RegulonDB
MarA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/MarA/MarA.EcolK12_2nt_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 /MarA.EcolK12_2nt_upstream.23.meme_quality_logo
; Input files
; input /MarA.EcolK12_2nt_upstream.23.meme_quality_matrix.tf
; prior /MarA.EcolK12_2nt_upstream.23.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /MarA.EcolK12_2nt_upstream.23.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 8 8 6 9 20 5 8 2 2 19 6 14 17 18 13 3 7 3 2 20 15 14 6
C 8 7 6 3 0 10 6 2 22 0 16 0 1 1 7 4 0 9 9 5 2 5 7
G 6 7 4 6 3 1 10 20 2 2 1 7 3 2 0 7 19 4 5 0 3 2 1
T 4 4 10 8 3 10 2 2 0 5 3 5 5 5 6 12 0 10 10 1 6 5 12
//
A 0.3 0.3 0.2 0.3 0.8 0.2 0.3 0.1 0.1 0.7 0.2 0.5 0.6 0.7 0.5 0.1 0.3 0.1 0.1 0.8 0.6 0.5 0.2
C 0.3 0.3 0.2 0.1 0.0 0.4 0.2 0.1 0.8 0.0 0.6 0.0 0.0 0.0 0.3 0.2 0.0 0.3 0.3 0.2 0.1 0.2 0.3
G 0.2 0.3 0.2 0.2 0.1 0.0 0.4 0.7 0.1 0.1 0.0 0.3 0.1 0.1 0.0 0.3 0.7 0.2 0.2 0.0 0.1 0.1 0.0
T 0.2 0.2 0.4 0.3 0.1 0.4 0.1 0.1 0.0 0.2 0.1 0.2 0.2 0.2 0.2 0.5 0.0 0.4 0.4 0.0 0.2 0.2 0.5
//
A 0.1 0.1 -0.2 0.2 0.9 -0.4 0.1 -1.2 -1.2 0.9 -0.2 0.6 0.8 0.8 0.5 -0.9 -0.1 -0.9 -1.2 0.9 0.7 0.6 -0.2
C 0.4 0.3 0.1 -0.6 -3.3 0.6 0.1 -0.9 1.4 -3.3 1.1 -3.3 -1.5 -1.5 0.3 -0.3 -3.3 0.5 0.5 -0.1 -0.9 -0.1 0.3
G 0.1 0.3 -0.3 0.1 -0.5 -1.5 0.6 1.3 -0.9 -0.9 -1.5 0.3 -0.5 -0.9 -3.3 0.3 1.2 -0.3 -0.1 -3.3 -0.5 -0.9 -1.5
T -0.6 -0.6 0.2 0.0 -0.9 0.2 -1.3 -1.3 -3.3 -0.4 -0.9 -0.4 -0.4 -0.4 -0.2 0.4 -3.3 0.2 0.2 -1.8 -0.2 -0.4 0.4
//
A 0.0 0.0 -0.1 0.1 0.7 -0.1 0.0 -0.1 -0.1 0.6 -0.1 0.3 0.5 0.6 0.3 -0.1 -0.0 -0.1 -0.1 0.7 0.4 0.3 -0.1
C 0.1 0.1 0.0 -0.1 -0.0 0.2 0.0 -0.1 1.1 -0.0 0.6 -0.0 -0.1 -0.1 0.1 -0.0 -0.0 0.2 0.2 -0.0 -0.1 -0.0 0.1
G 0.0 0.1 -0.0 0.0 -0.1 -0.1 0.2 1.0 -0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.0 0.1 0.9 -0.0 -0.0 -0.0 -0.1 -0.1 -0.1
T -0.1 -0.1 0.1 0.0 -0.1 0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 -0.0 0.1 0.1 -0.1 -0.1 -0.1 0.2
//
; Sites 26
>site_0
CACCACGGCACAAAATGACAAAT
>site_1
CCCTATGGCACGTAACGCCAACC
>site_2
ACATATGGCACGAAAAACCAAAC
>site_3
CGTAACGGCAAGAAATGCTCCAC
>site_4
AAAGGAGGCACTAACGGTTAAAT
>site_5
TTTGACAGCACTGAATGTCAAAA
>site_6
AACCGTGGCACAAATGGGCAATT
>site_7
GCTAAAAGCTATAACTGTTAAAC
>site_8
GCTGACCGCACAAAAGGGGAGTG
>site_9
TAAAACAGCAAAAAATGCTATTA
>site_10
CTGGAAGGCTCAATCGATCAAAT
>site_11
ACCGATGCCACGTTTTGCTAAAT
>site_12
GGCAAAAGCAGAAACTGTAAAAC
>site_13
CGTCATCGCATAAACCACTACAT
>site_14
CGTAATCGCACGGGTGGATAAGC
>site_15
GAAAGTCGCTCGTTACGTTAAAA
>site_16
ATGAACATGACAAAAGGTGCACT
>site_17
AGTTACAGCACTTTTTGCACTCA
>site_18
CCTTTTTGCAAAAAATGCTTGCT
>site_19
AAGTACGGCATTGATAATCATTT
>site_20
GGTAAGCGAGAAAAATGCGCTAT
>site_21
GTGGTTAGCGAAAGCTGGCATTT
>site_22
TAATACGACACGTTTCATTAAGA
>site_23
AGATACAACTCACACAATGCACC
>site_24
CCCAAATTGATAAAAGAGGAGAA
>site_25
TATTTTCCATCAACATGACATAT
;
; Matrix parameters
; Number of sites 26
; Columns 23
; 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 NNHDAHVGCACRAAMKGYBAAAH
; AC NNHDAHVGCACRAAMKGYBAAAH
; id NNHDAHVGCACRAAMKGYBAAAH
; name NNHDAHVGCACRAAMKGYBAAAH
; description vvydayvGCaCraamkGyyaaay
; statistical_basis 26 sequences
; sites 26
; nb_sites 26
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.89817
; information.per.column 0.299921
; max.possible.info.per.col 1.58952
; consensus.strict cgtaacgGCaCaaaatGccaaat
; consensus.strict.rc ATTTGGCATTTTGTGCCGTTACG
; consensus.IUPAC vvydayvGCaCraamkGyyaaay
; consensus.IUPAC.rc RTTTRRCMKTTYGTGCBRTHRBB
; consensus.regexp [acg][acg][ct][agt]a[ct][acg]GCaC[ag]aa[ac][gt]G[ct][ct]aaa[ct]
; consensus.regexp.rc [AG]TTT[AG][AG]C[AC][GT]TT[CT]GTGC[CGT][AG]T[ACT][AG][CGT][CGT]
; residues.content.crude.freq a:0.3763|c:0.2174|g:0.1923|t:0.2140
; G+C.content.crude.freq 0.409699
; residues.content.corrected.freq a:0.3731|c:0.2170|g:0.1927|t:0.2171
; G+C.content.corrected.freq 0.409778
; min(P(S|M)) 1.07305e-32
; max(P(S|M)) 1.93367e-07
; proba_range 1.93367e-07
; Wmin -40.2
; Wmax 16
; Wrange 56.2
; logo file:/MarA.EcolK12_2nt_upstream.23.meme_quality_logo_m1.png
; logo file:/MarA.EcolK12_2nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161014
; Job done 2019-06-03.161015
; Seconds 0.58
; user 0.58
; system 0.05
; cuser 0.42
; csystem 0.05