; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/en.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/en_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/en.tab ; Output files ; output html_ready/en_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : en ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 ; ----- |--------|-------|-------|-------|-------|-------| a | 4 23 28 0 0 10 c | 1 1 3 0 0 0 g | 0 7 0 0 6 21 t | 26 0 0 31 25 0 ; ----- |--------|-------|-------|-------|-------|-------| ; c.sum | 31 31 31 31 31 31 186 ; c.max | 26 23 28 31 25 21 31 ; c.min | 0 0 0 0 0 0 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 4 1 0 26 | 31 0.84 0.47 t t tttt 2 23 1 7 0 | 31 0.74 0.53 a r aaag 3 28 3 0 0 | 31 0.90 0.69 a a aaaaaac 4 0 0 0 31 | 31 1.00 0.89 t t tttttttttt 5 0 0 6 25 | 31 0.81 0.62 t k gtttt 6 10 0 21 0 | 31 0.68 0.97 G G aaGGGGG ; ; Matrix type: information ;P | 1 2 3 4 5 6 ;- |-----|----|----|----|----|----| a | -0.1 0.5 0.8 -0.0 -0.0 -0.0 c | -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 g | -0.0 0.1 -0.0 -0.0 0.1 1.1 t | 0.7 -0.0 -0.0 1.0 0.6 -0.0 ;- |-----|----|----|----|----|----| ; i.sum | 0.5 0.5 0.7 0.9 0.6 1.0 4.2 ; i.max | 0.7 0.5 0.8 1.0 0.6 1.1 1.1 ; i.min | -0.1 -0.0 -0.0 -0.0 -0.0 -0.0 -0.1 ; Sites 31 >en_chr2R_7044643_7044664 taattg >en_chr2L_2471447_2471454 taattg >en_chrX_1996644_1996665_ taattg >en_chr2L_2471225_2471232 taattg >en_chr2R_7041482_7041501 taattg >en_chr2R_7041421_7041430 taattg >en_chr4_80105_80117_D taattg >en_chrX_1996767_1996793_ taattg >en_chr2R_7044520_7044545 taattg >en_chr2R_7044683_7044718 taattg >en_chrX_1996582_1996641_ tgattg >en_chr3R_12599326_125993 tgattg >en_chrX_1996747_1996757_ tgattg >en_chrX_1980287_1980378_ taatgg >en_chr3R_12599167_125991 taatgg >en_chrX_1981649_1981669_ tgcttg >en_chrX_1996383_1996439_ tactgg >en_chr2R_7041389_7041401 taatta >en_chr2L_2471457_2471466 taatta >en_chr2L_2471427_2471434 taatta >en_chrX_1981450_1981495_ taatta >en_chrX_1980403_1980432_ taatta >en_chr4_80673_80681_D taatta >en_chrX_1981537_1981622_ tgatta >en_chr3R_2692105_2692143 tcattg >en_chrX_1981511_1981523_ agattg >en_chr3R_12599235_125992 taatga >en_chrX_1981689_1981725_ aaatgg >en_chr3R_12526988_125269 cgatgg >en_chr3R_12526804_125268 aaatta >en_chrX_1996473_1996534_ aactta ; ; Matrix parameters ; Columns 6 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.369|c:0.131|g:0.131|t:0.369 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/en_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 31 ; meme.llr 144 ; meme.E-value 0.00069 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.131 ; alphabet.size 4 ; max.bits 2 ; total.information 4.17709 ; information.per.column 0.696181 ; max.possible.info.per.col 2.03256 ; consensus.strict taattG ; consensus.strict.rc Caatta ; consensus.IUPAC tratkG ; consensus.IUPAC.rc Cmatya ; consensus.regexp t[ag]at[gt]G ; consensus.regexp.rc C[ac]at[ct]a ; residues.content.crude.freq a:0.3495|c:0.0269|g:0.1828|t:0.4409 ; G+C.content.crude.freq 0.209677 ; residues.content.corrected.freq a:0.3501|c:0.0301|g:0.1812|t:0.4386 ; G+C.content.corrected.freq 0.211313 ; min(P(S|M)) 1.32582e-14 ; max(P(S|M)) 0.27378 ; proba_range 0.27378 ; Wmin -21 ; Wmax 5.9 ; Wrange 26.9 ; Job started 2007_12_10.132054 ; Job done 2007_12_10.132054