; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Top2.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Top2_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Top2.tab ; Output files ; output html_ready/Top2_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : Top2 ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 0 2 1 4 0 3 0 4 1 3 0 4 0 3 1 4 0 4 0 4 0 c | 0 0 1 0 1 0 0 0 2 0 0 0 4 0 0 0 3 0 0 0 0 g | 0 2 0 0 1 0 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0 t | 4 0 2 0 2 1 4 0 1 0 4 0 0 1 3 0 0 0 4 0 4 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 84 ; c.max | 4 2 2 4 2 3 4 4 2 3 4 4 4 3 3 4 3 4 4 4 4 4 ; c.min | 0 0 0 0 0 0 0 0 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 0 0 4 | 4 1.00 0.52 t t ttttt 2 2 0 2 0 | 4 0.50 0.50 G R aG 3 1 1 0 2 | 4 0.50 0.12 c y 4 4 0 0 0 | 4 1.00 0.52 a a aaaaa 5 0 1 1 2 | 4 0.50 0.28 c b t 6 3 0 0 1 | 4 0.75 0.21 a a a 7 0 0 0 4 | 4 1.00 0.52 t t ttttt 8 4 0 0 0 | 4 1.00 0.52 a a aaaaa 9 1 2 0 1 | 4 0.50 0.34 C C C 10 3 0 1 0 | 4 0.75 0.37 g r aag 11 0 0 0 4 | 4 1.00 0.52 t t ttttt 12 4 0 0 0 | 4 1.00 0.52 a a aaaaa 13 0 4 0 0 | 4 1.00 1.36 C C CCCCCCCCCCCCCC 14 3 0 0 1 | 4 0.75 0.21 a a a 15 1 0 0 3 | 4 0.75 0.21 t t t 16 4 0 0 0 | 4 1.00 0.52 a a aaaaa 17 0 3 1 0 | 4 0.75 0.98 C S CCCCCgg 18 4 0 0 0 | 4 1.00 0.52 a a aaaaa 19 0 0 0 4 | 4 1.00 0.52 t t ttttt 20 4 0 0 0 | 4 1.00 0.52 a a aaaaa 21 0 0 0 4 | 4 1.00 0.52 t t ttttt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| a | -0.1 0.1 -0.1 0.7 -0.1 0.4 -0.1 0.7 -0.1 0.4 -0.1 0.7 -0.1 0.4 -0.1 0.7 -0.1 0.7 -0.1 0.7 -0.1 c | -0.0 -0.0 0.2 -0.0 0.2 -0.0 -0.0 -0.0 0.6 -0.0 -0.0 -0.0 1.6 -0.0 -0.0 -0.0 1.1 -0.0 -0.0 -0.0 -0.0 g | -0.0 0.6 -0.0 -0.0 0.2 -0.0 -0.0 -0.0 -0.0 0.2 -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 0.2 -0.0 -0.0 -0.0 -0.0 t | 0.7 -0.1 0.1 -0.1 0.1 -0.1 0.7 -0.1 -0.1 -0.1 0.7 -0.1 -0.1 -0.1 0.4 -0.1 -0.1 -0.1 0.7 -0.1 0.7 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 0.5 0.5 0.1 0.5 0.3 0.2 0.5 0.5 0.3 0.4 0.5 0.5 1.4 0.2 0.2 0.5 1.0 0.5 0.5 0.5 0.5 10.3 ; i.max | 0.7 0.6 0.2 0.7 0.2 0.4 0.7 0.7 0.6 0.4 0.7 0.7 1.6 0.4 0.4 0.7 1.1 0.7 0.7 0.7 0.7 1.6 ; 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 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 4 >Top2_chr3R_7783472_77835 tgtacatacatacatacatat >Top2_chr3R_7783127_77831 tacatatacatacatacatat >Top2_chr3R_7783360_77833 tgtatatatgtacatacatat >Top2_chr3R_7783072_77830 taaagttaaatactaagatat ; ; Matrix parameters ; Columns 21 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.389|c:0.111|g:0.111|t:0.389 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Top2_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 4 ; meme.llr 73 ; meme.E-value 0.0062 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.111 ; alphabet.size 4 ; max.bits 2 ; total.information 10.2824 ; information.per.column 0.48964 ; max.possible.info.per.col 2.19823 ; consensus.strict tGcacataCgtaCataCatat ; consensus.strict.rc atatGtatGtacGtatgtgCa ; consensus.IUPAC tRyabataCrtaCataSatat ; consensus.IUPAC.rc atatStatGtayGtatvtrYa ; consensus.regexp t[AG][ct]a[cgt]ataC[ag]taCata[CG]atat ; consensus.regexp.rc atat[CG]tatGta[ct]Gtat[acg]t[ag][CT]a ; residues.content.crude.freq a:0.4524|c:0.1310|g:0.0595|t:0.3571 ; G+C.content.crude.freq 0.190476 ; residues.content.corrected.freq a:0.4397|c:0.1270|g:0.0698|t:0.3635 ; G+C.content.corrected.freq 0.196781 ; min(P(S|M)) 2.30497e-34 ; max(P(S|M)) 0.00118556 ; proba_range 0.00118556 ; Wmin -33.6 ; Wmax 19.1 ; Wrange 52.7 ; Job started 2007_12_10.132133 ; Job done 2007_12_10.132133