; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/kni.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/kni_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/kni.tab ; Output files ; output html_ready/kni_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : kni ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 6 18 7 0 3 15 10 10 c | 2 7 6 33 4 7 8 2 g | 22 0 2 0 4 4 10 2 t | 3 8 18 0 22 7 5 19 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 33 33 33 33 33 33 33 33 264 ; c.max | 22 18 18 33 22 15 10 19 33 ; c.min | 2 0 2 0 3 4 5 2 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 6 2 22 3 | 33 0.67 0.46 G G cGGG 2 18 7 0 8 | 33 0.55 0.28 a a at 3 7 6 2 18 | 33 0.55 0.17 t t t 4 0 33 0 0 | 33 1.00 1.40 C C CCCCCCCCCCCCCCCCCCCCC 5 3 4 4 22 | 33 0.67 0.30 t t gtt 6 15 7 4 7 | 33 0.45 0.07 a a 7 10 8 10 5 | 33 0.30 0.05 g v 8 10 2 2 19 | 33 0.58 0.25 t w tt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | -0.1 0.3 -0.1 -0.0 -0.1 0.2 0.0 0.0 c | -0.1 -0.0 -0.0 1.5 -0.1 -0.0 0.0 -0.1 g | 0.7 -0.0 -0.1 -0.0 -0.1 -0.1 0.1 -0.1 t | -0.1 -0.0 0.3 -0.0 0.5 -0.1 -0.1 0.4 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.5 0.3 0.2 1.4 0.3 0.1 0.1 0.3 3.0 ; i.max | 0.7 0.3 0.3 1.5 0.5 0.2 0.1 0.4 1.5 ; i.min | -0.1 -0.0 -0.1 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 33 >kni_chr2R_5487348_548736 gatctagt >kni_chr2R_5487573_548758 gatctact >kni_chr3L_8638573_863859 gatctcgt >kni_chr3L_8639669_863967 gctctact >kni_chr3L_8639911_863992 gctctact >kni_chr3L_8638865_863889 gttctaat >kni_chr3L_8639837_863984 gatctgga >kni_chr2R_20730884_20730 gaactaaa >kni_chr2R_5487392_548740 gctctctt >kni_chr3L_8639205_863921 gccctcat >kni_chr3L_8640869_864091 gaactgat >kni_chr3R_12598893_12598 gttccagt >kni_chr3L_8641321_864133 gatcgtct >kni_chr2R_5487618_548762 gcgctagt >kni_chr3L_8639855_863986 gaactagg >kni_chr3L_8639264_863927 aatcttga >kni_chr2R_5487415_548742 gttcccat >kni_chr3L_8640806_864082 gatcgtaa >kni_chr3L_8638500_863850 gaccgaaa >kni_chr3L_8639165_863917 aatctgga >kni_chr3R_12598704_12598 gacccatt >kni_chr3L_8639485_863949 aacctaaa >kni_chr3L_8640835_864085 gacctccg >kni_chr3L_8639539_863954 atactcga >kni_chr3R_12600037_12600 gctcattt >kni_chr3L_8639054_863906 tttctttt >kni_chr3L_8639070_863907 ccacttct >kni_chr3R_12599333_12599 aatcataa >kni_chr3L_8639403_863941 attctggc >kni_chr3L_8639618_863962 ttactcca >kni_chr3L_8638757_863876 gagcgacc >kni_chr3R_12599841_12599 ttcccaat >kni_chr3L_8639096_863910 caacaatt ; ; Matrix parameters ; Columns 8 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.285|c:0.215|g:0.215|t:0.285 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/kni_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 33 ; meme.llr 107 ; meme.E-value 1.3e-06 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.215 ; alphabet.size 4 ; max.bits 2 ; total.information 2.99541 ; information.per.column 0.374426 ; max.possible.info.per.col 1.53712 ; consensus.strict GatCtagt ; consensus.strict.rc actaGatC ; consensus.IUPAC GatCtavw ; consensus.IUPAC.rc wbtaGatC ; consensus.regexp GatCta[acg][at] ; consensus.regexp.rc [at][cgt]taGatC ; residues.content.crude.freq a:0.2614|c:0.2614|g:0.1667|t:0.3106 ; G+C.content.crude.freq 0.42803 ; residues.content.corrected.freq a:0.2621|c:0.2600|g:0.1681|t:0.3099 ; G+C.content.corrected.freq 0.428088 ; min(P(S|M)) 2.05847e-11 ; max(P(S|M)) 0.00933343 ; proba_range 0.00933343 ; Wmin -12.9 ; Wmax 6.2 ; Wrange 19.1 ; Job started 2007_12_10.132112 ; Job done 2007_12_10.132112