; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Trl.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/Trl_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/Trl.tab ; Output files ; output html_ready/Trl_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : Trl ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 ; ----- |--------|-------|-------|-------|-------|-------| a | 49 1 70 0 44 17 c | 4 0 1 0 23 5 g | 7 72 0 73 0 51 t | 13 0 2 0 6 0 ; ----- |--------|-------|-------|-------|-------|-------| ; c.sum | 73 73 73 73 73 73 438 ; c.max | 49 72 70 73 44 51 73 ; c.min | 4 0 0 0 0 0 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 49 4 7 13 | 73 0.67 0.40 a a aaat 2 1 0 72 0 | 73 0.99 1.27 G G GGGGGGGGGGGGGGGGGGGGG 3 70 1 0 2 | 73 0.96 1.13 A A AAAAAAAAAAAAAAAAAt 4 0 0 73 0 | 73 1.00 1.33 G G GGGGGGGGGGGGGGGGGGGGGG 5 44 23 0 6 | 73 0.60 0.48 a m aacc 6 17 5 51 0 | 73 0.70 0.59 G G acGGGGG ; ; Matrix type: information ;P | 1 2 3 4 5 6 ;- |-----|----|----|----|----|----| a | 0.6 -0.0 1.3 -0.0 0.5 -0.0 c | -0.1 -0.0 -0.0 -0.0 0.1 -0.1 g | -0.1 1.3 -0.0 1.4 -0.0 0.7 t | -0.1 -0.0 -0.1 -0.0 -0.1 -0.0 ;- |-----|----|----|----|----|----| ; i.sum | 0.4 1.3 1.1 1.3 0.5 0.6 5.2 ; i.max | 0.6 1.3 1.3 1.4 0.5 0.7 1.4 ; i.min | -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 ; Sites 73 >Trl_chr3R_12589987_12589 agagag >Trl_chr3R_12589983_12590 agagag >Trl_chr3L_17584728_17584 agagag >Trl_chr2R_20734356_20734 agagag >Trl_chr3L_9351404_935142 agagag >Trl_chr3R_12589860_12589 agagag >Trl_chr3L_9351436_935144 agagag >Trl_chr3R_12590056_12590 agagag >Trl_chr2L_21441906_21441 agagag >Trl_chr3R_2912203_291221 agagag >Trl_chr3L_17584756_17584 agagag >Trl_chr3R_12589864_12589 agagag >Trl_chr3L_17584708_17584 agagag >Trl_chr3R_12589730_12589 agagag >Trl_chr3L_14722636_14722 agagag >Trl_chr3R_12560232_12560 agagag >Trl_chr2L_21517250_21517 agagag >Trl_chr3L_9351644_935166 agagag >Trl_chr3R_12560279_12560 agagag >Trl_chr3R_7782373_778240 agagag >Trl_chr3R_12589585_12589 agagag >Trl_chr3R_12589559_12589 agagag >Trl_chr3R_2912768_291279 agagag >Trl_chr3R_7782325_778234 agagag >Trl_chr3L_17584678_17584 agagcg >Trl_chr3L_14722665_14722 agagcg >Trl_chr3L_14723401_14723 agagcg >Trl_chr3L_9351685_935170 agagcg >Trl_chr3L_14722699_14722 agagcg >Trl_chr3R_12589950_12589 agagcg >Trl_chr3R_7782300_778231 agagcg >Trl_chr3R_12589906_12589 agagcg >Trl_chr2R_20734172_20734 agagcg >Trl_chr3R_12589700_12589 agagaa >Trl_chr3L_14723286_14723 agagaa >Trl_chr3L_17584662_17584 agagaa >Trl_chr3L_14723144_14723 agagaa >Trl_chr3R_7782411_778243 agagaa >Trl_chr3L_14723376_14723 agagaa >Trl_chr3R_2912848_291286 tgagag >Trl_chr2L_2454725_245473 agagca >Trl_chr3R_2912811_291282 agagca >Trl_chr3L_14723469_14723 agagca >Trl_chr3L_14722540_14722 agagca >Trl_chr2R_20734105_20734 tgagcg >Trl_chr3L_14723037_14723 tgagcg >Trl_chr3R_12589526_12589 ggagag >Trl_chr3R_2912222_291223 ggagag >Trl_chr3L_17584614_17584 tgagcg >Trl_chr3L_14723706_14723 agagtg >Trl_chr3L_14723011_14723 agagac >Trl_chr2L_14615337_14615 tgagaa >Trl_chr3R_12560330_12560 cgagag >Trl_chr3R_12589608_12589 cgagag >Trl_chr2R_20734155_20734 tgagaa >Trl_chr3L_14723440_14723 ggagcg >Trl_chr3L_14723092_14723 ggagcg >Trl_chr3R_26677844_26677 tgagca >Trl_chr3L_14723422_14723 cgagcg >Trl_chr3R_12590719_12590 agagta >Trl_chr3L_14722611_14722 agagta >Trl_chr3R_12590367_12590 tgagtg >Trl_chr3L_14722977_14722 tgagtg >Trl_chr3R_12560184_12560 agtgag >Trl_chr2L_14615550_14615 tgagac >Trl_chr3L_14722950_14722 tgagac >Trl_chr3L_14723240_14723 ggagca >Trl_chr3L_14723210_14723 tgagac >Trl_chr3L_14722415_14722 ggagac >Trl_chr3L_14722846_14722 agcgcg >Trl_chr3L_14722884_14722 tgtgcg >Trl_chr2R_20734273_20734 cgagta >Trl_chr3L_14722469_14722 gaagag ; ; Matrix parameters ; Columns 6 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.254|c:0.246|g:0.246|t:0.254 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/Trl_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 73 ; meme.llr 398 ; meme.E-value 3.1e-50 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.246 ; alphabet.size 4 ; max.bits 2 ; total.information 5.21291 ; information.per.column 0.868819 ; max.possible.info.per.col 1.40242 ; consensus.strict aGAGaG ; consensus.strict.rc CtCTCt ; consensus.IUPAC aGAGmG ; consensus.IUPAC.rc CkCTCt ; consensus.regexp aGAG[ac]G ; consensus.regexp.rc C[gt]CTCt ; residues.content.crude.freq a:0.4132|c:0.0753|g:0.4635|t:0.0479 ; G+C.content.crude.freq 0.538813 ; residues.content.corrected.freq a:0.4111|c:0.0776|g:0.4605|t:0.0507 ; G+C.content.corrected.freq 0.53818 ; min(P(S|M)) 2.40527e-14 ; max(P(S|M)) 0.25289 ; proba_range 0.25289 ; Wmin -23 ; Wmax 7.1 ; Wrange 30.1 ; Job started 2007_12_10.132135 ; Job done 2007_12_10.132135