; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/hb.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/hb_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/hb.tab ; Output files ; output html_ready/hb_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : hb ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 1 4 0 0 2 53 24 2 c | 0 4 2 0 2 4 14 20 g | 3 4 0 0 0 22 10 55 t | 99 91 101 103 99 24 55 26 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 103 103 103 103 103 103 103 103 824 ; c.max | 99 91 101 103 99 53 55 55 103 ; c.min | 0 4 0 0 0 4 10 2 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 1 0 3 99 | 103 0.96 0.82 t t ttttttttt 2 4 4 4 91 | 103 0.88 0.58 t t tttttt 3 0 2 0 101 | 103 0.98 0.89 t t tttttttttt 4 0 0 0 103 | 103 1.00 0.96 t t ttttttttttt 5 2 2 0 99 | 103 0.96 0.81 t t ttttttttt 6 53 4 22 24 | 103 0.51 0.12 g r 7 24 14 10 55 | 103 0.53 0.07 t y 8 2 20 55 26 | 103 0.53 0.64 G S GGGt ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | -0.0 -0.1 -0.0 -0.0 -0.1 0.2 -0.1 -0.1 c | -0.0 -0.0 -0.0 -0.0 -0.0 -0.0 0.0 0.1 g | -0.0 -0.0 -0.0 -0.0 -0.0 0.1 -0.0 0.7 t | 0.9 0.8 1.0 1.0 0.9 -0.1 0.2 -0.1 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.8 0.6 0.9 1.0 0.8 0.1 0.1 0.6 4.9 ; i.max | 0.9 0.8 1.0 1.0 0.9 0.2 0.2 0.7 1.0 ; i.min | -0.0 -0.1 -0.0 -0.0 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 103 >hb_chr3L_8639105_8639115 tttttgtg >hb_chr3L_8639879_8639888 tttttgtg >hb_chr2R_5487383_5487392 tttttgtg >hb_chr3L_8639057_8639066 tttttgtg >hb_chr3L_8638880_8638906 tttttatg >hb_chr3R_12599101_125991 tttttatg >hb_chr2R_20730351_207304 tttttatg >hb_chr3L_20630441_206304 tttttatg >hb_chr3L_8641225_8641239 tttttatg >hb_chr3L_8638470_8638480 tttttatg >hb_chr2R_5490020_5490029 tttttatg >hb_chr3R_12636860_126368 tttttatg >hb_chr3L_8638510_8638520 tttttatg >hb_chr3R_12637018_126370 tttttatg >hb_chr3R_12526870_125269 tttttatg >hb_chr2R_5487487_5487495 tttttatg >hb_chr3R_12526648_125266 tttttatg >hb_chr3R_12527040_125270 tttttatg >hb_chr3R_12590382_125904 tttttatg >hb_chr3L_8638435_8638444 tttttgcg >hb_chr3R_12636643_126366 tttttgcg >hb_chr3L_8640809_8640825 tttttacg >hb_chr3R_12590251_125902 tttttacg >hb_chr3R_12589546_125895 tttttacg >hb_chr2R_5487811_5487820 tttttacg >hb_chr3L_8639709_8639718 tttttggg >hb_chr3R_4524061_4524076 tttttggg >hb_chr3L_8639248_8639257 tttttttg >hb_chr3R_12589995_125900 tttttgag >hb_chr3L_8640993_8641034 tttttttg >hb_chr3L_20631266_206312 tttttagg >hb_chr3R_12599130_125991 tttttaag >hb_chr3R_12599383_125993 tttttaag >hb_chr3R_4524272_4524287 tttttaag >hb_chr3L_8640847_8640865 tttttaag >hb_chr3L_20631436_206314 tttttaag >hb_chr2R_20730829_207308 tttttaag >hb_chr3R_12590698_125907 tttttaag >hb_chr2R_5487763_5487771 tttttaag >hb_chr3L_8638728_8638755 tttttgtc >hb_chr3L_8641247_8641261 tttttgtc >hb_chr3R_12590594_125906 tttttatc >hb_chr3R_12590484_125905 tttttatc >hb_chr2R_20730588_207306 ttttttcg >hb_chr2R_5487610_5487618 ttttttcg >hb_chr3R_12599303_125993 tttttgcc >hb_chr3R_4523967_4523982 ttttttgg >hb_chr3R_12599053_125990 tttttacc >hb_chr2R_5487363_5487372 tttttgtt >hb_chr3L_8639755_8639764 tttttctg >hb_chr2R_5487589_5487598 tttttgtt >hb_chr3R_12590460_125904 tttttgtt >hb_chr3R_4520497_4520512 tttttgtt >hb_chr3R_4524457_4524472 ttttttag >hb_chr3L_8639038_8639048 tttttggc >hb_chr3L_20631140_206311 tttttatt >hb_chr3R_12636915_126369 tttttatt >hb_chr3L_8639903_8639912 tttttatt >hb_chr3L_8639011_8639021 tttttatt >hb_chr3L_8639229_8639238 tttttatt >hb_chr3R_4524373_4524388 tttttttc >hb_chr2R_20730613_207306 tttttttc >hb_chr3L_8639082_8639091 tttttagc >hb_chr3L_8638365_8638375 tttttttc >hb_chr2R_5487627_5487636 tttttttc >hb_chr3L_8638597_8638607 tttttagc >hb_chr3L_8640960_8640979 tttttgac >hb_chr3L_8638532_8638542 tttttttc >hb_chr3L_8638935_8638945 tctttgtg >hb_chr3L_20630773_206307 ttttttcc >hb_chr3R_12590281_125903 tttttagt >hb_chr2R_20730468_207304 tttttcag >hb_chr2L_11456122_114561 tttttcag >hb_chr3R_12590075_125901 gttttatg >hb_chr3L_8638773_8638783 tttttagt >hb_chr2R_5487401_5487410 tctttacg >hb_chr3R_12527001_125270 tttttaat >hb_chr3R_12599167_125991 tttttaat >hb_chr3L_20631099_206311 ttttttgc >hb_chr2R_5487659_5487669 tttttaat >hb_chr3L_20630794_206308 ttttttac >hb_chr3R_4520981_4520996 gttttgcg >hb_chr3L_20630484_206305 tctttttg >hb_chr3R_12590893_125909 tgtttgtc >hb_chr3L_20630962_206309 gttttttg >hb_chr3L_20630931_206309 ttttttat >hb_chr2R_20730424_207304 tttttctt >hb_chr2R_7044665_7044674 ttttcaag >hb_chr2R_5487438_5487447 tctttgtt >hb_chr3R_12589580_125895 tatttttg >hb_chr3R_12590862_125908 tatttttg >hb_chr3R_12590784_125908 tgtttttc >hb_chr3L_8641127_8641135 tgtttttt >hb_chr3R_12636603_126366 ttcttatt >hb_chr3R_4522755_4522770 tgtttaat >hb_chr2R_7044714_7044724 tatttatt >hb_chr3R_12589644_125896 ttttcact >hb_chr3R_12590519_125905 tttttaaa >hb_chr2R_5490102_5490111 tatttttt >hb_chr3L_8641169_8641178 ttctttat >hb_chr3R_12590429_125904 ttttaaat >hb_chr2R_5490185_5490194 attttttt >hb_chr3L_20630377_206303 ttttaaaa ; ; Matrix parameters ; Columns 8 ; Rows 4 ; Alphabet a|c|g|t ; Prior a:0.366|c:0.134|g:0.134|t:0.366 ; program meme ; matrix.nb 1 ; command meme ../data/oreganno_data/processed_data/regulons_for_one_factor/hb_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 103 ; meme.llr 521 ; meme.E-value 8.6e-89 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.134 ; alphabet.size 4 ; max.bits 2 ; total.information 4.90028 ; information.per.column 0.612535 ; max.possible.info.per.col 2.00992 ; consensus.strict tttttgtG ; consensus.strict.rc Cacaaaaa ; consensus.IUPAC tttttryS ; consensus.IUPAC.rc Sryaaaaa ; consensus.regexp ttttt[ag][ct][CG] ; consensus.regexp.rc [CG][ag][ct]aaaaa ; residues.content.crude.freq a:0.1044|c:0.0558|g:0.1141|t:0.7257 ; G+C.content.crude.freq 0.169903 ; residues.content.corrected.freq a:0.1069|c:0.0566|g:0.1143|t:0.7223 ; G+C.content.corrected.freq 0.170846 ; min(P(S|M)) 9.65359e-18 ; max(P(S|M)) 0.11251 ; proba_range 0.11251 ; Wmin -25 ; Wmax 7.3 ; Wrange 32.3 ; Job started 2007_12_10.132106 ; Job done 2007_12_10.132106