; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Espl.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Espl_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Espl.tab ; Output files ; output html_ready/Espl_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : Espl ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 0 3 0 1 2 1 0 1 3 2 3 1 0 c | 4 0 4 0 0 0 2 3 0 1 1 0 0 g | 0 1 0 3 0 3 0 0 1 1 0 0 4 t | 0 0 0 0 2 0 2 0 0 0 0 3 0 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 4 4 4 4 4 4 4 4 4 4 4 4 4 52 ; c.max | 4 3 4 3 2 3 2 3 3 2 3 3 4 4 ; c.min | 0 0 0 0 0 0 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 0 4 0 0 | 4 1.00 0.70 C C CCCCCCCCCC 2 3 0 1 0 | 4 0.75 0.53 A A AAAAgg 3 0 4 0 0 | 4 1.00 0.70 C C CCCCCCCCCC 4 1 0 3 0 | 4 0.75 0.41 g r aggg 5 2 0 0 2 | 4 0.50 0.48 a w att 6 1 0 3 0 | 4 0.75 0.41 g r aggg 7 0 2 0 2 | 4 0.50 0.38 t y ct 8 1 3 0 0 | 4 0.75 0.41 c m accc 9 3 0 1 0 | 4 0.75 0.53 A A AAAAgg 10 2 1 1 0 | 4 0.50 0.20 a a c 11 3 1 0 0 | 4 0.75 0.53 A A AAAAcc 12 1 0 0 3 | 4 0.75 0.57 T W aTTTTT 13 0 0 4 0 | 4 1.00 0.70 G G GGGGGGGGGG ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| a | -0.1 0.7 -0.1 0.0 0.3 0.0 -0.1 0.0 0.7 0.3 0.7 0.0 -0.1 c | 0.9 -0.1 0.9 -0.1 -0.1 -0.1 0.2 0.5 -0.1 -0.0 -0.0 -0.1 -0.1 g | -0.1 -0.0 -0.1 0.5 -0.1 0.5 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 0.9 t | -0.1 -0.1 -0.1 -0.1 0.3 -0.1 0.3 -0.1 -0.1 -0.1 -0.1 0.7 -0.1 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.7 0.5 0.7 0.4 0.5 0.4 0.4 0.4 0.5 0.2 0.5 0.6 0.7 6.5 ; i.max | 0.9 0.7 0.9 0.5 0.3 0.5 0.3 0.5 0.7 0.3 0.7 0.7 0.9 0.9 ; i.min | -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 4 >E(spl)_chrX_265912_26593 cacgtgtcaaatg >E(spl)_chrX_249927_24996 cacaaataaaatg >E(spl)_chr3R_21865771_21 cacgagccacaag >E(spl)_chrX_226541_22655 cgcgtgccggctg ; ; Matrix parameters ; Columns 13 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.207|c:0.293|g:0.293|t:0.207 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Espl_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 4 ; meme.llr 47 ; meme.E-value 2.3 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.207 ; alphabet.size 4 ; max.bits 2 ; total.information 6.54731 ; information.per.column 0.503639 ; max.possible.info.per.col 1.57504 ; consensus.strict CACgagtcAaATG ; consensus.strict.rc CATtTgactcGTG ; consensus.IUPAC CACrwrymAaAWG ; consensus.IUPAC.rc CWTtTkrywyGTG ; consensus.regexp CAC[ag][at][ag][ct][ac]AaA[AT]G ; consensus.regexp.rc C[AT]TtT[gt][ag][ct][at][ct]GTG ; residues.content.crude.freq a:0.3269|c:0.2885|g:0.2500|t:0.1346 ; G+C.content.crude.freq 0.538462 ; residues.content.corrected.freq a:0.3029|c:0.2894|g:0.2586|t:0.1491 ; G+C.content.corrected.freq 0.547969 ; min(P(S|M)) 2.1028e-18 ; max(P(S|M)) 0.00273434 ; proba_range 0.00273434 ; Wmin -20.8 ; Wmax 12.6 ; Wrange 33.4 ; Job started 2007_12_10.132055 ; Job done 2007_12_10.132055