; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bab1.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/bab1_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/bab1.tab ; Output files ; output html_ready/bab1_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : bab1 ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 1 2 2 1 6 0 2 4 2 0 4 0 0 c | 3 0 0 0 0 0 0 0 0 0 0 0 0 g | 2 1 0 0 0 0 0 1 0 0 2 0 2 t | 0 3 4 5 0 6 4 1 4 6 0 6 4 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 6 6 6 6 6 6 6 6 6 6 6 6 6 78 ; c.max | 3 3 4 5 6 6 4 4 4 6 4 6 4 6 ; 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 1 3 2 0 | 6 0.50 0.88 C S CCGG 2 2 0 1 3 | 6 0.50 0.09 g k 3 2 0 0 4 | 6 0.67 0.15 t t 4 1 0 0 5 | 6 0.83 0.28 t t tt 5 6 0 0 0 | 6 1.00 0.56 a a aaaaa 6 0 0 0 6 | 6 1.00 0.56 t t ttttt 7 2 0 0 4 | 6 0.67 0.15 t t 8 4 0 1 1 | 6 0.67 0.19 g r t 9 2 0 0 4 | 6 0.67 0.15 t t 10 0 0 0 6 | 6 1.00 0.56 t t ttttt 11 4 0 2 0 | 6 0.67 0.51 G R aaG 12 0 0 0 6 | 6 1.00 0.56 t t ttttt 13 0 0 2 4 | 6 0.67 0.51 G K Gtt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| a | -0.1 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 0.3 -0.1 -0.1 0.3 -0.1 -0.1 c | 0.8 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 g | 0.4 0.1 -0.0 -0.0 -0.0 -0.0 -0.0 0.1 -0.0 -0.0 0.4 -0.0 0.4 t | -0.1 0.1 0.3 0.5 -0.1 0.7 0.3 -0.1 0.3 0.7 -0.1 0.7 0.3 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.9 0.1 0.1 0.3 0.6 0.6 0.1 0.2 0.1 0.6 0.5 0.6 0.5 5.1 ; i.max | 0.8 0.1 0.3 0.5 0.7 0.7 0.3 0.3 0.3 0.7 0.4 0.7 0.4 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 6 >bab1_chr3L_1069333_10693 ctatatagttgtg >bab1_chr3L_1069625_10696 cgttattaatgtt >bab1_chr3L_1159108_11591 gtttattattatt >bab1_chr3L_1069513_10695 gataattattatt >bab1_chr3L_1159056_11590 atttattattatt >bab1_chr3L_1069304_10693 caatatatatatg ; ; Matrix parameters ; Columns 13 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.420|c:0.080|g:0.080|t:0.420 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/bab1_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 6 ; meme.llr 47 ; meme.E-value 29 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.08 ; alphabet.size 4 ; max.bits 2 ; total.information 5.10577 ; information.per.column 0.392751 ; max.possible.info.per.col 2.52573 ; consensus.strict CgttattgttGtG ; consensus.strict.rc CaCaacaataacG ; consensus.IUPAC SkttattrttRtK ; consensus.IUPAC.rc MaYaayaataamS ; consensus.regexp [CG][gt]ttatt[ag]tt[AG]t[GT] ; consensus.regexp.rc [AC]a[CT]aa[ct]aataa[ac][CG] ; residues.content.crude.freq a:0.3077|c:0.0385|g:0.1026|t:0.5513 ; G+C.content.crude.freq 0.141026 ; residues.content.corrected.freq a:0.3237|c:0.0444|g:0.0993|t:0.5325 ; G+C.content.corrected.freq 0.143736 ; min(P(S|M)) 2.97889e-25 ; max(P(S|M)) 0.00746406 ; proba_range 0.00746406 ; Wmin -24.7 ; Wmax 10.8 ; Wrange 35.5 ; Job started 2007_12_10.132033 ; Job done 2007_12_10.132033