; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/HLHm5.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/HLHm5_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/HLHm5.tab ; Output files ; output html_ready/HLHm5_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : HLHm5 ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 0 2 0 0 1 0 0 0 2 1 2 1 0 c | 3 0 3 0 0 0 2 3 0 1 1 0 0 g | 0 1 0 3 0 3 0 0 1 1 0 0 3 t | 0 0 0 0 2 0 1 0 0 0 0 2 0 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 3 3 3 3 3 3 3 3 3 3 3 3 3 39 ; c.max | 3 2 3 3 2 3 2 3 2 1 2 2 3 3 ; 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 3 0 0 | 3 1.00 0.56 c c ccccccc 2 2 0 1 0 | 3 0.67 0.44 A R AAgg 3 0 3 0 0 | 3 1.00 0.56 c c ccccccc 4 0 0 3 0 | 3 1.00 0.56 g g ggggggg 5 1 0 0 2 | 3 0.67 0.52 T W aTTT 6 0 0 3 0 | 3 1.00 0.56 g g ggggggg 7 0 2 0 1 | 3 0.67 0.32 c y ct 8 0 3 0 0 | 3 1.00 0.56 c c ccccccc 9 2 0 1 0 | 3 0.67 0.44 A R AAgg 10 1 1 1 0 | 3 0.33 0.10 a v 11 2 1 0 0 | 3 0.67 0.44 A M AAcc 12 1 0 0 2 | 3 0.67 0.52 T W aTTT 13 0 0 3 0 | 3 1.00 0.56 g g ggggggg ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| a | -0.1 0.6 -0.1 -0.1 0.1 -0.1 -0.1 -0.1 0.6 0.1 0.6 0.1 -0.1 c | 0.8 -0.1 0.8 -0.1 -0.1 -0.1 0.3 0.8 -0.1 0.0 0.0 -0.1 -0.1 g | -0.1 0.0 -0.1 0.8 -0.1 0.8 -0.1 -0.1 0.0 0.0 -0.1 -0.1 0.8 t | -0.1 -0.1 -0.1 -0.1 0.6 -0.1 0.1 -0.1 -0.1 -0.1 -0.1 0.6 -0.1 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.6 0.4 0.6 0.6 0.5 0.6 0.3 0.6 0.4 0.1 0.4 0.5 0.6 6.1 ; i.max | 0.8 0.6 0.8 0.8 0.6 0.8 0.3 0.8 0.6 0.1 0.6 0.6 0.8 0.8 ; 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 3 >HLHm5_chrX_265912_265932 cacgtgtcaaatg >HLHm5_chr3R_21865771_218 cacgagccacaag >HLHm5_chrX_226541_226558 cgcgtgccggctg ; ; Matrix parameters ; Columns 13 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.181|c:0.319|g:0.319|t:0.181 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/HLHm5_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 3 ; meme.llr 38 ; meme.E-value 4.2 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.181 ; alphabet.size 4 ; max.bits 2 ; total.information 6.13016 ; information.per.column 0.471551 ; max.possible.info.per.col 1.70926 ; consensus.strict cAcgTgccAaATg ; consensus.strict.rc cATtTggcAcgTg ; consensus.IUPAC cRcgWgycRvMWg ; consensus.IUPAC.rc cWKbYgrcWcgYg ; consensus.regexp c[AG]cg[AT]g[ct]c[AG][acg][AC][AT]g ; consensus.regexp.rc c[AT][GT][cgt][CT]g[ag]c[AT]cg[CT]g ; residues.content.crude.freq a:0.2308|c:0.3333|g:0.3077|t:0.1282 ; G+C.content.crude.freq 0.641026 ; residues.content.corrected.freq a:0.2183|c:0.3297|g:0.3105|t:0.1414 ; G+C.content.corrected.freq 0.640269 ; min(P(S|M)) 1.03578e-17 ; max(P(S|M)) 0.00300668 ; proba_range 0.00300668 ; Wmin -18.2 ; Wmax 12.7 ; Wrange 30.9 ; Job started 2007_12_10.132108 ; Job done 2007_12_10.132108