RegulonDB
CysB matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/CysB/CysB.EcolK12_2nt_upstream.43.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 /CysB.EcolK12_2nt_upstream.43.meme_quality_logo
; Input files
; input /CysB.EcolK12_2nt_upstream.43.meme_quality_matrix.tf
; prior /CysB.EcolK12_2nt_upstream.43.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /CysB.EcolK12_2nt_upstream.43.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 2 9 9 11 1 9 5 6 5 8 7 4 5 4 2 7 9 2 7 9 2 8 11 12 4 6 2 4 10 7 8 11 5 1 2 10 6 0 11 11 4 5 2
C 1 1 0 2 0 0 6 2 2 0 2 2 0 0 5 1 0 0 1 0 4 0 0 1 0 0 1 7 3 0 1 0 1 3 3 0 6 2 1 1 7 3 4
G 6 2 1 0 4 0 0 4 6 3 1 1 6 7 4 4 3 1 4 3 3 4 3 1 4 2 3 3 1 2 3 3 3 9 6 1 0 1 0 0 2 2 6
T 5 2 4 1 9 5 3 2 1 3 4 7 3 3 3 2 2 11 2 2 5 2 0 0 6 6 8 0 0 5 2 0 5 1 3 3 2 11 2 2 1 4 2
//
A 0.2 0.6 0.6 0.8 0.1 0.6 0.4 0.4 0.4 0.6 0.5 0.3 0.4 0.3 0.2 0.5 0.6 0.2 0.5 0.6 0.2 0.6 0.8 0.8 0.3 0.4 0.2 0.3 0.7 0.5 0.6 0.8 0.4 0.1 0.2 0.7 0.4 0.0 0.8 0.8 0.3 0.4 0.2
C 0.1 0.1 0.0 0.1 0.0 0.0 0.4 0.1 0.1 0.0 0.1 0.1 0.0 0.0 0.3 0.1 0.0 0.0 0.1 0.0 0.3 0.0 0.0 0.1 0.0 0.0 0.1 0.5 0.2 0.0 0.1 0.0 0.1 0.2 0.2 0.0 0.4 0.1 0.1 0.1 0.5 0.2 0.3
G 0.4 0.1 0.1 0.0 0.3 0.0 0.0 0.3 0.4 0.2 0.1 0.1 0.4 0.5 0.3 0.3 0.2 0.1 0.3 0.2 0.2 0.3 0.2 0.1 0.3 0.1 0.2 0.2 0.1 0.1 0.2 0.2 0.2 0.6 0.4 0.1 0.0 0.1 0.0 0.0 0.1 0.1 0.4
T 0.4 0.2 0.3 0.1 0.6 0.4 0.2 0.2 0.1 0.2 0.3 0.5 0.2 0.2 0.2 0.2 0.2 0.8 0.2 0.2 0.4 0.2 0.0 0.0 0.4 0.4 0.6 0.0 0.0 0.4 0.2 0.0 0.4 0.1 0.2 0.2 0.2 0.8 0.2 0.2 0.1 0.3 0.2
//
A -0.6 0.8 0.8 0.9 -1.2 0.8 0.2 0.4 0.2 0.6 0.5 -0.0 0.2 -0.0 -0.6 0.5 0.8 -0.6 0.5 0.8 -0.6 0.6 0.9 1.0 -0.0 0.4 -0.6 -0.0 0.9 0.5 0.6 0.9 0.2 -1.2 -0.6 0.9 0.4 -2.7 0.9 0.9 -0.0 0.2 -0.6
C -0.9 -0.9 -2.7 -0.3 -2.7 -2.7 0.7 -0.3 -0.3 -2.7 -0.3 -0.3 -2.7 -2.7 0.5 -0.9 -2.7 -2.7 -0.9 -2.7 0.3 -2.7 -2.7 -0.9 -2.7 -2.7 -0.9 0.8 0.0 -2.7 -0.9 -2.7 -0.9 0.0 0.0 -2.7 0.7 -0.3 -0.9 -0.9 0.8 0.0 0.3
G 0.7 -0.3 -0.9 -2.7 0.3 -2.7 -2.7 0.3 0.7 0.0 -0.9 -0.9 0.7 0.9 0.3 0.3 0.0 -0.9 0.3 0.0 0.0 0.3 0.0 -0.9 0.3 -0.3 0.0 0.0 -0.9 -0.3 0.0 0.0 0.0 1.1 0.7 -0.9 -2.7 -0.9 -2.7 -2.7 -0.3 -0.3 0.7
T 0.2 -0.7 -0.0 -1.2 0.7 0.2 -0.3 -0.7 -1.2 -0.3 -0.0 0.5 -0.3 -0.3 -0.3 -0.7 -0.7 0.9 -0.7 -0.7 0.2 -0.7 -2.7 -2.7 0.3 0.3 0.6 -2.7 -2.7 0.2 -0.7 -2.7 0.2 -1.2 -0.3 -0.3 -0.7 0.9 -0.7 -0.7 -1.2 -0.0 -0.7
//
A -0.1 0.5 0.5 0.7 -0.1 0.5 0.1 0.2 0.1 0.4 0.2 -0.0 0.1 -0.0 -0.1 0.2 0.5 -0.1 0.2 0.5 -0.1 0.4 0.7 0.8 -0.0 0.2 -0.1 -0.0 0.6 0.2 0.4 0.7 0.1 -0.1 -0.1 0.6 0.2 -0.1 0.7 0.7 -0.0 0.1 -0.1
C -0.1 -0.1 -0.0 -0.1 -0.0 -0.0 0.3 -0.1 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 0.2 -0.1 -0.0 -0.0 -0.1 -0.0 0.1 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1 0.4 0.0 -0.0 -0.1 -0.0 -0.1 0.0 0.0 -0.0 0.3 -0.1 -0.1 -0.1 0.4 0.0 0.1
