; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Hsf.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Hsf_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Hsf.tab ; Output files ; output html_ready/Hsf_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : Hsf ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 2 0 2 0 4 4 1 1 0 0 0 0 3 0 5 c | 3 0 3 0 0 0 0 1 0 0 5 0 2 0 0 g | 0 2 0 5 0 0 2 1 0 0 0 2 0 5 0 t | 0 3 0 0 1 1 2 2 5 5 0 3 0 0 0 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 75 ; c.max | 3 3 3 5 4 4 2 2 5 5 5 3 3 5 5 5 ; c.min | 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 2 3 0 0 | 5 0.60 0.43 c m accc 2 0 0 2 3 | 5 0.60 0.42 t k gttt 3 2 3 0 0 | 5 0.60 0.43 c m accc 4 0 0 5 0 | 5 1.00 0.90 G G GGGGGGGGGGGGGGG 5 4 0 0 1 | 5 0.80 0.53 A A AAAAAtt 6 4 0 0 1 | 5 0.80 0.53 A A AAAAAtt 7 1 0 2 2 | 5 0.40 0.19 g k t 8 1 1 1 2 | 5 0.40 0.03 t t 9 0 0 0 5 | 5 1.00 0.85 T T TTTTTTTTTTTTTT 10 0 0 0 5 | 5 1.00 0.85 T T TTTTTTTTTTTTTT 11 0 5 0 0 | 5 1.00 0.90 C C CCCCCCCCCCCCCCC 12 0 0 2 3 | 5 0.60 0.42 t k gttt 13 3 2 0 0 | 5 0.60 0.42 a m aacc 14 0 0 5 0 | 5 1.00 0.90 G G GGGGGGGGGGGGGGG 15 5 0 0 0 | 5 1.00 0.85 A A AAAAAAAAAAAAAA ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| a | 0.1 -0.1 0.1 -0.1 0.7 0.7 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 0.4 -0.1 1.1 c | 0.4 -0.1 0.4 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 1.1 -0.1 0.2 -0.1 -0.1 g | -0.1 0.2 -0.1 1.1 -0.1 -0.1 0.2 -0.0 -0.1 -0.1 -0.1 0.2 -0.1 1.1 -0.1 t | -0.1 0.4 -0.1 -0.1 -0.0 -0.0 0.1 0.1 1.1 1.1 -0.1 0.4 -0.1 -0.1 -0.1 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.4 0.4 0.4 0.9 0.5 0.5 0.2 0.0 0.8 0.8 0.9 0.4 0.4 0.9 0.8 8.6 ; i.max | 0.4 0.4 0.4 1.1 0.7 0.7 0.2 0.1 1.1 1.1 1.1 0.4 0.4 1.1 1.1 1.1 ; i.min | -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 5 >Hsf_chr3L_3176658_317669 ctagaagtttctaga >Hsf_chr3R_7782302_778232 ctcgaatgttcgcga >Hsf_chr3R_7782498_778252 agcgaatattctaga >Hsf_chr3R_7782428_778245 agagaaatttctcga >Hsf_chr3R_7782329_778235 ctcgttgcttcgaga ; ; Matrix parameters ; Columns 15 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.258|c:0.242|g:0.242|t:0.258 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Hsf_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 5 ; meme.llr 70 ; meme.E-value 0.012 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.242 ; alphabet.size 4 ; max.bits 2 ; total.information 8.62308 ; information.per.column 0.574872 ; max.possible.info.per.col 1.41882 ; consensus.strict ctcGAAgtTTCtaGA ; consensus.strict.rc TCtaGAAacTTCgag ; consensus.IUPAC mkmGAAktTTCkmGA ; consensus.IUPAC.rc TCkmGAAamTTCkmk ; consensus.regexp [ac][gt][ac]GAA[gt]tTTC[gt][ac]GA ; consensus.regexp.rc TC[gt][ac]GAAa[ac]TTC[gt][ac][gt] ; residues.content.crude.freq a:0.2933|c:0.1867|g:0.2267|t:0.2933 ; G+C.content.crude.freq 0.413333 ; residues.content.corrected.freq a:0.2874|c:0.1959|g:0.2292|t:0.2874 ; G+C.content.corrected.freq 0.425111 ; min(P(S|M)) 6.2412e-21 ; max(P(S|M)) 0.00149631 ; proba_range 0.00149631 ; Wmin -25.4 ; Wmax 14.1 ; Wrange 39.5 ; Job started 2007_12_10.132110 ; Job done 2007_12_10.132110