; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/z.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/z_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/z.tab ; Output files ; output html_ready/z_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : z ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 ; ----- |--------|-------|-------|-------|-------|-------| a | 2 0 41 0 7 1 c | 6 0 0 0 10 6 g | 3 41 0 41 0 29 t | 30 0 0 0 24 5 ; ----- |--------|-------|-------|-------|-------|-------| ; c.sum | 41 41 41 41 41 41 246 ; c.max | 30 41 41 41 24 29 41 ; c.min | 2 0 0 0 0 1 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 2 6 3 30 | 41 0.73 0.46 t t ctttt 2 0 0 41 0 | 41 1.00 1.39 G G GGGGGGGGGGGGGGGGGGGGGG 3 41 0 0 0 | 41 1.00 1.18 A A AAAAAAAAAAAAAAAAAA 4 0 0 41 0 | 41 1.00 1.39 G G GGGGGGGGGGGGGGGGGGGGGG 5 7 10 0 24 | 41 0.59 0.35 t y ctt 6 1 6 29 5 | 41 0.71 0.56 G G cGGGGt ; ; Matrix type: information ;P | 1 2 3 4 5 6 ;- |-----|----|----|----|----|----| a | -0.1 -0.0 1.2 -0.0 -0.1 -0.1 c | -0.1 -0.0 -0.0 -0.0 0.0 -0.1 g | -0.1 1.5 -0.0 1.5 -0.0 0.8 t | 0.7 -0.0 -0.0 -0.0 0.4 -0.1 ;- |-----|----|----|----|----|----| ; i.sum | 0.5 1.4 1.2 1.4 0.3 0.6 5.3 ; i.max | 0.7 1.5 1.2 1.5 0.4 0.8 1.5 ; i.min | -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 -0.1 ; Sites 41 >z_chrX_2653947_2653962_D tgagtg >z_chrX_2653050_2653055_D tgagtg >z_chr3R_12560289_1256030 tgagtg >z_chrX_2652760_2652765_D tgagtg >z_chr2L_2450934_2450939_ tgagtg >z_chr3R_12590374_1259039 tgagtg >z_chr2L_2450874_2450879_ tgagtg >z_chrX_2653816_2653821_D tgagtg >z_chrX_2653883_2653888_D tgagtg >z_chrX_2653080_2653085_D tgagtg >z_chr2L_2450912_2450917_ tgagtg >z_chr3R_12590108_1259012 tgagtg >z_chrX_2652777_2652782_D tgagtg >z_chr3R_12481491_1248150 tgagtg >z_chrX_2651357_2651368_D tgagtg >z_chrX_2653846_2653851_D tgagcg >z_chrX_2304183_2304188_D tgagcg >z_chr3R_12560269_1256028 tgagcg >z_chr3L_17584614_1758462 tgagcg >z_chr3R_12560246_1256026 tgagcg >z_chr3L_17584665_1758468 tgagcg >z_chr3R_12560212_1256023 cgagtg >z_chrX_2653989_2654004_D cgagtg >z_chrX_2304147_2304152_D cgagtg >z_chrX_2651309_2651314_D tgagtc >z_chr3R_12560189_1256020 tgagtc >z_chr3R_12590579_1259059 tgagtc >z_chr3R_12589999_1259001 tgagtt >z_chr3R_12481458_1248146 ggagtg >z_chr3R_12590088_1259010 tgagcc >z_chr3R_12590409_1259043 tgagcc >z_chr3R_12589608_1258962 cgagag >z_chr3R_12589741_1258975 tgagac >z_chr3R_12481511_1248151 tgagat >z_chr3R_12590730_1259075 tgagat >z_chr3R_12589954_1258997 agagcg >z_chr3R_12589873_1258989 ggagag >z_chr3R_12590699_1259072 cgagtt >z_chr3R_12589719_1258973 agagag >z_chr3R_12589443_1258946 cgagat >z_chr3R_12590301_1259033 ggagca ; ; Matrix parameters ; Columns 6 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.277|c:0.223|g:0.223|t:0.277 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/z_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 41 ; meme.llr 235 ; meme.E-value 7.2e-48 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.223 ; alphabet.size 4 ; max.bits 2 ; total.information 5.31955 ; information.per.column 0.886591 ; max.possible.info.per.col 1.50058 ; consensus.strict tGAGtG ; consensus.strict.rc CaCTCa ; consensus.IUPAC tGAGyG ; consensus.IUPAC.rc CrCTCa ; consensus.regexp tGAG[ct]G ; consensus.regexp.rc C[ag]CTCa ; residues.content.crude.freq a:0.2073|c:0.0894|g:0.4634|t:0.2398 ; G+C.content.crude.freq 0.552846 ; residues.content.corrected.freq a:0.2090|c:0.0926|g:0.4577|t:0.2407 ; G+C.content.corrected.freq 0.550302 ; min(P(S|M)) 1.31002e-12 ; max(P(S|M)) 0.274489 ; proba_range 0.274489 ; Wmin -18.6 ; Wmax 7.2 ; Wrange 25.8 ; Job started 2007_12_10.132142 ; Job done 2007_12_10.132142