; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Dref.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Dref_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Dref.tab ; Output files ; output html_ready/Dref_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : Dref ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 5 16 2 0 1 19 0 17 c | 3 0 0 18 0 0 0 1 g | 0 0 1 1 18 0 0 0 t | 11 3 16 0 0 0 19 1 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 19 19 19 19 19 19 19 19 152 ; c.max | 11 16 16 18 18 19 19 17 19 ; c.min | 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 5 3 0 11 | 19 0.58 0.23 t t t 2 16 0 0 3 | 19 0.84 0.61 a a aaaaatt 3 2 0 1 16 | 19 0.84 0.56 t t gttttt 4 0 18 1 0 | 19 0.95 1.30 C C CCCCCCCCCCCCCCCCg 5 1 0 18 0 | 19 0.95 1.28 G G GGGGGGGGGGGGGGGGG 6 19 0 0 0 | 19 1.00 0.97 A A AAAAAAAAAAAAA 7 0 0 0 19 | 19 1.00 0.97 T T TTTTTTTTTTTTT 8 17 1 0 1 | 19 0.89 0.67 A A AAAAAAAt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | -0.0 0.8 -0.1 -0.0 -0.1 1.1 -0.0 0.9 c | -0.0 -0.0 -0.0 1.5 -0.0 -0.0 -0.0 -0.1 g | -0.0 -0.0 -0.1 -0.1 1.5 -0.0 -0.0 -0.0 t | 0.3 -0.1 0.8 -0.0 -0.0 -0.0 1.1 -0.1 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.2 0.6 0.6 1.3 1.3 1.0 1.0 0.7 6.6 ; i.max | 0.3 0.8 0.8 1.5 1.5 1.1 1.1 0.9 1.5 ; i.min | -0.0 -0.1 -0.1 -0.1 -0.1 -0.0 -0.0 -0.1 -0.1 ; Sites 19 >Dref_chr3R_17497466_1749 tatcgata >Dref_chr3R_17497654_1749 tatcgata >Dref_chr3R_17497519_1749 tatcgata >Dref_chr3R_23064863_2306 tatcgata >Dref_chr3R_8877769_88777 tatcgata >Dref_chr3L_18787824_1878 tatcgata >Dref_chrX_10590263_10590 tatcgata >Dref_chr2L_10342665_1034 tatcgata >Dref_chr3R_12030978_1203 catcgata >Dref_chr3R_12030990_1203 catcgata >Dref_chr2L_20757380_2075 aatcgata >Dref_chrX_2196445_219645 aatcgata >Dref_chr2L_20756888_2075 tttcgata >Dref_chr3R_17458956_1745 attcgata >Dref_chr2L_20757791_2075 tatggata >Dref_chr3R_17458945_1745 aaacgata >Dref_chr3R_8877723_88777 aatcgatt >Dref_chr3R_23064812_2306 ctgcgata >Dref_chr3R_23064789_2306 taacaatc ; ; Matrix parameters ; Columns 8 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.318|c:0.182|g:0.182|t:0.318 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Dref_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 19 ; meme.llr 145 ; meme.E-value 3.9e-33 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.182 ; alphabet.size 4 ; max.bits 2 ; total.information 6.59029 ; information.per.column 0.823787 ; max.possible.info.per.col 1.70375 ; consensus.strict tatCGATA ; consensus.strict.rc TATCGata ; consensus.IUPAC tatCGATA ; consensus.IUPAC.rc TATCGata ; consensus.regexp tatCGATA ; consensus.regexp.rc TATCGata ; residues.content.crude.freq a:0.3947|c:0.1447|g:0.1316|t:0.3289 ; G+C.content.crude.freq 0.276316 ; residues.content.corrected.freq a:0.3909|c:0.1466|g:0.1341|t:0.3284 ; G+C.content.corrected.freq 0.2807 ; min(P(S|M)) 8.2165e-17 ; max(P(S|M)) 0.251518 ; proba_range 0.251518 ; Wmin -24 ; Wmax 8.9 ; Wrange 32.9 ; Job started 2007_12_10.132049 ; Job done 2007_12_10.132049