RegulonDB
GlpR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/GlpR/GlpR.EcolK12_1nt_upstream.22.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 /GlpR.EcolK12_1nt_upstream.22.meme_quality_logo
; Input files
; input /GlpR.EcolK12_1nt_upstream.22.meme_quality_matrix.tf
; prior /GlpR.EcolK12_1nt_upstream.22.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /GlpR.EcolK12_1nt_upstream.22.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 5 10 1 0 5 0 2 7 10 8 11 9 0 3 10 11 5 11 2 1
C 1 1 2 0 3 0 8 1 13 2 0 1 1 0 14 1 6 1 11 0 2 4
G 1 0 0 2 1 17 1 8 2 7 4 1 0 0 1 12 1 3 0 3 3 3
T 5 5 10 5 12 0 3 8 0 1 3 7 5 8 2 1 0 2 1 3 10 9
//
A 0.6 0.6 0.3 0.6 0.1 0.0 0.3 0.0 0.1 0.4 0.6 0.5 0.6 0.5 0.0 0.2 0.6 0.6 0.3 0.6 0.1 0.1
C 0.1 0.1 0.1 0.0 0.2 0.0 0.5 0.1 0.7 0.1 0.0 0.1 0.1 0.0 0.8 0.1 0.3 0.1 0.6 0.0 0.1 0.2
G 0.1 0.0 0.0 0.1 0.1 1.0 0.1 0.5 0.1 0.4 0.2 0.1 0.0 0.0 0.1 0.7 0.1 0.2 0.0 0.2 0.2 0.2
T 0.3 0.3 0.6 0.3 0.7 0.0 0.2 0.5 0.0 0.1 0.2 0.4 0.3 0.5 0.1 0.1 0.0 0.1 0.1 0.2 0.6 0.5
//
A 0.7 0.8 0.0 0.7 -1.4 -2.9 0.0 -2.9 -0.8 0.3 0.7 0.5 0.8 0.6 -2.9 -0.5 0.7 0.8 0.0 0.8 -0.8 -1.4
C -1.1 -1.1 -0.5 -2.9 -0.2 -2.9 0.8 -1.1 1.3 -0.5 -2.9 -1.1 -1.1 -2.9 1.3 -1.1 0.5 -1.1 1.1 -2.9 -0.5 0.1
G -1.1 -2.9 -2.9 -0.5 -1.1 1.5 -1.1 0.8 -0.5 0.7 0.1 -1.1 -2.9 -2.9 -1.1 1.2 -1.1 -0.1 -2.9 -0.1 -0.1 -0.1
T -0.0 -0.0 0.7 -0.0 0.8 -2.9 -0.5 0.4 -2.9 -1.4 -0.5 0.3 -0.0 0.4 -0.8 -1.4 -2.9 -0.8 -1.4 -0.5 0.7 0.6
//
A 0.4 0.5 0.0 0.4 -0.1 -0.0 0.0 -0.0 -0.1 0.1 0.4 0.2 0.5 0.3 -0.0 -0.1 0.4 0.5 0.0 0.5 -0.1 -0.1
C -0.1 -0.1 -0.1 -0.0 -0.0 -0.0 0.4 -0.1 0.9 -0.1 -0.0 -0.1 -0.1 -0.0 1.1 -0.1 0.2 -0.1 0.7 -0.0 -0.1 0.0
G -0.1 -0.0 -0.0 -0.1 -0.1 1.5 -0.1 0.4 -0.1 0.3 0.0 -0.1 -0.0 -0.0 -0.1 0.8 -0.1 -0.0 -0.0 -0.0 -0.0 -0.0
T -0.0 -0.0 0.4 -0.0 0.6 -0.0 -0.1 0.2 -0.0 -0.1 -0.1 0.1 -0.0 0.2 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.4 0.3
//
; Sites 17
>site_0
AATATGTTCGATAACGAACATT
>site_1
AATATGCGCGAAATCAAACAAT
>site_2
AATTTGCGCCAAAACGCAAACC
>site_3
AAATGGCGCGATAACGCTCATT
>site_4
AAAACGCGCGGATTCGAGCGAT
>site_5
ATTAAGCGCGGATTCGAATATT
>site_6
TTTTTGCTCGTTAACGATAAGT
>site_7
GATTTGCTCAAATTCGCGCTGC
>site_8
TAAATGGTAAAAAACGAACTTC
>site_9
TTTATGAGCTTTAACGAAAGTG
>site_10
AAAACGAGAAATATCGAACTTA
>site_11
AAAATGTTCAAAATGACGCATG
>site_12
AATGTGTGCGGCAATTCACATT
>site_13
CCCATGATGAATTTCGAAAATC
>site_14
ATCGTGATCCATTACGACCGCG
>site_15
TTTATGACGAGGCACACACATT
>site_16
TATTCGCTCATAATTCGAAAGT
;
; Matrix parameters
; Number of sites 17
; Columns 22
; 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 WAWWTGMKCRAWAWCGMACATT
; AC WAWWTGMKCRAWAWCGMACATT
; id WAWWTGMKCRAWAWCGMACATT
; name WAWWTGMKCRAWAWCGMACATT
; description aawatGmkCrrwawCGmaMaty
; statistical_basis 17 sequences
; sites 17
; nb_sites 17
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 9.10542
; information.per.column 0.413883
; max.possible.info.per.col 1.58873
; consensus.strict aatatGcgCgaaaaCGaaCatt
; consensus.strict.rc AATGTTCGTTTTCGCGCATATT
; consensus.IUPAC aawatGmkCrrwawCGmaMaty
; consensus.IUPAC.rc RATKTKCGWTWYYGMKCATWTT
; consensus.regexp aa[at]atG[ac][gt]C[ag][ag][at]a[at]CG[ac]a[AC]at[ct]
; consensus.regexp.rc [AG]AT[GT]T[GT]CG[AT]T[AT][CT][CT]G[AC][GT]CAT[AT]TT
; residues.content.crude.freq a:0.3529|c:0.1925|g:0.1872|t:0.2674
; G+C.content.crude.freq 0.379679
; residues.content.corrected.freq a:0.3495|c:0.1933|g:0.1881|t:0.2690
; G+C.content.corrected.freq 0.381461
; min(P(S|M)) 1.35268e-35
; max(P(S|M)) 9.03552e-06
; proba_range 9.03552e-06
; Wmin -48.6
; Wmax 18.3
; Wrange 66.9
; logo file:/GlpR.EcolK12_1nt_upstream.22.meme_quality_logo_m1.png
; logo file:/GlpR.EcolK12_1nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.6
; user 0.6
; system 0.06
; cuser 0.45
; csystem 0.04