; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/pan.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/pan_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/pan.tab ; Output files ; output html_ready/pan_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : pan ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 15 7 1 22 22 21 9 7 c | 1 2 23 0 1 1 2 6 g | 3 0 0 0 1 0 10 9 t | 6 16 1 3 1 3 4 3 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 25 25 25 25 25 25 25 25 200 ; c.max | 15 16 23 22 22 21 10 9 23 ; c.min | 1 0 0 0 1 0 2 3 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 15 1 3 6 | 25 0.60 0.19 a a a 2 7 2 0 16 | 25 0.64 0.31 t t ctt 3 1 23 0 1 | 25 0.92 1.20 C C CCCCCCCCCCCCCCCCt 4 22 0 0 3 | 25 0.88 0.69 a a aaaaaaaat 5 22 1 1 1 | 25 0.88 0.64 a a aaaaaaag 6 21 1 0 3 | 25 0.84 0.58 a a aaaaaat 7 9 2 10 4 | 25 0.40 0.17 g r 8 7 6 9 3 | 25 0.36 0.14 g s ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | 0.4 -0.0 -0.1 0.9 0.9 0.8 0.0 -0.0 c | -0.1 -0.1 1.4 -0.0 -0.1 -0.1 -0.1 0.1 g | -0.0 -0.0 -0.0 -0.0 -0.1 -0.0 0.3 0.2 t | -0.1 0.4 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.2 0.3 1.2 0.7 0.6 0.6 0.2 0.1 3.9 ; i.max | 0.4 0.4 1.4 0.9 0.9 0.8 0.3 0.2 1.4 ; i.min | -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 25 >pan_chr2L_3823994_382401 atcaaagc >pan_chr2R_5497302_549731 atcaaagc >pan_chr3R_22997721_22997 atcaaaag >pan_chr2L_3823211_382323 ttcaaagg >pan_chr3R_22997065_22997 atcaaaaa >pan_chr2L_3824023_382404 atcaaacg >pan_chr2L_3824346_382436 atcaaacg >pan_chr3R_22997245_22997 aacaaaac >pan_chr2L_3824173_382419 aacaaaac >pan_chr3R_22997606_22997 ttcaaatg >pan_chr2R_5497500_549751 tccaaagg >pan_chr2L_3824297_382432 ttcaaagt >pan_chr3R_22997400_22997 accaaaaa >pan_chr2L_3823447_382346 gacaaaac >pan_chr3R_22997361_22997 aactaagc >pan_chr2R_5497525_549753 attaaagg >pan_chr2R_5497184_549719 atcaatta >pan_chr2R_5497589_549760 atctaaat >pan_chr2L_3824209_382422 cacaaaaa >pan_chr3R_22997591_22997 ttcaatta >pan_chr2R_5497332_549734 ttcacagt >pan_chr3R_22997687_22997 aaaaaaga >pan_chr2R_5497348_549736 atcttaag >pan_chr2L_3823277_382329 gacaatta >pan_chr3R_22997264_22997 gtcagcgg ; ; Matrix parameters ; Columns 8 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.317|c:0.183|g:0.183|t:0.317 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/pan_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 25 ; meme.llr 108 ; meme.E-value 4.6 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.183 ; alphabet.size 4 ; max.bits 2 ; total.information 3.91725 ; information.per.column 0.489656 ; max.possible.info.per.col 1.69827 ; consensus.strict atCaaagg ; consensus.strict.rc cctttGat ; consensus.IUPAC atCaaars ; consensus.IUPAC.rc sytttGat ; consensus.regexp atCaaa[ag][cg] ; consensus.regexp.rc [cg][ct]tttGat ; residues.content.crude.freq a:0.5200|c:0.1800|g:0.1150|t:0.1850 ; G+C.content.crude.freq 0.295 ; residues.content.corrected.freq a:0.5122|c:0.1801|g:0.1176|t:0.1901 ; G+C.content.corrected.freq 0.297731 ; min(P(S|M)) 5.44235e-14 ; max(P(S|M)) 0.0275458 ; proba_range 0.0275458 ; Wmin -18.1 ; Wmax 7.5 ; Wrange 25.6 ; Job started 2007_12_10.132120 ; Job done 2007_12_10.132120