RegulonDB
FlhDC matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/FlhDC/FlhDC.EcolK12_1nt_upstream.19.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 /FlhDC.EcolK12_1nt_upstream.19.meme_quality_logo
; Input files
; input /FlhDC.EcolK12_1nt_upstream.19.meme_quality_matrix.tf
; prior /FlhDC.EcolK12_1nt_upstream.19.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /FlhDC.EcolK12_1nt_upstream.19.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 12 14 7 3 0 1 3 2 3 14 9 4 8 8 4 0 3 2 4
C 0 1 2 4 1 6 5 2 0 0 0 0 2 0 1 9 0 8 8
G 1 1 0 9 15 6 7 5 10 0 2 1 0 8 10 7 12 6 1
T 3 0 7 0 0 3 1 7 3 2 5 11 6 0 1 0 1 0 3
//
A 0.7 0.8 0.4 0.2 0.0 0.1 0.2 0.1 0.2 0.8 0.5 0.3 0.5 0.5 0.3 0.0 0.2 0.1 0.3
C 0.0 0.1 0.1 0.2 0.1 0.4 0.3 0.1 0.0 0.0 0.0 0.0 0.1 0.0 0.1 0.5 0.0 0.5 0.5
G 0.1 0.1 0.0 0.5 0.9 0.4 0.4 0.3 0.6 0.0 0.1 0.1 0.0 0.5 0.6 0.4 0.7 0.4 0.1
T 0.2 0.0 0.4 0.0 0.0 0.2 0.1 0.4 0.2 0.1 0.3 0.7 0.4 0.0 0.1 0.0 0.1 0.0 0.2
//
A 0.9 1.1 0.4 -0.4 -2.8 -1.3 -0.4 -0.8 -0.4 1.1 0.6 -0.1 0.5 0.5 -0.1 -2.8 -0.4 -0.8 -0.1
C -2.8 -1.1 -0.5 0.2 -1.1 0.6 0.4 -0.5 -2.8 -2.8 -2.8 -2.8 -0.5 -2.8 -1.1 1.0 -2.8 0.8 0.8
G -1.1 -1.1 -2.8 1.0 1.5 0.6 0.7 0.4 1.1 -2.8 -0.5 -1.1 -2.8 0.9 1.1 0.7 1.3 0.6 -1.1
T -0.4 -2.8 0.4 -2.8 -2.8 -0.4 -1.4 0.4 -0.4 -0.8 0.0 0.8 0.2 -2.8 -1.4 -2.8 -1.4 -2.8 -0.4
//
A 0.7 0.9 0.2 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 0.9 0.3 -0.0 0.3 0.3 -0.0 -0.0 -0.1 -0.1 -0.0
C -0.0 -0.1 -0.1 0.0 -0.1 0.2 0.1 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 0.5 -0.0 0.4 0.4
G -0.1 -0.1 -0.0 0.5 1.3 0.2 0.3 0.1 0.6 -0.0 -0.1 -0.1 -0.0 0.4 0.6 0.3 0.9 0.2 -0.1
T -0.1 -0.0 0.2 -0.0 -0.0 -0.1 -0.1 0.2 -0.1 -0.1 0.0 0.5 0.1 -0.0 -0.1 -0.0 -0.1 -0.0 -0.1
//
; Sites 16
>site_0
AATAGCGGGAATAAGGGGC
>site_1
AATGGCCGGAAAAGACGCC
>site_2
ACAGGCGGGATTTAGGGCT
>site_3
TATCGGCGGAATAAACGCA
>site_4
AATGGTTTGAGTAAGGGGC
>site_5
AAACGGGTTTATTGGCGGA
>site_6
GATGGCAAGAAATAGCGCC
>site_7
AATAGGCTGATTCAAGGCA
>site_8
AAAGCGGGGAAAAGACGCG
>site_9
AAAGGCGCTAAATAGCAAC
>site_10
AACGGCATAAATAGCGACC
>site_11
TGAGGGGTTATTTGGGGGT
>site_12
AACGGTCTAAATAGGCTGA
>site_13
AATCGGACGATTAGTGGGT
>site_14
TAACGTCAGAGGTAGCACC
>site_15
AAAAGAGTATTTCGGCGAC
;
; Matrix parameters
; Number of sites 16
; Columns 19
; 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 AAWGGBSKGAWTWRGSGSM
; AC AAWGGBSKGAWTWRGSGSM
; id AAWGGBSKGAWTWRGSGSM
; name AAWGGBSKGAWTWRGSGSM
; description aAwsGsskGAwtwrGsGsc
; statistical_basis 16 sequences
; sites 16
; nb_sites 16
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.74426
; information.per.column 0.460224
; max.possible.info.per.col 1.58873
; consensus.strict aAagGgggGAatagGcGcc
; consensus.strict.rc GGCGCCTATTCCCCCCTTT
; consensus.IUPAC aAwsGsskGAwtwrGsGsc
; consensus.IUPAC.rc GSCSCYWAWTCMSSCSWTT
; consensus.regexp aA[at][cg]G[cg][cg][gt]GA[at]t[at][ag]G[cg]G[cg]c
; consensus.regexp.rc G[CG]C[CG]C[CT][AT]A[AT]TC[AC][CG][CG]C[CG][AT]TT
; residues.content.crude.freq a:0.3322|c:0.1612|g:0.3322|t:0.1743
; G+C.content.crude.freq 0.493421
; residues.content.corrected.freq a:0.3298|c:0.1639|g:0.3247|t:0.1816
; G+C.content.corrected.freq 0.488617
; min(P(S|M)) 3.40524e-32
; max(P(S|M)) 1.98993e-05
; proba_range 1.98993e-05
; Wmin -45.6
; Wmax 16.5
; Wrange 62.1
; logo file:/FlhDC.EcolK12_1nt_upstream.19.meme_quality_logo_m1.png
; logo file:/FlhDC.EcolK12_1nt_upstream.19.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 0.04
; cuser 0.44
; csystem 0.05