RegulonDB
TyrR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/TyrR/TyrR.EcolK12_2nt_upstream.21.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 /TyrR.EcolK12_2nt_upstream.21.meme_quality_logo
; Input files
; input /TyrR.EcolK12_2nt_upstream.21.meme_quality_matrix.tf
; prior /TyrR.EcolK12_2nt_upstream.21.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /TyrR.EcolK12_2nt_upstream.21.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 0 0 1 13 8 10 4 8 6 10 8 6 3 0 0 17 0 13 0 7 5
C 4 0 0 3 4 2 0 6 4 2 2 4 1 0 1 2 19 0 10 5 3
G 0 19 3 0 0 1 7 2 3 2 1 7 1 1 2 0 0 4 5 2 3
T 15 0 15 3 7 6 8 3 6 5 8 2 14 18 16 0 0 2 4 5 8
//
A 0.0 0.0 0.1 0.7 0.4 0.5 0.2 0.4 0.3 0.5 0.4 0.3 0.2 0.0 0.0 0.9 0.0 0.7 0.0 0.4 0.3
C 0.2 0.0 0.0 0.2 0.2 0.1 0.0 0.3 0.2 0.1 0.1 0.2 0.1 0.0 0.1 0.1 1.0 0.0 0.5 0.3 0.2
G 0.0 1.0 0.2 0.0 0.0 0.1 0.4 0.1 0.2 0.1 0.1 0.4 0.1 0.1 0.1 0.0 0.0 0.2 0.3 0.1 0.2
T 0.8 0.0 0.8 0.2 0.4 0.3 0.4 0.2 0.3 0.3 0.4 0.1 0.7 0.9 0.8 0.0 0.0 0.1 0.2 0.3 0.4
//
A -3.0 -3.0 -1.5 0.8 0.4 0.6 -0.3 0.4 0.1 0.6 0.4 0.1 -0.6 -3.0 -3.0 1.1 -3.0 0.8 -3.0 0.2 -0.1
C 0.0 -3.0 -3.0 -0.3 0.0 -0.6 -3.0 0.4 0.0 -0.6 -0.6 0.0 -1.2 -3.0 -1.2 -0.6 1.5 -3.0 0.9 0.2 -0.3
G -3.0 1.5 -0.2 -3.0 -3.0 -1.2 0.6 -0.6 -0.2 -0.6 -1.2 0.6 -1.2 -1.2 -0.6 -3.0 -3.0 0.0 0.2 -0.6 -0.2
T 0.9 -3.0 0.9 -0.6 0.2 0.1 0.3 -0.6 0.1 -0.1 0.3 -1.0 0.9 1.1 1.0 -3.0 -3.0 -1.0 -0.3 -0.1 0.3
//
A -0.0 -0.0 -0.1 0.5 0.1 0.3 -0.1 0.1 0.0 0.3 0.1 0.0 -0.1 -0.0 -0.0 0.9 -0.0 0.5 -0.0 0.1 -0.0
C 0.0 -0.0 -0.0 -0.0 0.0 -0.1 -0.0 0.1 0.0 -0.1 -0.1 0.0 -0.1 -0.0 -0.1 -0.1 1.5 -0.0 0.5 0.1 -0.0
G -0.0 1.5 -0.0 -0.0 -0.0 -0.1 0.2 -0.1 -0.0 -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.0 -0.0 0.0 0.1 -0.1 -0.0
T 0.7 -0.0 0.7 -0.1 0.1 0.0 0.1 -0.1 0.0 -0.0 0.1 -0.1 0.6 1.0 0.8 -0.0 -0.0 -0.1 -0.1 -0.0 0.1
//
; Sites 19
>site_0
TGTATAGATAAATTTACACTC
>site_1
TGTACATTTATATTTACACCA
>site_2
TGTAAAACCCCGTTTACACAT
>site_3
TGTAATTTATTATTTACACTT
>site_4
TGTATATATTATTTTACAGAT
>site_5
CGTAAATCACACTTTACAGCT
>site_6
TGTATTAATTTGTTTACATCA
>site_7
CGTACATTTTTATTTACACAG
>site_8
TGTAAAGAAAAAATTCCACTT
>site_9
TGTTCAGCGATGATTACGCAT
>site_10
TGTCAATGATTGTTGACAGAA
>site_11
TGTTTCAAAAAGTTGACGCCT
>site_12
TGGATTGAAAACTTTACTTTA
>site_13
CGGAATTGCAAACTTACACAC
>site_14
TGACCGGATATCTTTACGCCG
>site_15
CGTCAAACCGACGTTACATAT
>site_16
TGGTTCTCCAGGTTTACGGGC
>site_17
TGTATTGAGATTTTCACTTTA
>site_18
TGTAATGCGGCGAGTCCAGGG
;
; Matrix parameters
; Number of sites 19
; Columns 21
; 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 TGTAHWDMNWWVTTTACASHW
; AC TGTAHWDMNWWVTTTACASHW
; id TGTAHWDMNWWVTTTACASHW
; name TGTAHWDMNWWVTTTACASHW
; description yGtahwkmhawvtTTACrsmt
; statistical_basis 19 sequences
; sites 19
; nb_sites 19
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 9.0151
; information.per.column 0.42929
; max.possible.info.per.col 1.58952
; consensus.strict tGtaaagcaaagtTTACacct
; consensus.strict.rc AGGTGTAAACTTTGCTTTACA
; consensus.IUPAC yGtahwkmhawvtTTACrsmt
; consensus.IUPAC.rc AKSYGTAAABWTDKMWDTACR
; consensus.regexp [ct]Gta[act][at][gt][ac][act]a[at][acg]tTTAC[ag][cg][ac]t
; consensus.regexp.rc A[GT][CG][CT]GTAAA[CGT][AT]T[AGT][GT][AC][AT][AGT]TAC[AG]
; residues.content.crude.freq a:0.2982|c:0.1805|g:0.1579|t:0.3634
; G+C.content.crude.freq 0.338346
; residues.content.corrected.freq a:0.2979|c:0.1818|g:0.1602|t:0.3601
; G+C.content.corrected.freq 0.34202
; min(P(S|M)) 2.4403e-33
; max(P(S|M)) 7.52485e-06
; proba_range 7.52485e-06
; Wmin -43
; Wmax 15.7
; Wrange 58.7
; logo file:/TyrR.EcolK12_2nt_upstream.21.meme_quality_logo_m1.png
; logo file:/TyrR.EcolK12_2nt_upstream.21.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161114
; Job done 2019-06-03.161115
; Seconds 0.55
; user 0.55
; system 0.06
; cuser 0.43
; csystem 0.05