RegulonDB
IscR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/IscR/IscR.EcolK12_1nt_upstream.27.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 /IscR.EcolK12_1nt_upstream.27.meme_quality_logo
; Input files
; input /IscR.EcolK12_1nt_upstream.27.meme_quality_matrix.tf
; prior /IscR.EcolK12_1nt_upstream.27.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /IscR.EcolK12_1nt_upstream.27.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 4 3 9 2 1 2 2 7 2 2 3 6 1 3 0 7 1 2 5 0 0 0 1 5 2 3 5
C 3 1 0 2 2 2 5 2 8 4 3 3 1 0 2 1 2 3 3 0 0 0 0 1 0 0 0
G 1 1 0 3 1 1 4 0 0 0 4 0 2 1 1 0 5 2 1 7 10 10 0 1 1 1 1
T 3 6 2 4 7 6 0 2 1 5 1 2 7 7 8 3 3 4 2 4 1 1 10 4 8 7 5
//
A 0.4 0.3 0.8 0.2 0.1 0.2 0.2 0.6 0.2 0.2 0.3 0.5 0.1 0.3 0.0 0.6 0.1 0.2 0.4 0.0 0.0 0.0 0.1 0.4 0.2 0.3 0.4
C 0.3 0.1 0.0 0.2 0.2 0.2 0.4 0.2 0.7 0.4 0.3 0.3 0.1 0.0 0.2 0.1 0.2 0.3 0.3 0.0 0.0 0.0 0.0 0.1 0.0 0.0 0.0
G 0.1 0.1 0.0 0.3 0.1 0.1 0.4 0.0 0.0 0.0 0.4 0.0 0.2 0.1 0.1 0.0 0.4 0.2 0.1 0.6 0.9 0.9 0.0 0.1 0.1 0.1 0.1
T 0.3 0.5 0.2 0.4 0.6 0.5 0.0 0.2 0.1 0.4 0.1 0.2 0.6 0.6 0.7 0.3 0.3 0.4 0.2 0.4 0.1 0.1 0.9 0.4 0.7 0.6 0.4
//
A 0.2 -0.1 1.0 -0.4 -1.0 -0.4 -0.4 0.7 -0.4 -0.4 -0.1 0.6 -1.0 -0.1 -2.5 0.7 -1.0 -0.4 0.4 -2.5 -2.5 -2.5 -1.0 0.4 -0.4 -0.1 0.4
C 0.3 -0.7 -2.5 -0.1 -0.1 -0.1 0.7 -0.1 1.2 0.5 0.3 0.3 -0.7 -2.5 -0.1 -0.7 -0.1 0.3 0.3 -2.5 -2.5 -2.5 -2.5 -0.7 -2.5 -2.5 -2.5
G -0.7 -0.7 -2.5 0.3 -0.7 -0.7 0.5 -2.5 -2.5 -2.5 0.5 -2.5 -0.1 -0.7 -0.7 -2.5 0.8 -0.1 -0.7 1.1 1.4 1.4 -2.5 -0.7 -0.7 -0.7 -0.7
T -0.1 0.6 -0.4 0.2 0.7 0.6 -2.5 -0.4 -1.0 0.4 -1.0 -0.4 0.7 0.7 0.8 -0.1 -0.1 0.2 -0.4 0.2 -1.0 -1.0 1.1 0.2 0.8 0.7 0.4
//
A 0.1 -0.0 0.8 -0.1 -0.1 -0.1 -0.1 0.4 -0.1 -0.1 -0.0 0.3 -0.1 -0.0 -0.1 0.4 -0.1 -0.1 0.2 -0.1 -0.1 -0.1 -0.1 0.2 -0.1 -0.0 0.2
C 0.1 -0.1 -0.0 -0.0 -0.0 -0.0 0.3 -0.0 0.8 0.2 0.1 0.1 -0.1 -0.0 -0.0 -0.1 -0.0 0.1 0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0
G -0.1 -0.1 -0.0 0.1 -0.1 -0.1 0.2 -0.0 -0.0 -0.0 0.2 -0.0 -0.0 -0.1 -0.1 -0.0 0.3 -0.0 -0.1 0.6 1.2 1.2 -0.0 -0.1 -0.1 -0.1 -0.1
T -0.0 0.3 -0.1 0.1 0.4 0.3 -0.1 -0.1 -0.1 0.2 -0.1 -0.1 0.4 0.4 0.6 -0.0 -0.0 0.1 -0.1 0.1 -0.1 -0.1 0.9 0.1 0.6 0.4 0.2
//
; Sites 11
>site_0
TTACTTGACTGATTTAGTCGGGTATTT
>site_1
ATAGTTGACCAATTTACTCGGGAATGT
>site_2
ATACTTGAACGAAATACCAGGGTATTA
>site_3
ATAGTTGACTATTTTAGTTGGTTATAA
>site_4
AAATCAATACACTTCAGGGGGGTATTA
>site_5
TAAATCCACACAGTTTGTATTGTTTTG
>site_6
CCTGTTAACCCACACATCAGGGTCTAT
>site_7
TAAAGCCCCTGCGTTTGCTGGGTTGAA
>site_8
CTTTTGCTCACATTTCAAATGGTTATA
>site_9
GTATCTCATTGTTAGATAATGGTTATT
>site_10
CGATAACCCTTCTGTTTGCTGGTGTTT
;
; Matrix parameters
; Number of sites 11
; Columns 27
; 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 HWANTTSACYVMTTTAKNMKGGTWTTW
; AC HWANTTSACYVMTTTAKNMKGGTWTTW
; id HWANTTSACYVMTTTAKNMKGGTWTTW
; name HWANTTSACYVMTTTAKNMKGGTWTTW
; description mtakttsaCysmtttagymKGGTwttw
; statistical_basis 11 sequences
; sites 11
; nb_sites 11
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.99332
; information.per.column 0.333086
; max.possible.info.per.col 1.58873
; consensus.strict ctagttcaCcgatttagcaGGGTatta
; consensus.strict.rc TAATACCCTGCTAAATCGGTGAACTAG
; consensus.IUPAC mtakttsaCysmtttagymKGGTwttw
; consensus.IUPAC.rc WAAWACCMKRCTAAAKSRGTSAAMTAK
; consensus.regexp [ac]ta[gt]tt[cg]aC[ct][cg][ac]tttag[ct][ac][GT]GGT[at]tt[at]
; consensus.regexp.rc [AT]AA[AT]ACC[AC][GT][AG]CTAAA[GT][CG][AG]GT[CG]AA[AC]TA[GT]
; residues.content.crude.freq a:0.2626|c:0.1616|g:0.1953|t:0.3805
; G+C.content.crude.freq 0.356902
; residues.content.corrected.freq a:0.2650|c:0.1654|g:0.1960|t:0.3735
; G+C.content.corrected.freq 0.361473
; min(P(S|M)) 4.63966e-39
; max(P(S|M)) 7.87341e-08
; proba_range 7.87341e-08
; Wmin -48.2
; Wmax 19.5
; Wrange 67.7
; logo file:/IscR.EcolK12_1nt_upstream.27.meme_quality_logo_m1.png
; logo file:/IscR.EcolK12_1nt_upstream.27.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161000
; Job done 2019-06-03.161001
; Seconds 0.52
; user 0.52
; system 0.04
; cuser 0.44
; csystem 0.04