; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/byn.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/byn_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/byn.tab ; Output files ; output html_ready/byn_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : byn ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 7 4 1 0 0 1 2 7 4 5 2 0 0 c | 2 0 0 1 0 7 0 1 2 0 0 4 2 g | 0 3 6 0 9 0 4 1 0 0 0 1 1 t | 0 2 2 8 0 1 3 0 3 4 7 4 6 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 9 9 9 9 9 9 9 9 9 9 9 9 9 117 ; c.max | 7 4 6 8 9 7 4 7 4 5 7 4 6 9 ; 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 7 2 0 0 | 9 0.78 0.56 a m aaaaac 2 4 0 3 2 | 9 0.44 0.20 g r g 3 1 0 6 2 | 9 0.67 0.48 G G GGGt 4 0 1 0 8 | 9 0.89 0.67 T T TTTTTTTT 5 0 0 9 0 | 9 1.00 1.21 G G GGGGGGGGGGGGGGGGGG 6 1 7 0 1 | 9 0.78 0.65 C C CCCCCCt 7 2 0 4 3 | 9 0.44 0.23 g k g 8 7 1 1 0 | 9 0.78 0.46 a a aaaag 9 4 2 0 3 | 9 0.44 0.16 a h t 10 5 0 0 4 | 9 0.56 0.37 a w att 11 2 0 0 7 | 9 0.78 0.50 t t atttt 12 0 4 1 4 | 9 0.44 0.33 c y ct 13 0 2 1 6 | 9 0.67 0.36 t y gtt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| a | 0.7 0.2 -0.1 -0.1 -0.1 -0.1 -0.1 0.7 0.2 0.3 -0.1 -0.1 -0.1 c | 0.0 -0.0 -0.0 -0.1 -0.0 0.9 -0.0 -0.1 0.0 -0.0 -0.0 0.3 0.0 g | -0.0 0.1 0.7 -0.0 1.4 -0.0 0.3 -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 t | -0.1 -0.1 -0.1 0.8 -0.1 -0.1 0.0 -0.1 0.0 0.2 0.7 0.2 0.5 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.6 0.2 0.5 0.7 1.2 0.7 0.2 0.5 0.2 0.4 0.5 0.3 0.4 6.2 ; i.max | 0.7 0.2 0.7 0.8 1.4 0.9 0.3 0.7 0.2 0.3 0.7 0.3 0.5 1.4 ; i.min | -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 ; Sites 9 >byn_chr2R_16406573_16406 aggtgcgatatct >byn_chr2R_16406726_16406 aagtgcgactttt >byn_chr2R_16406263_16406 aagtgctaatttt >byn_chr2R_16406874_16406 aagtgcgatttcg >byn_chr2R_16407647_16407 atttgcacaattt >byn_chr2R_16407702_16407 cgacgcgatttct >byn_chr2R_16406990_16407 atgtgttacaact >byn_chr2R_16406967_16406 aggtgaaaaaatc >byn_chr2R_16407819_16407 cattgctgaatgc ; ; Matrix parameters ; Columns 13 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.298|c:0.202|g:0.202|t:0.298 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/byn_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 9 ; meme.llr 75 ; meme.E-value 0.029 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.202 ; alphabet.size 4 ; max.bits 2 ; total.information 6.19712 ; information.per.column 0.476701 ; max.possible.info.per.col 1.59949 ; consensus.strict agGTGCgaaatct ; consensus.strict.rc agatttcGCACct ; consensus.IUPAC mrGTGCkahwtyy ; consensus.IUPAC.rc rrawdtmGCACyk ; consensus.regexp [ac][ag]GTGC[gt]a[act][at]t[ct][ct] ; consensus.regexp.rc [ag][ag]a[at][agt]t[ac]GCAC[ct][gt] ; residues.content.crude.freq a:0.2821|c:0.1624|g:0.2137|t:0.3419 ; G+C.content.crude.freq 0.376068 ; residues.content.corrected.freq a:0.2836|c:0.1664|g:0.2125|t:0.3375 ; G+C.content.corrected.freq 0.378862 ; min(P(S|M)) 2.99338e-22 ; max(P(S|M)) 0.00147578 ; proba_range 0.00147578 ; Wmin -29.9 ; Wmax 11.3 ; Wrange 41.2 ; Job started 2007_12_10.132042 ; Job done 2007_12_10.132042