; convert-matrix -v 1 -i /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/CRP/CRP_1cgp_AB.tab -from tab -to tab -o /export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB.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,profile,sites,logo -logo_format png,pdf -logo_opt '-e -M -t CRP_1cgp_AB ' ; Input files ; input /export/internal_use2/amedina/matrix_eval/data/Matrices_contact/CRP/CRP_1cgp_AB.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/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB.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 6 0 96 72 24 24 24 24 6 0 0 78 0 96 c | 0 0 12 0 0 6 24 24 24 24 12 0 96 6 96 0 g | 0 96 6 96 0 12 24 24 24 24 66 12 0 6 0 0 t | 96 0 72 0 0 6 24 24 24 24 12 84 0 6 0 0 // a | 0.0 0.0 0.1 0.0 1.0 0.7 0.3 0.3 0.3 0.3 0.1 0.0 0.0 0.8 0.0 1.0 c | 0.0 0.0 0.1 0.0 0.0 0.1 0.2 0.2 0.2 0.2 0.1 0.0 1.0 0.1 1.0 0.0 g | 0.0 1.0 0.1 1.0 0.0 0.1 0.2 0.2 0.2 0.2 0.7 0.1 0.0 0.1 0.0 0.0 t | 1.0 0.0 0.7 0.0 0.0 0.1 0.3 0.3 0.3 0.3 0.1 0.9 0.0 0.1 0.0 0.0 // a | -4.6 -4.6 -1.5 -4.6 1.2 0.9 -0.2 -0.2 -0.2 -0.2 -1.5 -4.6 -4.6 1.0 -4.6 1.2 c | -4.6 -4.6 -0.5 -4.6 -4.6 -1.2 0.2 0.2 0.2 0.2 -0.5 -4.6 1.6 -1.2 1.6 -4.6 g | -4.6 1.6 -1.2 1.6 -4.6 -0.5 0.2 0.2 0.2 0.2 1.2 -0.5 -4.6 -1.2 -4.6 -4.6 t | 1.2 -4.6 0.9 -4.6 -4.6 -1.5 -0.2 -0.2 -0.2 -0.2 -0.9 1.1 -4.6 -1.5 -4.6 -4.6 // ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 0.0 0.0 0.0 96.0 | 96.0 1.0 1.2 T T TTTTTTTTTTTTTTTTT 2 0.0 0.0 96.0 0.0 | 96.0 1.0 1.5 G G GGGGGGGGGGGGGGGGGGGGGGG 3 6.0 12.0 6.0 72.0 | 96.0 0.8 0.5 t t gtttt 4 0.0 0.0 96.0 0.0 | 96.0 1.0 1.5 G G GGGGGGGGGGGGGGGGGGGGGGG 5 96.0 0.0 0.0 0.0 | 96.0 1.0 1.2 A A AAAAAAAAAAAAAAAAA 6 72.0 6.0 12.0 6.0 | 96.0 0.8 0.5 a a aaact 7 24.0 24.0 24.0 24.0 | 96.0 0.2 0.0 g s 8 24.0 24.0 24.0 24.0 | 96.0 0.2 0.0 g s 9 24.0 24.0 24.0 24.0 | 96.0 0.2 0.0 g s 10 24.0 24.0 24.0 24.0 | 96.0 0.2 0.0 g s 11 6.0 12.0 66.0 12.0 | 96.0 0.7 0.6 G G cGGGG 12 0.0 0.0 12.0 84.0 | 96.0 0.9 0.8 T T gTTTTTTTTTT 13 0.0 96.0 0.0 0.0 | 96.0 1.0 1.5 C C CCCCCCCCCCCCCCCCCCCCCC 14 78.0 6.0 6.0 6.0 | 96.0 0.8 0.6 A A AAAAAct 15 0.0 96.0 0.0 0.0 | 96.0 1.0 1.5 C C CCCCCCCCCCCCCCCCCCCCCC 16 96.0 0.0 0.0 0.0 | 96.0 1.0 1.2 A A AAAAAAAAAAAAAAAAA a | -0.0 -0.0 -0.1 -0.0 1.2 0.7 -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 -0.0 0.8 -0.0 1.2 c | -0.0 -0.0 -0.1 -0.0 -0.0 -0.1 0.0 0.0 0.0 0.0 -0.1 -0.0 1.6 -0.1 1.6 -0.0 g | -0.0 1.6 -0.1 1.6 -0.0 -0.1 0.0 0.0 0.0 0.0 0.8 -0.1 -0.0 -0.1 -0.0 -0.0 t | 1.2 -0.0 0.7 -0.0 -0.0 -0.1 -0.0 -0.0 -0.0 -0.0 -0.1 0.9 -0.0 -0.1 -0.0 -0.0 // ; Sites ; ; Matrix parameters ; Columns 16 ; 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 12.5775 ; information.per.column 0.786091 ; max.possible.info.per.col 1.5879 ; consensus.strict TGtGAaggggGTCACA ; consensus.strict.rc TGTGACCCCCTTCACA ; consensus.IUPAC TGtGAassssGTCACA ; consensus.IUPAC.rc TGTGACSSSSTTCACA ; consensus.regexp TGtGAa[cg][cg][cg][cg]GTCACA ; consensus.regexp.rc TGTGAC[CG][CG][CG][CG]TTCACA ; residues.content.crude.freq a:0.2930|c:0.2109|g:0.2539|t:0.2422 ; G+C.content.crude.freq 0.464844 ; residues.content.corrected.freq a:0.2929|c:0.2109|g:0.2534|t:0.2428 ; G+C.content.corrected.freq 0.464296 ; min(P(S|M)) 2.66953e-29 ; max(P(S|M)) 0.000991032 ; proba_range 0.000991032 ; Wmin -43.4 ; Wmax 16 ; Wrange 59.4 ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB_m1_logo.png ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB_m1_logo.pdf ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB_m1_logo_rc.png ; logo file:/export/internal_use2/amedina/matrix_eval/results/contact/matrix_quality_200100311/CRP/CRP_1cgp_AB.tab/CRP_1cgp_AB_m1_logo_rc.pdf ; Job started 2010_03_11.180547 ; Job done 2010_03_11.180617