.0 -0.0 0.1 -0.1 -0.0 -0.0 -0.0 0.1 -0.1 -0.1 -0.0 0.1 0.3
T -0.1 -0.1 -0.1 0.9 0.9 1.1 -0.1 -0.1 0.4 1.1 0.9 0.3 -0.1 0.7 0.9 0.9 -0.1 0.1 0.4 0.7 0.7 0.3 -0.0
//
; Sites 11
>site_0
AACTTTCGTTTCATTTCGTTTTG
>site_1
GCCTTTCTTTTTCTTTCGTTTTG
>site_2
GCCTTTCGTTTCATTTCACTTGG
>site_3
AAATTTCGTTTTATTTCTTTTTT
>site_4
ATCTTTCGTTTTGTTTCAGTTGA
>site_5
GACTTTCATTATGTTTCTTTTGT
>site_6
ATCTTTCGTTTTATTTTTATCTC
>site_7
AACTTTCAGTTTCTTTTCTATAG
>site_8
CCCTTTTGCTTCCTTTATCTTTT
>site_9
CAGGGTCAATTAGCTTCGTTTTG
>site_10
GCCTTTCTATTAAGCAAATGCAA
;
; Matrix parameters
; Number of sites 11
; 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 RMCTTTCRTTTYVTTTCDTTTKK
; AC RMCTTTCRTTTYVTTTCDTTTKK
; id RMCTTTCRTTTYVTTTCDTTTKK
; name RMCTTTCRTTTYVTTTCDTTTKK
; description rmCTTTCgtTTyvtTTCktttkg
; statistical_basis 11 sequences
; sites 11
; nb_sites 11
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 11.6387
; information.per.column 0.50603
; max.possible.info.per.col 1.58873
; consensus.strict gcCTTTCgtTTtatTTCgttttg
; consensus.strict.rc CAAAACGAAATAAAACGAAAGGC
; consensus.IUPAC rmCTTTCgtTTyvtTTCktttkg
; consensus.IUPAC.rc CMAAAMGAAABRAAACGAAAGKY
; consensus.regexp [ag][ac]CTTTCgtTT[ct][acg]tTTC[gt]ttt[gt]g
; consensus.regexp.rc C[AC]AAA[AC]GAAA[CGT][AG]AAACGAAAG[GT][CT]
; residues.content.crude.freq a:0.1423|c:0.1858|g:0.1225|t:0.5494
; G+C.content.crude.freq 0.3083
; residues.content.corrected.freq a:0.1547|c:0.1876|g:0.1293|t:0.5284
; G+C.content.corrected.freq 0.316921
; min(P(S|M)) 1.18434e-37
; max(P(S|M)) 5.26993e-05
; proba_range 5.26993e-05
; Wmin -50.4
; Wmax 20.3
; Wrange 70.7
; logo file:/AgaR.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/AgaR.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.62
; user 0.62
; system 0.06
; cuser 0.46
; csystem 0.04