G 0.3 -0.0 -0.1 -0.0 0.1 -0.0 -0.0 0.1 0.3 0.0 -0.1 -0.1 0.3 0.4 0.1 0.1 0.0 -0.1 0.1 0.0 0.0 0.1 0.0 -0.1 0.1 -0.0 0.0 0.0 -0.1 -0.0 0.0 0.0 0.0 0.7 0.3 -0.1 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 0.3
T 0.1 -0.1 -0.0 -0.1 0.5 0.1 -0.1 -0.1 -0.1 -0.1 -0.0 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 0.1 0.1 0.3 -0.1 -0.1 0.1 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 -0.0 -0.1
//
; Sites 14
>site_0
GAAAGACGGATCGGCGATAACAAATATCAGAAAGGTATAACAG
>site_1
TAAAGACGGGATAGCGATAACTAATAACCAAATCGACTAACCT
>site_2
TATATACAGAAGGGAAATAATGACATGCAAGATGGAATAAGGG
>site_3
TATATACCGTTTGGTGATTTGGAAGTTGAAAAGGGAATAAGAA
>site_4
GAAAGTCACGGTAGGAATTATAAAGTTCATAGGGGACTATTCC
>site_5
GAAATTATAAATATAAATAATGAATTAGCAGAAGCATCAACAG
>site_6
GAAATATTCAATAATAGTGATGAATGGGCAAATCAACTAAAAC
>site_7
GGAATAACGATTTGGCAAAGCTAATATCAAAAAGTGCTTAAGG
>site_8
TATCGTAAATAAAAGGATGACAAATAGCATAACCCAATACCCT
>site_9
ATTATATGTATTGATATTGATAGAAATAATGAAGTAATAAATC
>site_10
TAGCAAAAAAACGGCTAAGGAAAGATTAAATATGCAATTACTC
>site_11
CTATTTTAAGAATAGAGGATGAAAGGTCATTGGGGATTATCTG
>site_12
GGAATAAAAACATTCATTAAAAGAATTAGTCGTTATCGCACAG
>site_13
ACAATTCGGTCAGTCTGTCGGAGAGACAAGAAAATTCCAAATA
;
; Matrix parameters
; Number of sites 14
; Columns 43
; 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 KAAATWHRRAWWDRBRATRABRAADWTMAWAADGBAMTAAMHS
; AC KAAATWHRRAWWDRBRATRABRAADWTMAWAADGBAMTAAMHS
; id KAAATWHRRAWWDRBRATRABRAADWTMAWAADGBAMTAAMHS
; name KAAATWHRRAWWDRBRATRABRAADWTMAWAADGBAMTAAMHS
; description kaaakwmrrratrgsrrtrrbrrAkwksmwrrdSsamtaacms
; statistical_basis 14 sequences
; sites 14
; nb_sites 14
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 12.7347
; information.per.column 0.296156
; max.possible.info.per.col 1.58952
; consensus.strict gaaatacagaatggcaataacaaAtatcaaaaaGgactaacag
; consensus.strict.rc CTGTTAGTCCTTTTTGATATTTGTTATTGCCATTCTGTATTTC
; consensus.IUPAC kaaakwmrrratrgsrrtrrbrrAkwksmwrrdSsamtaacms
; consensus.IUPAC.rc SKGTTAKTSSHYYWKSMWMTYYVYYAYYSCYATYYYKWMTTTM
; consensus.regexp [gt]aaa[gt][at][ac][ag][ag][ag]at[ag]g[cg][ag][ag]t[ag][ag][cgt][ag][ag]A[gt][at][gt][cg][ac][at][ag][ag][agt][CG][cg]a[ac]taac[ac][cg]
; consensus.regexp.rc [CG][GT]GTTA[GT]T[CG][CG][ACT][CT][CT][AT][GT][CG][AC][AT][AC]T[CT][CT][ACG][CT][CT]A[CT][CT][CG]C[CT]AT[CT][CT][CT][GT][AT][AC]TTT[AC]
; residues.content.crude.freq a:0.4369|c:0.1213|g:0.2027|t:0.2392
; G+C.content.crude.freq 0.32392
; residues.content.corrected.freq a:0.4272|c:0.1270|g:0.2027|t:0.2431
; G+C.content.corrected.freq 0.329781
; min(P(S|M)) 1.35885e-64
; max(P(S|M)) 1.22309e-12
; proba_range 1.22309e-12
; Wmin -83.5
; Wmax 29.8
; Wrange 113.3
; logo file:/CysB.EcolK12_2nt_upstream.43.meme_quality_logo_m1.png
; logo file:/CysB.EcolK12_2nt_upstream.43.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.160931
; Job done 2019-06-03.160931
; Seconds 0.62
; user 0.62
; system 0.06
; cuser 0.51
; csystem 0.05