; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/tll.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/tll_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/tll.tab ; Output files ; output html_ready/tll_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : tll ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 2 0 5 18 1 1 0 3 c | 4 0 0 2 21 3 4 6 g | 0 0 17 1 0 0 0 0 t | 16 22 0 1 0 18 18 13 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 22 22 22 22 22 22 22 22 176 ; c.max | 16 22 17 18 21 18 18 13 22 ; c.min | 0 0 0 1 0 0 0 0 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 2 4 0 16 | 22 0.73 0.45 t t cttt 2 0 0 0 22 | 22 1.00 1.03 T T TTTTTTTTTTTTTTT 3 5 0 17 0 | 22 0.77 0.87 G G aaGGGGGGGG 4 18 2 1 1 | 22 0.82 0.53 a a aaaaag 5 1 21 0 0 | 22 0.95 1.27 C C CCCCCCCCCCCCCCCCC 6 1 3 0 18 | 22 0.82 0.59 t t ctttttt 7 0 4 0 18 | 22 0.82 0.68 t t cttttttt 8 3 6 0 13 | 22 0.59 0.32 t y ct ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | -0.1 -0.0 -0.1 0.8 -0.1 -0.1 -0.0 -0.1 c | -0.0 -0.0 -0.0 -0.1 1.4 -0.0 -0.0 0.1 g | -0.0 -0.0 1.0 -0.1 -0.0 -0.0 -0.0 -0.0 t | 0.6 1.1 -0.0 -0.1 -0.0 0.8 0.8 0.4 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.4 1.0 0.9 0.5 1.3 0.6 0.7 0.3 5.7 ; i.max | 0.6 1.1 1.0 0.8 1.4 0.8 0.8 0.4 1.4 ; i.min | -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.1 -0.1 ; Sites 22 >tll_chr3L_8641202_864123 ttgacttt >tll_chr3L_20630381_20630 ttgacttt >tll_chr3L_20630598_20630 ttgacttt >tll_chr3L_20630716_20630 ttgacttt >tll_chr2R_20730810_20730 ttgacttc >tll_chr3R_9720721_972073 ctgacttt >tll_chr3L_20630701_20630 ctgacttc >tll_chr3R_12599144_12599 ttgacctt >tll_chr3R_12527089_12527 ttgactta >tll_chr3R_12526966_12526 ttaacttt >tll_chr3R_4526654_452668 ttgccttc >tll_chr3R_12599286_12599 ctgacctt >tll_chr3L_20630476_20630 ttggcttt >tll_chr3L_20630429_20630 ttaactct >tll_chr3R_9720621_972063 ttgcctct >tll_chr2R_20730328_20730 ttaactta >tll_chr3R_4527125_452715 ttgtcttc >tll_chr3L_8639774_863978 ctgactca >tll_chr3R_4527487_452750 ataacttt >tll_chr3R_12526878_12526 atgacctc >tll_chr3L_8640905_864092 ttgacacc >tll_chr2R_20730463_20730 ttaaattt ; ; Matrix parameters ; Columns 8 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.305|c:0.195|g:0.195|t:0.305 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/tll_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 22 ; meme.llr 144 ; meme.E-value 4.1e-06 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.195 ; alphabet.size 4 ; max.bits 2 ; total.information 5.74505 ; information.per.column 0.718131 ; max.possible.info.per.col 1.63476 ; consensus.strict tTGaCttt ; consensus.strict.rc aaaGtCAa ; consensus.IUPAC tTGaCtty ; consensus.IUPAC.rc raaGtCAa ; consensus.regexp tTGaCtt[ct] ; consensus.regexp.rc [ag]aaGtCAa ; residues.content.crude.freq a:0.1705|c:0.2273|g:0.1023|t:0.5000 ; G+C.content.crude.freq 0.329545 ; residues.content.corrected.freq a:0.1763|c:0.2259|g:0.1063|t:0.4915 ; G+C.content.corrected.freq 0.332174 ; min(P(S|M)) 1.63602e-16 ; max(P(S|M)) 0.138121 ; proba_range 0.138121 ; Wmin -23.4 ; Wmax 8.6 ; Wrange 32 ; Job started 2007_12_10.132131 ; Job done 2007_12_10.132131