; convert-matrix -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A.tab_quality_matrix_info.txt -bgfile /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq -bg_format oligos -return counts,frequencies,weights,info,parameters,sites,logo -logo_format png,pdf -logo_opt '-e -M -t MarA_1b10_A ' ; Input files ; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/MarA/MarA_1b10_A.tab ; prior /export/space2/rsa-tools/data/genomes/Escherichia_coli_K12/oligo-frequencies/1nt_upstream-noorf_Escherichia_coli_K12-ovlp-1str.freq ; Input format tab ; Output files ; output /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A.tab_quality_matrix_info.txt ; Output format tab ; pseudo-weight 1 ; Background model ; Bernoulli model (order=0) ; Strand sensitive ; Background pseudo-frequency 0.01 ; Residue probabilities ; a 0.29107 ; c 0.20737 ; g 0.20436 ; t 0.29721 a | 0 0 0 64 12 24 24 24 24 10 0 0 24 96 96 c | 0 96 96 10 64 24 24 24 24 0 0 96 24 0 0 g | 96 0 0 12 10 24 24 24 24 12 96 0 24 0 0 t | 0 0 0 10 10 24 24 24 24 74 0 0 24 0 0 // a | 0.0 0.0 0.0 0.7 0.1 0.3 0.3 0.3 0.3 0.1 0.0 0.0 0.3 1.0 1.0 c | 0.0 1.0 1.0 0.1 0.7 0.2 0.2 0.2 0.2 0.0 0.0 1.0 0.2 0.0 0.0 g | 1.0 0.0 0.0 0.1 0.1 0.2 0.2 0.2 0.2 0.1 1.0 0.0 0.2 0.0 0.0 t | 0.0 0.0 0.0 0.1 0.1 0.3 0.3 0.3 0.3 0.8 0.0 0.0 0.3 0.0 0.0 // a | -4.6 -4.6 -4.6 0.8 -0.8 -0.2 -0.2 -0.2 -0.2 -1.0 -4.6 -4.6 -0.2 1.2 1.2 c | -4.6 1.6 1.6 -0.7 1.2 0.2 0.2 0.2 0.2 -4.6 -4.6 1.6 0.2 -4.6 -4.6 g | 1.6 -4.6 -4.6 -0.5 -0.7 0.2 0.2 0.2 0.2 -0.5 1.6 -4.6 0.2 -4.6 -4.6 t | -4.6 -4.6 -4.6 -1.0 -1.0 -0.2 -0.2 -0.2 -0.2 0.9 -4.6 -4.6 -0.2 -4.6 -4.6 // a | -0.0 -0.0 -0.0 0.5 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 1.2 1.2 c | -0.0 1.6 1.6 -0.1 0.8 0.0 0.0 0.0 0.0 -0.0 -0.0 1.6 0.0 -0.0 -0.0 g | 1.6 -0.0 -0.0 -0.1 -0.1 0.0 0.0 0.0 0.0 -0.1 1.6 -0.0 0.0 -0.0 -0.0 t | -0.0 -0.0 -0.0 -0.1 -0.1 -0.0 -0.0 -0.0 -0.0 0.7 -0.0 -0.0 -0.0 -0.0 -0.0 // ; Sites ; ; Matrix parameters ; Columns 15 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.291066898814656|c:0.207372933914605|g:0.204355073413807|t:0.297205093856932 ; program tab ; matrix.nb 1 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.204355 ; alphabet.size 4 ; max.bits 2 ; total.information 11.3843 ; information.per.column 0.758955 ; max.possible.info.per.col 1.5879 ; consensus.strict GCCaCggggtGCgAA ; consensus.strict.rc TTCGCACCCCGTGGC ; consensus.IUPAC GCCaCsssstGCsAA ; consensus.IUPAC.rc TTSGCASSSSGTGGC ; consensus.regexp GCCaC[cg][cg][cg][cg]tGC[cg]AA ; consensus.regexp.rc TT[CG]GCA[CG][CG][CG][CG]GTGGC ; residues.content.crude.freq a:0.2764|c:0.3347|g:0.2403|t:0.1486 ; G+C.content.crude.freq 0.575 ; residues.content.corrected.freq a:0.2765|c:0.3334|g:0.2399|t:0.1501 ; G+C.content.corrected.freq 0.573317 ; min(P(S|M)) 4.34285e-27 ; max(P(S|M)) 0.000313401 ; proba_range 0.000313401 ; Wmin -39.6 ; Wmax 14.3 ; Wrange 53.9 ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo.png ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo.pdf ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo_rc.png ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/MarA/MarA_1b10_A.tab/MarA_1b10_A_m1_logo_rc.pdf ; Job started 2010_03_11.191418 ; Job done 2010_03_11.191429