RegulonDB
FadR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/FadR/FadR.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 /FadR.EcolK12_1nt_upstream.20.meme_quality_logo
; Input files
; input /FadR.EcolK12_1nt_upstream.20.meme_quality_matrix.tf
; prior /FadR.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 /FadR.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 1 11 4 0 5 2 5 0 6 4 0 18 0 1 11 1 1 5 4 10
C 7 7 3 16 2 0 1 2 13 6 0 1 14 11 0 6 1 5 8 0
G 4 2 6 4 0 18 12 1 0 4 20 0 0 5 0 11 2 1 1 4
T 8 0 7 0 13 0 2 17 1 6 0 1 6 3 9 2 16 9 7 6
//
A 0.1 0.5 0.2 0.0 0.3 0.1 0.3 0.0 0.3 0.2 0.0 0.9 0.0 0.1 0.5 0.1 0.1 0.3 0.2 0.5
C 0.3 0.3 0.2 0.8 0.1 0.0 0.1 0.1 0.6 0.3 0.0 0.1 0.7 0.5 0.0 0.3 0.1 0.2 0.4 0.0
G 0.2 0.1 0.3 0.2 0.0 0.9 0.6 0.1 0.0 0.2 1.0 0.0 0.0 0.2 0.0 0.5 0.1 0.1 0.1 0.2
T 0.4 0.0 0.3 0.0 0.6 0.0 0.1 0.8 0.1 0.3 0.0 0.1 0.3 0.2 0.4 0.1 0.8 0.4 0.3 0.3
//
A -1.6 0.6 -0.4 -3.0 -0.1 -1.0 -0.1 -3.0 0.0 -0.4 -3.0 1.1 -3.0 -1.6 0.6 -1.6 -1.6 -0.1 -0.4 0.5
C 0.5 0.5 -0.3 1.3 -0.7 -3.0 -1.3 -0.7 1.1 0.4 -3.0 -1.3 1.2 0.9 -3.0 0.4 -1.3 0.2 0.6 -3.0
G -0.0 -0.7 0.4 -0.0 -3.0 1.4 1.0 -1.3 -3.0 -0.0 1.6 -3.0 -3.0 0.2 -3.0 1.0 -0.7 -1.3 -1.3 -0.0
T 0.3 -3.0 0.2 -3.0 0.8 -3.0 -1.0 1.0 -1.6 0.0 -3.0 -1.6 0.0 -0.6 0.4 -1.0 1.0 0.4 0.2 0.0
//
A -0.1 0.3 -0.1 -0.0 -0.0 -0.1 -0.0 -0.0 0.0 -0.1 -0.0 1.0 -0.0 -0.1 0.3 -0.1 -0.1 -0.0 -0.1 0.3
C 0.2 0.2 -0.0 1.0 -0.1 -0.0 -0.1 -0.1 0.7 0.1 -0.0 -0.1 0.8 0.5 -0.0 0.1 -0.1 0.0 0.2 -0.0
G -0.0 -0.1 0.1 -0.0 -0.0 1.3 0.6 -0.1 -0.0 -0.0 1.5 -0.0 -0.0 0.0 -0.0 0.5 -0.1 -0.1 -0.1 -0.0
T 0.1 -0.0 0.1 -0.0 0.5 -0.0 -0.1 0.8 -0.1 0.0 -0.0 -0.1 0.0 -0.1 0.2 -0.1 0.7 0.2 0.1 0.0
//
; Sites 20
>site_0
GATCAGGTCAGACCACTTTA
>site_1
CCTCTGGTATGATGAGTCCA
>site_2
CATCTGGTACGACCAGATCA
>site_3
CAGCTGGTCCGACCTATACT
>site_4
TATGTGGTCGGATGAGTTCT
>site_5
GAACTGATCGGACTTGTTCA
>site_6
GAACTGATCCGATGAGTTAA
>site_7
TCCCTGATAAGACCAGTATT
>site_8
TGGCTGATCGGACTTGTTCG
>site_9
GCTCCGGTCGGACCTGGCAA
>site_10
TAGGAGGTCTGACCACTTGT
>site_11
AAGCTGGTATGATGAGTTAA
>site_12
CCACTGGTCTGATTTCTAAG
>site_13
TCCGCGGTTCGACCACTTTT
>site_14
CATCAAAGCTGACCTGTCCG
>site_15
TACCAGTTATGACCTCTGTA
>site_16
CCTCAACCCCGACCAGTATA
>site_17
CGGCTGGTCCGCTGTTTCTG
>site_18
TAGCTGGCCAGTCATCGACA
>site_19
TCAGTGTTAAGACCATCCTT
;
; Matrix parameters
; Number of sites 20
; 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 BMDCTGGTCNGACCWSTHHW
; AC BMDCTGGTCNGACCWSTHHW
; id BMDCTGGTCNGACCWSTHHW
; name BMDCTGGTCNGACCWSTHHW
; description ymkCtGGTMyGAYswstyyw
; statistical_basis 20 sequences
; sites 20
; nb_sites 20
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 9.68292
; information.per.column 0.484146
; max.possible.info.per.col 1.58873
; consensus.strict cagCtGGTCcGACcagttca
; consensus.strict.rc TGAACTGGTCGGACCAGCTG
; consensus.IUPAC ymkCtGGTMyGAYswstyyw
; consensus.IUPAC.rc WRRASWSRTCRKACCAGMKR
; consensus.regexp [ct][ac][gt]CtGGT[AC][ct]GA[CT][cg][at][cg]t[ct][ct][at]
; consensus.regexp.rc [AT][AG][AG]A[CG][AT][CG][AG]TC[AG][GT]ACCAG[AC][GT][AG]
; residues.content.crude.freq a:0.2225|c:0.2575|g:0.2375|t:0.2825
; G+C.content.crude.freq 0.495
; residues.content.corrected.freq a:0.2258|c:0.2551|g:0.2359|t:0.2832
; G+C.content.corrected.freq 0.491036
; min(P(S|M)) 1.76093e-32
; max(P(S|M)) 1.6126e-05
; proba_range 1.6126e-05
; Wmin -44.3
; Wmax 17.4
; Wrange 61.7
; logo file:/FadR.EcolK12_1nt_upstream.20.meme_quality_logo_m1.png
; logo file:/FadR.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 0.61
; user 0.61
; system 0.08
; cuser 0.44
; csystem 0.05