RegulonDB
PhoP matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/PhoP/PhoP.EcolK12_2nt_upstream.18.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 /PhoP.EcolK12_2nt_upstream.18.meme_quality_logo
; Input files
; input /PhoP.EcolK12_2nt_upstream.18.meme_quality_matrix.tf
; prior /PhoP.EcolK12_2nt_upstream.18.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /PhoP.EcolK12_2nt_upstream.18.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 7 11 1 4 6 26 8 4 9 12 6 3 6 1 1 5 31
C 8 3 3 2 1 1 3 2 16 7 5 13 8 0 0 0 1 0
G 5 3 17 1 3 2 3 9 8 7 5 5 4 25 3 2 5 3
T 13 21 3 30 26 25 2 15 6 11 12 10 19 3 30 31 23 0
//
A 0.2 0.2 0.3 0.0 0.1 0.2 0.8 0.2 0.1 0.3 0.4 0.2 0.1 0.2 0.0 0.0 0.2 0.9
C 0.2 0.1 0.1 0.1 0.0 0.0 0.1 0.1 0.5 0.2 0.1 0.4 0.2 0.0 0.0 0.0 0.0 0.0
G 0.1 0.1 0.5 0.0 0.1 0.1 0.1 0.3 0.2 0.2 0.1 0.1 0.1 0.7 0.1 0.1 0.1 0.1
T 0.4 0.6 0.1 0.9 0.8 0.7 0.1 0.4 0.2 0.3 0.4 0.3 0.6 0.1 0.9 0.9 0.7 0.0
//
A -0.2 -0.3 0.1 -2.1 -0.9 -0.5 0.9 -0.2 -0.9 -0.1 0.2 -0.5 -1.1 -0.5 -2.1 -2.1 -0.7 1.1
C 0.1 -0.8 -0.8 -1.2 -1.8 -1.8 -0.8 -1.2 0.8 -0.0 -0.3 0.6 0.1 -3.6 -3.6 -3.6 -1.8 -3.6
G -0.3 -0.8 0.9 -1.8 -0.8 -1.2 -0.8 0.3 0.1 0.0 -0.3 -0.3 -0.5 1.3 -0.8 -1.2 -0.3 -0.8
T 0.2 0.7 -1.1 1.1 0.9 0.9 -1.5 0.4 -0.5 0.1 0.2 -0.0 0.6 -1.1 1.1 1.1 0.8 -3.6
//
A -0.0 -0.1 0.0 -0.1 -0.1 -0.1 0.7 -0.0 -0.1 -0.0 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 1.0
C 0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.4 -0.0 -0.0 0.2 0.0 -0.0 -0.0 -0.0 -0.1 -0.0
G -0.0 -0.1 0.4 -0.1 -0.1 -0.1 -0.1 0.1 0.0 0.0 -0.0 -0.0 -0.1 0.9 -0.1 -0.1 -0.0 -0.1
T 0.1 0.4 -0.1 0.9 0.7 0.6 -0.1 0.2 -0.1 0.0 0.1 -0.0 0.3 -0.1 0.9 1.0 0.5 -0.0
//
; Sites 34
>site_0
TTGTTTAGGTTTTGTTTA
>site_1
TTGTTTAGGGTTTGTTTA
>site_2
GAGTTTAAGCTCCGTTTA
>site_3
TGGTTTATCGTTGGTTTA
>site_4
TGGTTTATTTAATGTTTA
>site_5
TTGTTTAACATCCATTGA
>site_6
CTGTTTATGGGCGGTGTA
>site_7
TTGTTTATAATTGGTTGA
>site_8
TAATTTCACATTTGTTTA
>site_9
TATTTAATCTATTGTTTA
>site_10
GCGTATAGCTTATGTTTA
>site_11
CTGTATATGTCATGTTGA
>site_12
ATATTGCTCCACTGTTTA
>site_13
TTCTTTAAGTTTTATTTA
>site_14
ATAGTTAGGCGCTGTTTA
>site_15
ATGTTTGACGAGTATTTA
>site_16
CTATTAAGGTTATGTTAA
>site_17
CTATTTAACTCCCGGTAA
>site_18
TAATTCAGCCTTCGTTTA
>site_19
TTGTTTAGAAACGATTGA
>site_20
GGGTTTATTAACTTTTGA
>site_21
TTTTCAATCTGCCGTTTA
>site_22
ACGTTTGACTGCCGTTTG
>site_23
CCATTAACACAATGTTTA
>site_24
ATGTTTATTTAGCGGATA
>site_25
CTGATTAACGATTTTTAA
>site_26
ATTTATAGCCTTAGTGTA
>site_27
AACTGTTTTGACCGTTTA
>site_28
CTATTTACAAGCTGATAA
>site_29
AACTATGTCACGTGTTAA
>site_30
TAATGAATTACGTGTTCA
>site_31
GTATGAATCAAAAATTTG
>site_32
GTGCTGCTCCAGTTGTTA
>site_33
CTACTTTGTGCCAATTTG
;
; Matrix parameters
; Number of sites 34
; Columns 18
; 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 HTRTTTADSNWYTGTTTA
; AC HTRTTTADSNWYTGTTTA
; id HTRTTTADSNWYTGTTTA
; name HTRTTTADSNWYTGTTTA
; description ytrTttakskwcyGTTtA
; statistical_basis 34 sequences
; sites 34
; nb_sites 34
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.68648
; information.per.column 0.371471
; max.possible.info.per.col 1.58952
; consensus.strict ttgTttatctactGTTtA
; consensus.strict.rc TAAACAGTAGATAAACAA
; consensus.IUPAC ytrTttakskwcyGTTtA
; consensus.IUPAC.rc TAAACRGWMSMTAAAYAR
; consensus.regexp [ct]t[ag]Ttta[gt][cg][gt][at]c[ct]GTTtA
; consensus.regexp.rc TAAAC[AG]G[AT][AC][CG][AC]TAAA[CT]A[AG]
; residues.content.crude.freq a:0.2435|c:0.1193|g:0.1797|t:0.4575
; G+C.content.crude.freq 0.29902
; residues.content.corrected.freq a:0.2448|c:0.1218|g:0.1804|t:0.4529
; G+C.content.corrected.freq 0.302243
; min(P(S|M)) 4.76017e-25
; max(P(S|M)) 6.35586e-05
; proba_range 6.35586e-05
; Wmin -29.6
; Wmax 13.8
; Wrange 43.4
; logo file:/PhoP.EcolK12_2nt_upstream.18.meme_quality_logo_m1.png
; logo file:/PhoP.EcolK12_2nt_upstream.18.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.59
; user 0.59
; system 0.06
; cuser 0.43
; csystem 0.04