RegulonDB
NtrC matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/NtrC/NtrC.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 /NtrC.EcolK12_2nt_upstream.20.meme_quality_logo
; Input files
; input /NtrC.EcolK12_2nt_upstream.20.meme_quality_matrix.tf
; prior /NtrC.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 /NtrC.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 9 10 5 2 1 18 1 3 20 2 1 2 3 6 2 3 0 3 18 12
C 0 2 5 0 25 4 21 13 1 0 2 3 4 1 3 3 4 21 2 9
G 11 4 1 25 0 5 0 7 3 0 7 7 1 15 20 10 22 3 5 4
T 7 11 16 0 1 0 5 4 3 25 17 15 19 5 2 11 1 0 2 2
//
A 0.3 0.4 0.2 0.1 0.0 0.7 0.0 0.1 0.7 0.1 0.0 0.1 0.1 0.2 0.1 0.1 0.0 0.1 0.7 0.4
C 0.0 0.1 0.2 0.0 0.9 0.2 0.8 0.5 0.0 0.0 0.1 0.1 0.2 0.0 0.1 0.1 0.2 0.8 0.1 0.3
G 0.4 0.2 0.0 0.9 0.0 0.2 0.0 0.3 0.1 0.0 0.3 0.3 0.0 0.5 0.7 0.4 0.8 0.1 0.2 0.2
T 0.3 0.4 0.6 0.0 0.0 0.0 0.2 0.2 0.1 0.9 0.6 0.5 0.7 0.2 0.1 0.4 0.0 0.0 0.1 0.1
//
A 0.1 0.2 -0.4 -1.3 -1.8 0.8 -1.8 -0.9 0.9 -1.3 -1.8 -1.3 -0.9 -0.3 -1.3 -0.9 -3.3 -0.9 0.8 0.4
C -3.3 -1.0 -0.1 -3.3 1.5 -0.3 1.3 0.8 -1.6 -3.3 -1.0 -0.6 -0.3 -1.6 -0.6 -0.6 -0.3 1.3 -1.0 0.5
G 0.7 -0.3 -1.6 1.5 -3.3 -0.1 -3.3 0.2 -0.6 -3.3 0.2 0.2 -1.6 1.0 1.3 0.6 1.4 -0.6 -0.1 -0.3
T -0.1 0.3 0.7 -3.3 -1.9 -3.3 -0.5 -0.7 -0.9 1.1 0.7 0.6 0.8 -0.5 -1.3 0.3 -1.9 -3.3 -1.3 -1.3
//
A 0.0 0.1 -0.1 -0.1 -0.1 0.5 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 0.5 0.2
C -0.0 -0.1 -0.0 -0.0 1.3 -0.0 1.0 0.4 -0.1 -0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.0 1.0 -0.1 0.2
G 0.3 -0.0 -0.1 1.3 -0.0 -0.0 -0.0 0.1 -0.1 -0.0 0.1 0.1 -0.1 0.5 0.9 0.2 1.1 -0.1 -0.0 -0.0
T -0.0 0.1 0.4 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 1.0 0.5 0.3 0.6 -0.1 -0.1 0.1 -0.1 -0.0 -0.1 -0.1
//
; Sites 27
>site_0
GATGCACCATTCTGGGGCAC
>site_1
TAAGCACCATGTTGGTGCAA
>site_2
GTTGCACCATTTTAGTGCAT
>site_3
TTCGCACCATTGCGGGGCGC
>site_4
AGTGCACAATTTTAGCGCAC
>site_5
AATGCACGTTTTCAGGGCAA
>site_6
ATTGCCTGATTTTTGGGCAA
>site_7
GAAGCACTATATTGGTGCAA
>site_8
AATGCCCGCTTTTGGTGCGC
>site_9
GTTGCCCTGTTTCAGGGCAA
>site_10
TGCGCCACATTTTGGCGCAA
>site_11
GGGGCACCAATCTGGTGCGC
>site_12
GATGCATGTTTTATGTGCAA
>site_13
AACGCACTATGACAGTGCAC
>site_14
AATGAACCATCGTGGTGCAT
>site_15
GACGCACCATGTTGTGCGGC
>site_16
ACTGCGCCATTCTGACGCAG
>site_17
ATAACGCCTTTTAGGGGCAA
>site_18
GTAGTGCAGTTTTGGTGCAA
>site_19
TGTGCGCGATGAGAGTGCAG
>site_20
GATGCACGATTTATAGGGCA
>site_21
TTTGCACGATGGTGCGCATG
>site_22
ATAGCATCATGTTGTGCGGA
>site_23
GTTGCATTATTGTCCTGAAG
>site_24
GCTGCACAAATGTTGATCAA
>site_25
TTTGCGCCATCGTTGACATC
>site_26
TTCACATCGTGGTGCAGCCC
;
; Matrix parameters
; Number of sites 27
; 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 DWTGCACSATTTTGGKGCAM
; AC DWTGCACSATTTTGGKGCAM
; id DWTGCACSATTTTGGKGCAM
; name DWTGCACSATTTTGGKGCAM
; description rwtGCaCsaTkktgGkGCam
; statistical_basis 27 sequences
; sites 27
; nb_sites 27
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.80982
; information.per.column 0.490491
; max.possible.info.per.col 1.58952
; consensus.strict gttGCaCcaTtttgGgGCac
; consensus.strict.rc GTGCCCCAAAATGGTGCAAC
; consensus.IUPAC rwtGCaCsaTkktgGkGCam
; consensus.IUPAC.rc KTGCMCCAMMATSGTGCAWY
; consensus.regexp [ag][at]tGCaC[cg]aT[gt][gt]tgG[gt]GCa[ac]
; consensus.regexp.rc [GT]TGC[AC]CCA[AC][AC]AT[CG]GTGCA[AT][CT]
; residues.content.crude.freq a:0.2241|c:0.2278|g:0.2778|t:0.2704
; G+C.content.crude.freq 0.505556
; residues.content.corrected.freq a:0.2265|c:0.2271|g:0.2751|t:0.2713
; G+C.content.corrected.freq 0.502208
; min(P(S|M)) 1.81926e-31
; max(P(S|M)) 7.36925e-05
; proba_range 7.36925e-05
; Wmin -42.7
; Wmax 18.5
; Wrange 61.2
; logo file:/NtrC.EcolK12_2nt_upstream.20.meme_quality_logo_m1.png
; logo file:/NtrC.EcolK12_2nt_upstream.20.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161045
; Job done 2019-06-03.161045
; Seconds 0.61
; user 0.61
; system 0.05
; cuser 0.44
; csystem 0.04