RegulonDB
CpxR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CpxR/CpxR.EcolK12_1nt_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 /CpxR.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /CpxR.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /CpxR.EcolK12_1nt_upstream.20.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /CpxR.EcolK12_1nt_upstream.20.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 6 6 8 39 9 19 14 18 14 8 7 7 4 42 4 18 14 19 13 17
C 17 0 0 0 43 11 12 13 4 18 9 0 0 3 44 16 18 12 15 14
G 3 7 9 3 2 18 10 9 17 10 13 0 4 7 5 12 17 6 6 14
T 34 47 43 18 6 12 24 20 25 24 31 53 52 8 7 14 11 23 26 15
//
A 0.1 0.1 0.1 0.6 0.2 0.3 0.2 0.3 0.2 0.1 0.1 0.1 0.1 0.7 0.1 0.3 0.2 0.3 0.2 0.3
C 0.3 0.0 0.0 0.0 0.7 0.2 0.2 0.2 0.1 0.3 0.2 0.0 0.0 0.1 0.7 0.3 0.3 0.2 0.2 0.2
G 0.1 0.1 0.2 0.1 0.0 0.3 0.2 0.2 0.3 0.2 0.2 0.0 0.1 0.1 0.1 0.2 0.3 0.1 0.1 0.2
T 0.6 0.8 0.7 0.3 0.1 0.2 0.4 0.3 0.4 0.4 0.5 0.9 0.9 0.1 0.1 0.2 0.2 0.4 0.4 0.3
//
A -1.0 -1.0 -0.8 0.8 -0.6 0.1 -0.2 0.0 -0.2 -0.8 -0.9 -0.9 -1.4 0.9 -1.4 0.0 -0.2 0.1 -0.3 -0.0
C 0.3 -4.1 -4.1 -4.1 1.2 -0.1 -0.0 0.0 -1.1 0.4 -0.3 -4.1 -4.1 -1.4 1.3 0.2 0.4 -0.0 0.2 0.1
G -1.4 -0.5 -0.3 -1.4 -1.7 0.4 -0.2 -0.3 0.3 -0.2 0.1 -4.1 -1.1 -0.5 -0.9 -0.0 0.3 -0.7 -0.7 0.1
T 0.6 1.0 0.9 0.0 -1.1 -0.4 0.3 0.1 0.3 0.3 0.5 1.1 1.1 -0.8 -0.9 -0.2 -0.5 0.3 0.4 -0.2
//
A -0.1 -0.1 -0.1 0.5 -0.1 0.0 -0.1 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 0.6 -0.1 0.0 -0.1 0.0 -0.1 -0.0
C 0.1 -0.0 -0.0 -0.0 0.9 -0.0 -0.0 0.0 -0.1 0.1 -0.0 -0.0 -0.0 -0.1 0.9 0.1 0.1 -0.0 0.0 0.0
G -0.1 -0.1 -0.0 -0.1 -0.1 0.1 -0.0 -0.0 0.1 -0.0 0.0 -0.0 -0.1 -0.1 -0.1 -0.0 0.1 -0.1 -0.1 0.0
T 0.4 0.7 0.6 0.0 -0.1 -0.1 0.1 0.0 0.1 0.1 0.3 0.9 0.9 -0.1 -0.1 -0.1 -0.1 0.1 0.2 -0.0
//
; Sites 60
>site_0
TTTACGTTGTTTTACACCCC
>site_1
TTTACGTCTTTTTACTGCCC
>site_2
TTTACCCATCTTTACGCATT
>site_3
TTTTCGCCGCTTTACGGTTA
>site_4
TTTACCCTTCTTTACACACT
>site_5
CTTTCATTGTTTTACCGTTG
>site_6
TTTACATTTTTTTGCACTCG
>site_7
CTTACCAGGTTTTACCGATG
>site_8
TTTACGCCACGTTACGGACA
>site_9
TTTACCTTACTTTACGCGCG
>site_10
TTTACCTAATTTTACGTATC
>site_11
TTTACGCGTTTTTACCTGCG
>site_12
CTTACGGCGTTTTGCTGTTT
>site_13
TTATCCCCGCTTTACCGTTC
>site_14
TTTACTTTTGGTTACATATT
>site_15
CTTACAAGCTTTTACTCTTT
>site_16
TTTATATATTTTTACATTTC
>site_17
CTTTCAGTGCTTTACCTGCA
>site_18
TTAACGCTGCGTTACGATGG
>site_19
TTTACACAGGCTGACACTTT
>site_20
CTGACGGTAATTTACTGACA
>site_21
CTGACGCATGTTTGCAGCCT
