RegulonDB
CsgD matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CsgD/CsgD.EcolK12_1nt_upstream.14.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 /CsgD.EcolK12_1nt_upstream.14.meme_quality_logo
; Input files
; input /CsgD.EcolK12_1nt_upstream.14.meme_quality_matrix.tf
; prior /CsgD.EcolK12_1nt_upstream.14.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /CsgD.EcolK12_1nt_upstream.14.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 8 15 21 14 1 5 8 10 3 14 20 8 15 7
C 7 1 1 0 2 6 0 7 3 7 0 10 5 10
G 2 4 0 9 5 11 14 4 2 1 0 2 0 1
T 7 4 2 1 16 2 2 3 16 2 4 4 4 6
//
A 0.3 0.6 0.9 0.6 0.1 0.2 0.3 0.4 0.1 0.6 0.8 0.3 0.6 0.3
C 0.3 0.0 0.0 0.0 0.1 0.2 0.0 0.3 0.1 0.3 0.0 0.4 0.2 0.4
G 0.1 0.2 0.0 0.4 0.2 0.4 0.6 0.2 0.1 0.0 0.0 0.1 0.0 0.0
T 0.3 0.2 0.1 0.1 0.7 0.1 0.1 0.1 0.7 0.1 0.2 0.2 0.2 0.3
//
A 0.1 0.7 1.1 0.7 -1.7 -0.3 0.1 0.3 -0.8 0.7 1.0 0.1 0.7 0.0
C 0.3 -1.5 -1.5 -3.2 -0.9 0.2 -3.2 0.3 -0.5 0.3 -3.2 0.7 0.0 0.7
G -0.8 -0.2 -3.2 0.6 0.0 0.8 1.0 -0.2 -0.8 -1.4 -3.2 -0.8 -3.2 -1.4
T -0.0 -0.5 -1.2 -1.7 0.8 -1.2 -1.2 -0.8 0.8 -1.2 -0.5 -0.5 -0.5 -0.2
//
A 0.0 0.5 0.9 0.4 -0.1 -0.1 0.0 0.1 -0.1 0.4 0.8 0.0 0.5 0.0
C 0.1 -0.1 -0.1 -0.0 -0.1 0.0 -0.0 0.1 -0.1 0.1 -0.0 0.3 0.0 0.3
G -0.1 -0.0 -0.0 0.2 0.0 0.4 0.6 -0.0 -0.1 -0.1 -0.0 -0.1 -0.0 -0.1
T -0.0 -0.1 -0.1 -0.1 0.5 -0.1 -0.1 -0.1 0.5 -0.1 -0.1 -0.1 -0.1 -0.0
//
; Sites 24
>site_0
AAAATGGCTCACCC
>site_1
TAAATGGGTAAAAT
>site_2
TAAGTCAATAAGAC
>site_3
CTAATGGATTACAT
>site_4
AAAGGCGCTAAATA
>site_5
TAAATAAGCAACAC
>site_6
TTAATAACTCACCC
>site_7
AGAATAGATATCAT
>site_8
CAAATGGTGATAAC
>site_9
CTTGTCGATCACCC
>site_10
ACAGGGAGTAAAAC
>site_11
AAAAGCGCCCTCAA
>site_12
GAAACGGATAATCA
>site_13
CAAAGTATTAAAAC
>site_14
AAAGTGGAATATAA
>site_15
CAAATGTACAACTT
>site_16
TTCGTAGCTCACCC
>site_17
TAAGCCGCTCTTAT
>site_18
CGATGAGATAAAAA
>site_19
TGAGTTATTAAAAA
>site_20
AAAAAGAAAAATAC
>site_21
GATATGGCAAAATA
>site_22
AAAGTCTGGCACTT
>site_23
CGAATGAATGAGAG
;
; Matrix parameters
; Number of sites 24
; Columns 14
; 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 HAARTSRMTMAMAH
; AC HAARTSRMTMAMAH
; id HAARTSRMTMAMAH
; name HAARTSRMTMAMAH
; description maArksRmtmAmmm
; statistical_basis 24 sequences
; sites 24
; nb_sites 24
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 4.58487
; information.per.column 0.327491
; max.possible.info.per.col 1.58873
; consensus.strict caAatgGataAcac
; consensus.strict.rc GTGTTATCCATTTG
; consensus.IUPAC maArksRmtmAmmm
; consensus.IUPAC.rc KKKTKAKYSMYTTK
; consensus.regexp [ac]aA[ag][gt][cg][AG][ac]t[ac]A[ac][ac][ac]
; consensus.regexp.rc [GT][GT][GT]T[GT]A[GT][CT][CG][AC][CT]TT[GT]
; residues.content.crude.freq a:0.4435|c:0.1756|g:0.1637|t:0.2173
; G+C.content.crude.freq 0.339286
; residues.content.corrected.freq a:0.4374|c:0.1769|g:0.1653|t:0.2205
; G+C.content.corrected.freq 0.342184
; min(P(S|M)) 1.80521e-21
; max(P(S|M)) 0.000208092
; proba_range 0.000208092
; Wmin -26.7
; Wmax 10.4
; Wrange 37.1
; logo file:/CsgD.EcolK12_1nt_upstream.14.meme_quality_logo_m1.png
; logo file:/CsgD.EcolK12_1nt_upstream.14.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160930
; Job done 2019-06-03.160931
; Seconds 0.61
; user 0.61
; system 0.05
; cuser 0.43
; csystem 0.04