RSAT - matrix-quality result
Analysis: matrix-quality result: LexA.RegulonDB2012 (21/03/2018 17:50)
matrix-quality result: LexA and CTCF matrices from RegulonDB 2015 LexA.RegulonDB2012
Command: matrix-quality -v 0 -html_title ' LexA and CTCF matrices from RegulonDB 2015 ' -ms $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/input_matrix -matrix_format transfac -pseudo 1 -seq LexA_peaks $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/sequence1.fasta -seq_format fasta -plot LexA_peaks nwd -seq CRP_binding_sites $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/sequence2.fasta -plot CRP_binding_sites nwd -perm LexA_peaks 1 -perm CRP_binding_sites 1 -bgfile $RSAT/public_html/data/genomes/Escherichia_coli_GCF_000005845.2_ASM584v2/oligo-frequencies/2nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz -bg_format oligo-analysis -bg_pseudo 0.01 -archive -o $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.175002
Figures
Matrix logo
Decreasing cumulative distributions (dCDF)
Decreasing cumulative distributions (dCDF), logarithmic Y axis
ROC curve (logarithmic X axis)
NWD curve
Matrix information
; convert-matrix -v 1 -from transfac -i $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_matrix.tf -to tab -o $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_matrix_info.txt -bgfile $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.1750022nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab -bg_format inclusive -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png -logo_opt '-e -M -t LexA.RegulonDB2012 ' -logo_file $RSAT/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_logo
; Input files
; input /space23/rsat/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_matrix.tf
; prior /space23/rsat/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/matrix-quality_2018-03-21.1750022nt_upstream-noorf_Escherichia_coli_GCF_000005845.2_ASM584v2-ovlp-1str.freq.gz_inclusive.tab
; Input format transfac
; Output files
; output /space23/rsat/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012/matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_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 16 26 1 2 0 6 30 1 31 16 33 18 25 16 23 1 37 4 2 21
C 6 4 39 1 1 3 5 3 1 4 0 7 1 9 16 38 1 0 12 4
G 1 7 0 0 39 8 0 5 6 6 2 1 5 3 1 1 0 35 7 7
T 17 3 0 37 0 23 5 31 2 14 5 14 9 12 0 0 2 1 19 8
//
A 0.4 0.6 0.0 0.1 0.0 0.2 0.7 0.0 0.8 0.4 0.8 0.4 0.6 0.4 0.6 0.0 0.9 0.1 0.1 0.5
C 0.2 0.1 1.0 0.0 0.0 0.1 0.1 0.1 0.0 0.1 0.0 0.2 0.0 0.2 0.4 0.9 0.0 0.0 0.3 0.1
G 0.0 0.2 0.0 0.0 1.0 0.2 0.0 0.1 0.2 0.2 0.1 0.0 0.1 0.1 0.0 0.0 0.0 0.9 0.2 0.2
T 0.4 0.1 0.0 0.9 0.0 0.6 0.1 0.8 0.1 0.3 0.1 0.3 0.2 0.3 0.0 0.0 0.1 0.0 0.5 0.2
//
A 0.3 0.8 -2.2 -1.7 -3.7 -0.6 0.9 -2.2 1.0 0.3 1.0 0.4 0.8 0.3 0.7 -2.2 1.1 -1.0 -1.7 0.6
C -0.3 -0.7 1.5 -2.0 -2.0 -1.0 -0.5 -1.0 -2.0 -0.7 -3.7 -0.2 -2.0 0.1 0.6 1.5 -2.0 -3.7 0.4 -0.7
G -1.9 -0.1 -3.7 -3.7 1.5 -0.0 -3.7 -0.5 -0.3 -0.3 -1.3 -1.9 -0.5 -1.0 -1.9 -1.9 -3.7 1.4 -0.1 -0.1
T 0.4 -1.3 -3.7 1.1 -3.7 0.6 -0.8 0.9 -1.7 0.2 -0.8 0.2 -0.3 0.0 -3.7 -3.7 -1.7 -2.2 0.5 -0.4
//