>site_22
TTTACTCTCATTTACGCTGC
>site_23
GTTACGGAACTTTACAAAAA
>site_24
TGGACAATTTTTTACTGCAA
>site_25
TAAACGGGGTTTTACACTAT
>site_26
ATTACGAAAAATTACAATTA
>site_27
TTTACAAATTCTTTGCACTT
>site_28
TTATCTACGCGTTAGCGATA
>site_29
GTTACGGAATATTACATTGC
>site_30
ATTACATCTGATTTCAATCT
>site_31
CTTTGTTGCCTTTACCAATG
>site_32
TGTACATTTGGTTTTTATTG
>site_33
TGGTGATCTCTTTACCGGTC
>site_34
TTTTATTAAGTTTAGAAATG
>site_35
TTTTCTTTTTGAAACCAAAT
>site_36
TTGACCGTTTGTTTAACCAC
>site_37
ATTACATTAACTGACTTTCC
>site_38
TTGACTTATACTTGCCTGGG
>site_39
TTTAAGATTTGTAATGGCTA
>site_40
TTTTATAAACATTCCGCTTG
>site_41
GTTTCAGGGAGTTGCGGCGC
>site_42
TGTAAATTATCATGCCCTTT
>site_43
CTTTTGTCTCGATATACATT
>site_44
CGATAGAGAGTTTACGATTC
>site_45
CTTTTCTATCATTTCTAAAC
>site_46
TTATCTGTTTGTTAAGTCAA
>site_47
CTTATTTCGCCATTCCGCAA
>site_48
ATTGTTCGTCTTTACAAAAG
>site_49
TAAACTAAGCGTTGTCCCCA
>site_50
CTGACCAAAGAATACTTGCA
>site_51
AGTTACATGTTTAACACTTG
>site_52
ATTACGTCAATATTTTCATA
>site_53
CATACAAATGGTGATAACTT
>site_54
TATTAAAATGTTAACCTTAA
>site_55
TATATGCATTATTAGTAAGT
>site_56
CGGTAATGGTTTTCGTCTAC
>site_57
CTTGCATTTACATTTTGAAA
>site_58
CTGGAATCGTCTGAATGACG
>site_59
TAAACCGCCTCTTCACCTAA
;
; Matrix parameters
; Number of sites 60
; Columns 20
; 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 YTTACNHHDYTTTACNNHHN
; AC YTTACNHHDYTTTACNNHHN
; id YTTACNHHDYTTTACNNHHN
; name YTTACNHHDYTTTACNNHHN
; description yttwCrthkykTTaCmswys
; statistical_basis 60 sequences
; sites 60
; nb_sites 60
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 5.41751
; information.per.column 0.270876
; max.possible.info.per.col 1.58873
; consensus.strict tttaCgtttctTTaCccttg
; consensus.strict.rc CAAGGGTAAAGAAACGTAAA
; consensus.IUPAC yttwCrthkykTTaCmswys
; consensus.IUPAC.rc SRWSKGTAAMRMDAYGWAAR
; consensus.regexp [ct]tt[at]C[ag]t[act][gt][ct][gt]TTaC[ac][cg][at][ct][cg]
; consensus.regexp.rc [CG][AG][AT][CG][GT]GTAA[AC][AG][AC][AGT]A[CT]G[AT]AA[AG]
; residues.content.crude.freq a:0.2383|c:0.2075|g:0.1433|t:0.4108
; G+C.content.crude.freq 0.350833
; residues.content.corrected.freq a:0.2392|c:0.2075|g:0.1443|t:0.4090
; G+C.content.corrected.freq 0.351832
; min(P(S|M)) 1.46104e-27
; max(P(S|M)) 7.88417e-07
; proba_range 7.88417e-07
; Wmin -32.4
; Wmax 12.2
; Wrange 44.6
; logo file:/CpxR.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/CpxR.EcolK12_1nt_upstream.20.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 0.61
; system 0.09
; cuser 0.43
; csystem 0.05