RegulonDB
NagC matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/NagC/NagC.EcolK12_1nt_upstream.25.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 /NagC.EcolK12_1nt_upstream.25.meme_quality_logo
; Input files
; input /NagC.EcolK12_1nt_upstream.25.meme_quality_matrix.tf
; prior /NagC.EcolK12_1nt_upstream.25.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /NagC.EcolK12_1nt_upstream.25.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 15 4 8 4 17 6 1 0 0 7 4 4 13 7 5 9 9 19 20 10 3 18 10 3 9
C 1 6 1 1 0 0 0 0 15 0 10 3 3 6 0 6 0 1 0 0 2 0 2 9 6
G 2 4 0 0 0 1 0 0 0 12 0 11 1 2 11 2 7 0 0 3 2 2 3 5 0
T 2 6 11 15 3 13 19 20 5 1 6 2 3 5 4 3 4 0 0 7 13 0 5 3 5
//
A 0.7 0.2 0.4 0.2 0.8 0.3 0.1 0.0 0.0 0.3 0.2 0.2 0.6 0.3 0.3 0.4 0.4 0.9 1.0 0.5 0.2 0.9 0.5 0.2 0.4
C 0.1 0.3 0.1 0.1 0.0 0.0 0.0 0.0 0.7 0.0 0.5 0.2 0.2 0.3 0.0 0.3 0.0 0.1 0.0 0.0 0.1 0.0 0.1 0.4 0.3
G 0.1 0.2 0.0 0.0 0.0 0.1 0.0 0.0 0.0 0.6 0.0 0.5 0.1 0.1 0.5 0.1 0.3 0.0 0.0 0.2 0.1 0.1 0.2 0.2 0.0
T 0.1 0.3 0.5 0.7 0.2 0.6 0.9 1.0 0.3 0.1 0.3 0.1 0.2 0.3 0.2 0.2 0.2 0.0 0.0 0.3 0.6 0.0 0.3 0.2 0.3
//
A 0.9 -0.4 0.3 -0.4 1.0 0.0 -1.6 -3.0 -3.0 0.2 -0.4 -0.4 0.8 0.2 -0.1 0.4 0.4 1.1 1.2 0.5 -0.6 1.1 0.5 -0.6 0.4
C -1.3 0.4 -1.3 -1.3 -3.0 -3.0 -3.0 -3.0 1.2 -3.0 0.9 -0.3 -0.3 0.4 -3.0 0.4 -3.0 -1.3 -3.0 -3.0 -0.7 -3.0 -0.7 0.7 0.4
G -0.7 -0.0 -3.0 -3.0 -3.0 -1.3 -3.0 -3.0 -3.0 1.0 -3.0 1.0 -1.3 -0.7 1.0 -0.7 0.5 -3.0 -3.0 -0.3 -0.7 -0.7 -0.3 0.2 -3.0
T -1.0 0.0 0.6 0.9 -0.6 0.8 1.1 1.2 -0.2 -1.6 0.0 -1.0 -0.6 -0.2 -0.4 -0.6 -0.4 -3.0 -3.0 0.2 0.8 -3.0 -0.2 -0.6 -0.2
//
A 0.7 -0.1 0.1 -0.1 0.9 0.0 -0.1 -0.0 -0.0 0.1 -0.1 -0.1 0.5 0.1 -0.0 0.2 0.2 1.1 1.2 0.3 -0.1 1.0 0.3 -0.1 0.2
C -0.1 0.1 -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 0.9 -0.0 0.4 -0.0 -0.0 0.1 -0.0 0.1 -0.0 -0.1 -0.0 -0.0 -0.1 -0.0 -0.1 0.3 0.1
G -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 0.6 -0.0 0.5 -0.1 -0.1 0.5 -0.1 0.2 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 0.0 -0.0
T -0.1 0.0 0.3 0.7 -0.1 0.5 1.0 1.1 -0.0 -0.1 0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 -0.0 0.1 0.5 -0.0 -0.0 -0.1 -0.0
//
; Sites 20
>site_0
AAATAATTCGCGAAGATAATTAAGA
>site_1
ACATATTTCATGATGAGAATTATGC
>site_2
AGTAATTTTACGAAGAGAAATAAGT
>site_3
CTATTTTTCGCGACGCGAATTATCA
>site_4
AATTAATTCGCGAAGAAAAGCAGAA
>site_5
ATTAATTTCGCGCATCAAAATAATT
>site_6
ATTTAATTCGTATCGCAAATTAAAC
>site_7
TCTTAATTCACAATAAAAAATAACC
>site_8
AATTAGTTCGTCACGGTAAATAACA
>site_9
AGAAATTTCGAAAGGTAAAATATCC
>site_10
ATATAATTCGAATAGTGAATTACCC
>site_11
ACATATTTTGTGACACGAATTGCAA
>site_12
ACTTATTTTATCATTCAAAAAATCA
>site_13
AGTAATTTCTCGCCGATAAACAACT
>site_14
ATATTTTTCAATATAAAAAATAAGA
>site_15
TCTTATTTCGATCAATGAATAAACA
>site_16
GGTTATTTTACCTGTATAAATAACC
>site_17
GTCCATTTCACGATGAAAAAAATGT
>site_18
ACTTTTTTTGTGGCTGAAAGGAGTA
>site_19
AAATAAATCGCGAAACGCAGGGGTT
;
; Matrix parameters
; Number of sites 20
; Columns 25
; 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 ANWTATTTCRYGAHGMRAAWTAWSH
; AC ANWTATTTCRYGAHGMRAAWTAWSH
; id ANWTATTTCRYGAHGMRAAWTAWSH
; name ANWTATTTCRYGAHGMRAAWTAWSH
; description aywtAwTTCRygamgmrAAwtAasm
; statistical_basis 20 sequences
; sites 20
; nb_sites 20
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 11.0147
; information.per.column 0.440589
; max.possible.info.per.col 1.58873
; consensus.strict acttAtTTCGcgacgagAAatAaca
; consensus.strict.rc TGTTATTTCTCGTCGCGAAATAAGT
; consensus.IUPAC aywtAwTTCRygamgmrAAwtAasm
; consensus.IUPAC.rc KSTTAWTTYKCKTCRYGAAWTAWRT
; consensus.regexp a[ct][at]tA[at]TTC[AG][ct]ga[ac]g[ac][ag]AA[at]tAa[cg][ac]
; consensus.regexp.rc [GT][CG]TTA[AT]TT[CT][GT]C[GT]TC[AG][CT]GAA[AT]TA[AT][AG]T
; residues.content.crude.freq a:0.4100|c:0.1440|g:0.1360|t:0.3100
; G+C.content.crude.freq 0.28
; residues.content.corrected.freq a:0.4043|c:0.1470|g:0.1392|t:0.3094
; G+C.content.corrected.freq 0.286274
; min(P(S|M)) 9.68512e-42
; max(P(S|M)) 2.26304e-06
; proba_range 2.26304e-06
; Wmin -56
; Wmax 20.5
; Wrange 76.5
; logo file:/NagC.EcolK12_1nt_upstream.25.meme_quality_logo_m1.png
; logo file:/NagC.EcolK12_1nt_upstream.25.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161029
; Job done 2019-06-03.161030
; Seconds 0.53
; user 0.53
; system 0.05
; cuser 0.43
; csystem 0.04