A 0.1 0.5 -0.1 -0.1 -0.0 -0.1 0.7 -0.1 0.7 0.1 0.8 0.2 0.5 0.1 0.4 -0.1 1.0 -0.1 -0.1 0.3
C -0.0 -0.1 1.5 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 0.0 0.3 1.4 -0.1 -0.0 0.1 -0.1
G -0.1 -0.0 -0.0 -0.0 1.5 -0.0 -0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 1.2 -0.0 -0.0
T 0.1 -0.1 -0.0 1.0 -0.0 0.4 -0.1 0.7 -0.1 0.1 -0.1 0.1 -0.1 0.0 -0.0 -0.0 -0.1 -0.1 0.2 -0.1
//
; Sites 40
>site_0
GACTGTATAAAACCACAGCC
>site_1
TCCTCTCTGCAATACGCAGA
>site_2
AGCTGAATAAATATACAGCA
>site_3
CACTGTATACTTTACCAGTG
>site_4
ACCAGAATATACATAATAGT
>site_5
CACTGTATAAATAAACAGCT
>site_6
AACTGATTAAAAACCCAGCG
>site_7
AACTGTCGATAAGCGCAGCC
>site_8
CGCTGCCCTGAAAGCCAGGC
>site_9
TACTGGATAAAAAAACAGTT
>site_10
TACTGTATAAACAGCCAATA
>site_11
TGCTGTATGGATTAACAGGA
>site_12
TACTGTATGGATGTACAGTA
>site_13
ACCTGTATAAATAACCAGTA
>site_14
ATCTGCTGGCAAGAACAGAC
>site_15
TACTGTATATAAAAACAGTA
>site_16
CACTGTATAAAAATCCTATA
>site_17
AACTGTCGATACGTACAGTA
>site_18
CACTGGATAGATAACCAGCA
>site_19
TACTGTATAAAATCACAGTT
>site_20
TGCTGGATAGATATCCAGCG
>site_21
AACTGAAAAATGGCACAGTA
>site_22
TACCGGATCGTTTCACAGTA
>site_23
TACTGTATATAAAAACAGTA
>site_24
AACTGGATAAAATTACAGGG
>site_25
TACTGTATATAAAACCAGTT
>site_26
TACTGTACACAATAACAGTA
>site_27
TACTGTATGAGCATACAGTA
>site_28
CTATGTTTATATAACCATCA
>site_29
AGCTGGCGTTGATGCCAGCG
>site_30
AACTGGATAATCATACAGTA
>site_31
TGCAGGTTATAAAACCAGCA
>site_32
AACTGTATATAAATACAGTT
>site_33
TACTGTATAAATAAACAGTA
>site_34
ATCTGTATATATACCCAGCT
>site_35
AACTGCACAATAAACCAGAG
>site_36
TGCTGTATATACTCACAGCA
>site_37
AACTGTATATACACCCAGGG
>site_38
ACCTGAATGAATATACAGTA
>site_39
TACTGATGATATATACAGGT
;
; Matrix parameters
; Number of sites 40
; Columns 20
; 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 LexA.RegulonDB2012
; AC LexA.RegulonDB2012
; id LexA.RegulonDB2012
; name LexA.RegulonDB2012
; description waCTGtatawAwahmCAGya
; statistical_basis 40 sequences
; sites 40
; nb_sites 40
; min.prior 0.204024
; alphabet.size 4
; max.bits 2
; total.information 11.0099
; information.per.column 0.550495
; max.possible.info.per.col 1.58952
; consensus.strict taCTGtataaAaaaaCAGta
; consensus.strict.rc TACTGTTTTTTTATACAGTA
; consensus.IUPAC waCTGtatawAwahmCAGya
; consensus.IUPAC.rc TRCTGKDTWTWTATACAGTW
; consensus.regexp [at]aCTGtata[at]A[at]a[act][ac]CAG[ct]a
; consensus.regexp.rc T[AG]CTG[GT][AGT]T[AT]T[AT]TATACAGT[AT]
; residues.content.crude.freq A:0.3863|C:0.1937|G:0.1675|T:0.2525
; G+C.content.crude.freq 0.36125
; residues.content.corrected.freq A:0.3839|C:0.1941|G:0.1684|T:0.2536
; G+C.content.corrected.freq 0.362484
; min(P(S|M)) 4.00406e-35
; max(P(S|M)) 0.000196197
; proba_range 0.000196197
; Wmin -49.8
; Wmax 17.5
; Wrange 67.3
; logo file:/space23/rsat/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012//matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_logo_m1.png
; logo file:/space23/rsat/public_html/tmp/apache/2018/03/21/matrix-quality_2018-03-21.175002_zdBRpm/LexA.RegulonDB2012//matrix-quality_2018-03-21.175002_LexA.RegulonDB2012_logo_m1_rc.png
;
; Host name sinik
; Job started 2018-03-21.175004
; Job done 2018-03-21.175004
; Seconds 0.32
; user 0.32
; system 0.03
; cuser 0.38
; csystem 0.07
Result files