; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/eve.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/eve_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/eve.tab ; Output files ; output html_ready/eve_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : eve ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| a | 0 5 3 6 1 2 7 0 0 8 4 2 3 1 0 c | 8 0 4 2 3 3 0 0 1 1 0 5 0 6 7 g | 1 4 2 1 0 3 2 0 0 0 4 2 6 2 0 t | 0 0 0 0 5 1 0 9 8 0 1 0 0 0 2 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 135 ; c.max | 8 5 4 6 5 3 7 9 8 8 4 5 6 6 7 9 ; c.min | 0 0 0 0 0 1 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 8 1 0 | 9 0.89 1.10 C C CCCCCCCCCCCg 2 5 0 4 0 | 9 0.56 0.52 g r aag 3 3 4 2 0 | 9 0.44 0.36 c v cg 4 6 2 1 0 | 9 0.67 0.35 a m aag 5 1 3 0 5 | 9 0.56 0.29 c y tt 6 2 3 3 1 | 9 0.33 0.20 c s 7 7 0 2 0 | 9 0.78 0.52 a r aaaag 8 0 0 0 9 | 9 1.00 0.81 T T TTTTTTTTTT 9 0 1 0 8 | 9 0.89 0.61 t t ttttttt 10 8 1 0 0 | 9 0.89 0.61 a a aaaaaac 11 4 0 4 1 | 9 0.44 0.33 g r gt 12 2 5 2 0 | 9 0.56 0.48 C S CCg 13 3 0 6 0 | 9 0.67 0.69 G R aaGGGG 14 1 6 2 0 | 9 0.67 0.66 C S CCCCg 15 0 7 0 2 | 9 0.78 0.85 C C CCCCCCtt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| a | -0.1 0.3 0.0 0.4 -0.1 -0.1 0.6 -0.1 -0.1 0.8 0.1 -0.1 0.0 -0.1 -0.1 c | 1.3 -0.0 0.4 0.1 0.2 0.2 -0.0 -0.0 -0.0 -0.0 -0.0 0.6 -0.0 0.8 1.0 g | -0.0 0.4 0.1 -0.0 -0.0 0.2 0.1 -0.0 -0.0 -0.0 0.4 0.1 0.8 0.1 -0.0 t | -0.1 -0.1 -0.1 -0.1 0.3 -0.1 -0.1 1.0 0.8 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ;- |-----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| ; i.sum | 1.1 0.5 0.4 0.3 0.3 0.2 0.5 0.8 0.6 0.6 0.3 0.5 0.7 0.7 0.8 8.4 ; i.max | 1.3 0.4 0.4 0.4 0.3 0.2 0.6 1.0 0.8 0.8 0.4 0.6 0.8 0.8 1.0 1.3 ; 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 ; Sites 9 >eve_chr2R_5490987_549101 cgcacgattagcacc >eve_chr2R_20564746_20564 cgcatgattaggggc >eve_chr2R_5490935_549096 cgcctcgttatcgcc >eve_chr2R_20564632_20564 caaaccattaacacc >eve_chr3R_12560060_12560 cacattatcagcggc >eve_chr3R_12559847_12559 caaatcgttaaaacc >eve_chr3R_17205862_17205 caggcaattaaggac >eve_chr2R_15777955_15777 ggaatgattaaagct >eve_chr2R_5485790_548582 cagcaaattcgcgct ; ; Matrix parameters ; Columns 15 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.333|c:0.167|g:0.167|t:0.333 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/eve_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 9 ; meme.llr 101 ; meme.E-value 0.55 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.167 ; alphabet.size 4 ; max.bits 2 ; total.information 8.37624 ; information.per.column 0.558416 ; max.possible.info.per.col 1.78976 ; consensus.strict CgcaccaTtagCGCC ; consensus.strict.rc GGCGctaAtggtgcG ; consensus.IUPAC CrvmysrTtarSRSC ; consensus.IUPAC.rc GSYSytaAysrkbyG ; consensus.regexp C[ag][acg][ac][ct][cg][ag]Tta[ag][CG][AG][CG]C ; consensus.regexp.rc G[CG][CT][CG][ct]taA[ct][cg][ag][gt][cgt][ct]G ; residues.content.crude.freq a:0.3111|c:0.2963|g:0.2000|t:0.1926 ; G+C.content.crude.freq 0.496296 ; residues.content.corrected.freq a:0.3133|c:0.2834|g:0.1967|t:0.2066 ; G+C.content.corrected.freq 0.480067 ; min(P(S|M)) 5.51442e-25 ; max(P(S|M)) 0.000562996 ; proba_range 0.000562996 ; Wmin -33.1 ; Wmax 15 ; Wrange 48.1 ; Job started 2007_12_10.132056 ; Job done 2007_12_10.132056