RegulonDB
SlyA matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/SlyA/SlyA.EcolK12_2nt_upstream.15.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 /SlyA.EcolK12_2nt_upstream.15.meme_quality_logo
; Input files
; input /SlyA.EcolK12_2nt_upstream.15.meme_quality_matrix.tf
; prior /SlyA.EcolK12_2nt_upstream.15.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /SlyA.EcolK12_2nt_upstream.15.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 10 1 1 10 4 3 3 10 3 9 4 12 13 10 0
C 0 0 2 1 5 2 0 3 0 0 0 1 0 2 1
G 1 0 2 3 1 0 5 0 3 0 0 0 1 0 1
T 3 13 9 0 4 9 6 1 8 5 10 1 0 2 12
//
A 0.7 0.1 0.1 0.7 0.3 0.2 0.2 0.7 0.2 0.6 0.3 0.8 0.9 0.7 0.0
C 0.0 0.0 0.1 0.1 0.3 0.1 0.0 0.2 0.0 0.0 0.0 0.1 0.0 0.1 0.1
G 0.1 0.0 0.1 0.2 0.1 0.0 0.3 0.0 0.2 0.0 0.0 0.0 0.1 0.0 0.1
T 0.2 0.9 0.6 0.0 0.3 0.6 0.4 0.1 0.6 0.4 0.7 0.1 0.0 0.2 0.8
//
A 0.9 -1.2 -1.2 0.9 -0.0 -0.3 -0.3 0.9 -0.3 0.8 -0.0 1.0 1.1 0.9 -2.7
C -2.7 -2.7 -0.3 -0.9 0.5 -0.3 -2.7 0.0 -2.7 -2.7 -2.7 -0.9 -2.7 -0.3 -0.9
G -0.9 -2.7 -0.3 0.0 -0.9 -2.7 0.5 -2.7 0.0 -2.7 -2.7 -2.7 -0.9 -2.7 -0.9
T -0.3 1.1 0.7 -2.7 -0.0 0.7 0.3 -1.2 0.6 0.2 0.8 -1.2 -2.7 -0.7 1.0
//
A 0.6 -0.1 -0.1 0.6 -0.0 -0.1 -0.1 0.6 -0.1 0.5 -0.0 0.8 1.0 0.6 -0.1
C -0.0 -0.0 -0.1 -0.1 0.2 -0.1 -0.0 0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1 -0.1
G -0.1 -0.0 -0.0 0.0 -0.1 -0.0 0.2 -0.0 0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1
T -0.1 1.0 0.5 -0.1 -0.0 0.5 0.1 -0.1 0.3 0.1 0.6 -0.1 -0.1 -0.1 0.8
//
; Sites 14
>site_0
ATTACTAATATAAAT
>site_1
ATTAAATATATAAAT
>site_2
ATGATTTATAAAAAT
>site_3
ATTAATGCATTAAAT
>site_4
TTTAAATATATAAAT
>site_5
ATTATTGAATTAATT
>site_6
ATTAATATGATAAAT
>site_7
TTTATTTCTATTAAT
>site_8
TTCGCCTCTTTAAAT
>site_9
ATTCGCGATTTAACT
>site_10
ATAGTTAAGTAAAAT
>site_11
AACACTTAGAAAAAC
>site_12
ATGACTGAAATCGTT
>site_13
GTTGCAGATAAAACG
;
; Matrix parameters
; Number of sites 14
; Columns 15
; 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 ATTAHTDATWTAAAT
; AC ATTAHTDATWTAAAT
; id ATTAHTDATWTAAAT
; name ATTAHTDATWTAAAT
; description aTtrctkmkwtAAaT
; statistical_basis 14 sequences
; sites 14
; nb_sites 14
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.67422
; information.per.column 0.444948
; max.possible.info.per.col 1.58952
; consensus.strict aTtactgatatAAaT
; consensus.strict.rc ATTTATATCAGTAAT
; consensus.IUPAC aTtrctkmkwtAAaT
; consensus.IUPAC.rc ATTTAWMKMAGYAAT
; consensus.regexp aTt[ag]ct[gt][ac][gt][at]tAAaT
; consensus.regexp.rc ATTTA[AT][AC][GT][AC]AG[CT]AAT
; residues.content.crude.freq a:0.4429|c:0.0810|g:0.0810|t:0.3952
; G+C.content.crude.freq 0.161905
; residues.content.corrected.freq a:0.4327|c:0.0894|g:0.0892|t:0.3887
; G+C.content.corrected.freq 0.178567
; min(P(S|M)) 8.42516e-27
; max(P(S|M)) 0.00153949
; proba_range 0.00153949
; Wmin -37.4
; Wmax 12.5
; Wrange 49.9
; logo file:/SlyA.EcolK12_2nt_upstream.15.meme_quality_logo_m1.png
; logo file:/SlyA.EcolK12_2nt_upstream.15.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161114
; Job done 2019-06-03.161115
; Seconds 0.59
; user 0.59
; system 0.05
; cuser 0.4
; csystem 0.05