RegulonDB
Rob matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/Rob/Rob.EcolK12_1nt_upstream.23.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 /Rob.EcolK12_1nt_upstream.23.meme_quality_logo
; Input files
; input /Rob.EcolK12_1nt_upstream.23.meme_quality_matrix.tf
; prior /Rob.EcolK12_1nt_upstream.23.meme_quality1nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /Rob.EcolK12_1nt_upstream.23.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 5 4 3 2 0 9 5 1 6 6 4 5 3 2 2 0 0 0 7 0 4 6 3
C 2 1 2 2 0 1 1 9 3 0 1 3 6 0 1 0 11 5 0 1 3 1 2
G 4 4 2 1 1 4 6 0 4 2 0 0 0 10 1 14 1 4 6 0 2 3 4
T 3 5 7 9 13 0 2 4 1 6 9 6 5 2 10 0 2 5 1 13 5 4 5
//
A 0.4 0.3 0.2 0.2 0.0 0.6 0.4 0.1 0.4 0.4 0.3 0.4 0.2 0.2 0.2 0.0 0.0 0.0 0.5 0.0 0.3 0.4 0.2
C 0.1 0.1 0.1 0.1 0.0 0.1 0.1 0.6 0.2 0.0 0.1 0.2 0.4 0.0 0.1 0.0 0.7 0.3 0.0 0.1 0.2 0.1 0.1
G 0.3 0.3 0.1 0.1 0.1 0.3 0.4 0.0 0.3 0.1 0.0 0.0 0.0 0.7 0.1 0.9 0.1 0.3 0.4 0.0 0.1 0.2 0.3
T 0.2 0.4 0.5 0.6 0.9 0.0 0.2 0.3 0.1 0.4 0.6 0.4 0.4 0.2 0.7 0.0 0.2 0.4 0.1 0.9 0.4 0.3 0.4
//
A 0.2 -0.0 -0.3 -0.6 -2.7 0.8 0.2 -1.2 0.4 0.4 -0.0 0.2 -0.3 -0.6 -0.6 -2.7 -2.7 -2.7 0.5 -2.7 -0.0 0.4 -0.3
C -0.3 -0.9 -0.3 -0.3 -2.7 -0.9 -0.9 1.1 0.0 -2.7 -0.9 0.0 0.7 -2.7 -0.9 -2.7 1.3 0.5 -2.7 -0.9 0.0 -0.9 -0.3
G 0.3 0.3 -0.3 -0.9 -0.9 0.3 0.7 -2.7 0.3 -0.3 -2.7 -2.7 -2.7 1.2 -0.9 1.5 -0.9 0.3 0.7 -2.7 -0.3 0.0 0.3
T -0.3 0.2 0.5 0.7 1.1 -2.7 -0.7 -0.0 -1.2 0.3 0.7 0.3 0.2 -0.7 0.8 -2.7 -0.7 0.2 -1.2 1.1 0.2 -0.0 0.2
//
A 0.1 -0.0 -0.1 -0.1 -0.1 0.5 0.1 -0.1 0.2 0.2 -0.0 0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 0.2 -0.1 -0.0 0.2 -0.1
C -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 0.7 0.0 -0.0 -0.1 0.0 0.3 -0.0 -0.1 -0.0 1.0 0.2 -0.0 -0.1 0.0 -0.1 -0.1
G 0.1 0.1 -0.0 -0.1 -0.1 0.1 0.3 -0.0 0.1 -0.0 -0.0 -0.0 -0.0 0.8 -0.1 1.5 -0.1 0.1 0.3 -0.0 -0.0 0.0 0.1
T -0.1 0.1 0.2 0.5 1.0 -0.1 -0.1 -0.0 -0.1 0.1 0.5 0.1 0.1 -0.1 0.6 -0.1 -0.1 0.1 -0.1 1.0 0.1 -0.0 0.1
//
; Sites 14
>site_0
AGGTTGGCGTTACGTGCCATAGG
>site_1
GTTTTGACATTCAGTGCTGTCAA
>site_2
GATTTAGCAAAACGTGGCATCGG
>site_3
TGTTTGGTCTTTCGTGCCATGTA
>site_4
ATAATAGCATTTTTTGCTGTTTT
>site_5
CGCTTATCCACCCGTGCGATTAC
>site_6
ATCTTAATGAAACGTGTCGTATT
>site_7
TTTTTAACGTAACGAGCGACTTT
>site_8
CTTTTATCAATTTGGGTTGTTAT
>site_9
GCACTCCCCTTTTGTGCGGTCAG
>site_10
GATGTAGTGGTTTATGCGATGAC
>site_11
TGTTTAACAGTTATAGCTTTTAG
>site_12
AAAATGATTATCAATGCCGTACT
>site_13
AAGCGAGAAAAATGCGCTATAGA
;
; Matrix parameters
; Number of sites 14
; Columns 23
; 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 DDTTTARCVWTHHGTGCBRTHDD
; AC DDTTTARCVWTHHGTGCBRTHDD
; id DDTTTARCVWTHHGTGCBRTHDD
; name DDTTTARCVWTHHGTGCBRTHDD
; description rkttTrrCvwthyGtGCbrTyrk
; statistical_basis 14 sequences
; sites 14
; nb_sites 14
; min.prior 0.204185
; alphabet.size 4
; max.bits 2
; total.information 8.01128
; information.per.column 0.348316
; max.possible.info.per.col 1.58873
; consensus.strict ggttTagCaattcGtGCcgTtag
; consensus.strict.rc CTAACGGCACGAATTGCTAAACC
; consensus.IUPAC rkttTrrCvwthyGtGCbrTyrk
; consensus.IUPAC.rc MYRAYVGCACRDAWBGYYAAAMY
; consensus.regexp [ag][gt]ttT[ag][ag]C[acg][at]t[act][ct]GtGC[cgt][ag]T[ct][ag][gt]
; consensus.regexp.rc [AC][CT][AG]A[CT][ACG]GCAC[AG][AGT]A[AT][CGT]G[CT][CT]AAA[AC][CT]
; residues.content.crude.freq a:0.2391|c:0.1708|g:0.2267|t:0.3634
; G+C.content.crude.freq 0.397516
; residues.content.corrected.freq a:0.2426|c:0.1733|g:0.2252|t:0.3590
; G+C.content.corrected.freq 0.398464
; min(P(S|M)) 2.40455e-34
; max(P(S|M)) 2.61115e-07
; proba_range 2.61115e-07
; Wmin -42.6
; Wmax 16.1
; Wrange 58.7
; logo file:/Rob.EcolK12_1nt_upstream.23.meme_quality_logo_m1.png
; logo file:/Rob.EcolK12_1nt_upstream.23.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.61
; user 0.61
; system 0.06
; cuser 0.44
; csystem 0.04