RegulonDB
OmpR matrix and aligment
matrix-quality result
Command: matrix-quality -v 1 -ms ./data/Matrices_NR/OmpR/OmpR.EcolK12_2nt_upstream.22.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 /OmpR.EcolK12_2nt_upstream.22.meme_quality_logo
; Input files
; input /OmpR.EcolK12_2nt_upstream.22.meme_quality_matrix.tf
; prior /OmpR.EcolK12_2nt_upstream.22.meme_quality2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /OmpR.EcolK12_2nt_upstream.22.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 12 6 11 3 2 3 14 15 3 6 17 16 15 8 6 4 10 13 8 13 9
C 0 3 5 4 4 0 3 1 0 15 7 0 2 0 2 3 0 0 0 7 3 3
G 3 3 2 4 2 15 1 0 1 0 2 3 2 5 2 7 0 4 0 2 0 2
T 8 3 8 2 12 4 14 6 5 3 6 1 1 1 9 5 17 7 8 4 5 7
//
A 0.5 0.6 0.3 0.5 0.1 0.1 0.1 0.6 0.7 0.1 0.3 0.8 0.7 0.7 0.4 0.3 0.2 0.5 0.6 0.4 0.6 0.4
C 0.0 0.1 0.2 0.2 0.2 0.0 0.1 0.1 0.0 0.7 0.3 0.0 0.1 0.0 0.1 0.1 0.0 0.0 0.0 0.3 0.1 0.1
G 0.1 0.1 0.1 0.2 0.1 0.7 0.1 0.0 0.1 0.0 0.1 0.1 0.1 0.2 0.1 0.3 0.0 0.2 0.0 0.1 0.0 0.1
T 0.4 0.1 0.4 0.1 0.6 0.2 0.6 0.3 0.2 0.1 0.3 0.1 0.1 0.1 0.4 0.2 0.8 0.3 0.4 0.2 0.2 0.3
//
A 0.5 0.7 -0.0 0.6 -0.7 -1.0 -0.7 0.8 0.9 -0.7 -0.0 1.0 0.9 0.9 0.3 -0.0 -0.4 0.5 0.7 0.3 0.7 0.4
C -3.1 -0.4 0.1 -0.1 -0.1 -3.1 -0.4 -1.3 -3.1 1.2 0.5 -3.1 -0.7 -3.1 -0.7 -0.4 -3.1 -3.1 -3.1 0.5 -0.4 -0.4
G -0.3 -0.3 -0.7 -0.1 -0.7 1.2 -1.3 -3.1 -1.3 -3.1 -0.7 -0.3 -0.7 0.1 -0.7 0.5 -3.1 -0.1 -3.1 -0.7 -3.1 -0.7
T 0.2 -0.7 0.2 -1.0 0.6 -0.4 0.8 -0.0 -0.2 -0.7 -0.0 -1.6 -1.6 -1.6 0.4 -0.2 1.0 0.1 0.2 -0.4 -0.2 0.1
//
A 0.2 0.4 -0.0 0.3 -0.1 -0.1 -0.1 0.5 0.6 -0.1 -0.0 0.8 0.7 0.6 0.1 -0.0 -0.1 0.2 0.4 0.1 0.4 0.2
C -0.0 -0.1 0.0 -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 0.8 0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 0.1 -0.1 -0.1
G -0.0 -0.0 -0.1 -0.0 -0.1 0.8 -0.1 -0.0 -0.1 -0.0 -0.1 -0.0 -0.1 0.0 -0.1 0.2 -0.0 -0.0 -0.0 -0.1 -0.0 -0.1
T 0.1 -0.1 0.1 -0.1 0.4 -0.1 0.5 -0.0 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 0.1 -0.1 0.8 0.0 0.1 -0.1 -0.1 0.0
//
; Sites 21
>site_0
AATATGTAACCAAAAGTAAAAT
>site_1
AACATGTAACTAAATGTAACTC
>site_2
AACGAGAAACCAAAACTTACAT
>site_3
AAAGTGTAACCAAAGGTTTGCA
>site_4
AATATGATACTAAAACTTTTAA
>site_5
TATATGTAACAGATTATTACAA
>site_6
TAGATGTTTCAAAATGTAAATG
>site_7
ATCCTGTTACGGAATATTACAT
>site_8
GAAATGCAACGAGGTGTGTAAA
>site_9
AAAGTGCTACAAAGATAAAGAT
>site_10
TATAGGCAAACATAAATAACAT
>site_11
ATTTGGTTTCAAAAAGAAAAAA
>site_12
AGCACGTAACATAGTTTGTATA
>site_13
TACACTTATCTAAGATTTTTCC
>site_14
TATCTTTTTTCAAATATGATCT
>site_15
TGACCGAAATCACACTTAAAAA
>site_16
GCAGCTTAACAACAAATATTTA
>site_17
TTAAAATAATTAAATCAGTAAA
>site_18
ACTTTGTAAACAGGGTTTTCTG
>site_19
GGGCATTATCTGAACATAAAAC
>site_20
TCTATAGCGATAAATGAAACAT
;
; Matrix parameters
; Number of sites 21
; Columns 22
; 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 WAHATGTAACHAAAWDTWWHAW
; AC WAHATGTAACHAAAWDTWWHAW
; id WAHATGTAACHAAAWDTWWHAW
; name WAHATGTAACHAAAWDTWWHAW
; description wayatGtaaCcaarwgtwwmaw
; statistical_basis 21 sequences
; sites 21
; nb_sites 21
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 6.71066
; information.per.column 0.30503
; max.possible.info.per.col 1.58952
; consensus.strict aatatGtaaCcaaatgtaacaa
; consensus.strict.rc TTGTTACATTTGGTTACATATT
; consensus.IUPAC wayatGtaaCcaarwgtwwmaw
; consensus.IUPAC.rc WTKWWACWYTTGGTTACATRTW
; consensus.regexp [at]a[ct]atGtaaCcaa[ag][at]gt[at][at][ac]a[at]
; consensus.regexp.rc [AT]T[GT][AT][AT]AC[AT][CT]TTGGTTACAT[AG]T[AT]
; residues.content.crude.freq a:0.4416|c:0.1342|g:0.1299|t:0.2944
; G+C.content.crude.freq 0.264069
; residues.content.corrected.freq a:0.4347|c:0.1375|g:0.1332|t:0.2945
; G+C.content.corrected.freq 0.270786
; min(P(S|M)) 3.52424e-34
; max(P(S|M)) 1.55302e-06
; proba_range 1.55302e-06
; Wmin -43.4
; Wmax 15.3
; Wrange 58.7
; logo file:/OmpR.EcolK12_2nt_upstream.22.meme_quality_logo_m1.png
; logo file:/OmpR.EcolK12_2nt_upstream.22.meme_quality_logo_m1_rc.png
;
; Host name sinik
; Job started 2019-06-03.161059
; Job done 2019-06-03.161100
; Seconds 0.57
; user 0.57
; system 0.05
; cuser 0.43
; csystem 0.05