; convert-matrix -v -i /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ftz.tab -from meme -to tab -return counts,info,margins,parameters,profile,sites -o html_ready/ftz_parameters.txt ; Input files ; input /Users/jturatsi/research/project/drosophila/data/oreganno_data/matrices_from_oreganno/ftz.tab ; Output files ; output html_ready/ftz_parameters.txt ; pseudo-weight 1 ; ; MATRIX 1/1 : ftz ; ; ; Matrix type: counts ; Pos | 1 2 3 4 5 6 7 8 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| a | 11 15 32 56 2 8 57 32 c | 16 35 27 7 0 5 1 4 g | 23 6 0 0 0 4 5 16 t | 14 8 5 1 62 47 1 12 ; ----- |--------|-------|-------|-------|-------|-------|-------|-------| ; c.sum | 64 64 64 64 64 64 64 64 512 ; c.max | 23 35 32 56 62 47 57 32 62 ; c.min | 11 6 0 0 0 4 1 4 0 ; Profile matrix ;pos a c g t | sum max_frq inf_sum strict IUPAC -----------1-----------2 1 11 16 23 14 | 64 0.36 0.17 g s 2 15 35 6 8 | 64 0.55 0.38 C C CC 3 32 27 0 5 | 64 0.50 0.46 c m act 4 56 7 0 1 | 64 0.88 0.72 a a aaaaaaac 5 2 0 0 62 | 64 0.97 0.91 T T TTTTTTTTTTTT 6 8 5 4 47 | 64 0.73 0.33 t t ttt 7 57 1 5 1 | 64 0.89 0.70 a a aaaaaaag 8 32 4 16 12 | 64 0.50 0.13 a r ; ; Matrix type: information ;P | 1 2 3 4 5 6 7 8 ;- |-----|----|----|----|----|----|----|----| a | -0.1 -0.1 0.2 0.8 -0.1 -0.1 0.9 0.2 c | 0.1 0.6 0.4 -0.0 -0.0 -0.1 -0.0 -0.1 g | 0.3 -0.1 -0.0 -0.0 -0.0 -0.1 -0.1 0.1 t | -0.1 -0.1 -0.1 -0.1 1.0 0.6 -0.1 -0.1 ;- |-----|----|----|----|----|----|----|----| ; i.sum | 0.2 0.4 0.5 0.7 0.9 0.3 0.7 0.1 3.8 ; i.max | 0.3 0.6 0.4 0.8 1.0 0.6 0.9 0.2 1.0 ; i.min | -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 -0.1 ; Sites 64 >ftz_chr3R_12599161_12599 gccattaa >ftz_chr3R_2684909_268493 gcaattaa >ftz_chr3R_2759093_275911 gcaattaa >ftz_chr2R_7041422_704143 ccaattag >ftz_chr3R_2823452_282346 tccattaa >ftz_chr3R_2685240_268526 tccattaa >ftz_chr3R_2684593_268461 gccattac >ftz_chr2R_20564746_20564 gccattac >ftz_chr3R_2824505_282455 cccattat >ftz_chr2R_20564632_20564 accattaa >ftz_chr3R_2685625_268563 gccatcaa >ftz_chr2R_7044642_704466 tcaattaa >ftz_chr2R_7044685_704471 tcaattaa >ftz_chr3R_2825819_282583 tcaattaa >ftz_chr2R_7041636_704164 tcaattaa >ftz_chr2R_7041491_704150 tcaattaa >ftz_chr3R_2685720_268573 gccataag >ftz_chr3R_12526853_12526 gcacttaa >ftz_chr3R_2685823_268583 gcaattac >ftz_chr2R_7041624_704163 gcacttaa >ftz_chr2R_7042027_704203 acaattag >ftz_chr3R_2827314_282737 gaaattaa >ftz_chr3R_2686061_268607 cccattga >ftz_chr3R_2684774_268479 cgcattag >ftz_chr2R_7041524_704153 ggaattaa >ftz_chr3R_2684955_268501 gcaattgg >ftz_chr2L_21841173_21841 caaattag >ftz_chr3R_12599438_12599 caaattaa >ftz_chr3R_2685573_268558 gacattat >ftz_chr3R_2686026_268604 ccaatcaa >ftz_chr3R_12599231_12599 ctcattag >ftz_chr3R_2684880_268489 tccataaa >ftz_chr2L_21840984_21840 tgcattag >ftz_chr3R_2825835_282585 acaattat >ftz_chr2R_7041393_704140 ctaattag >ftz_chr3R_2823481_282349 gacataag >ftz_chr2R_7041613_704162 accataaa >ftz_chr3R_2685777_268579 gcaatgat >ftz_chr3R_2824602_282463 aaaattag >ftz_chr3R_2827254_282726 cacatcag >ftz_chr2R_7041879_704188 cacataaa >ftz_chr3R_2824641_282467 ccaattgt >ftz_chr3R_12527016_12527 cacatgag >ftz_chr3R_12526956_12527 atcattaa >ftz_chr3R_2823468_282347 actattag >ftz_chr3R_2826123_282613 ttaattaa >ftz_chr3R_2685888_268590 gcaattca >ftz_chr2R_7042051_704206 gtcataaa >ftz_chr3R_2826055_282607 gtacttaa >ftz_chr3R_2685337_268535 ggtattaa >ftz_chr3R_2685371_268539 ttcattat >ftz_chr2L_21841081_21841 aaaattat >ftz_chr3R_2685802_268582 cgaataag >ftz_chr3R_12599333_12599 acaatcat >ftz_chr3R_2686177_268619 taaatgaa >ftz_chr3R_12599313_12599 gctaataa >ftz_chr3R_12599408_12599 taccttga >ftz_chr3R_2827240_282725 attattaa >ftz_chr2L_21841132_21841 cactttag >ftz_chr3R_2684547_268456 gacatttt >ftz_chr3R_2824588_282459 cgactgat >ftz_chr3R_2685535_268554 taccttgt >ftz_chr3R_2685478_268549 actataac >ftz_chr3R_12527038_12527 gcacacat ; ; Matrix parameters ; Columns 8 ; 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/ftz_factor_binding_sites_sequences.fa -dna -mod zoops -nmotifs 1 -revcomp -minw 6 -maxw 25 -dir /Users/jturatsi ; sites 64 ; meme.llr 253 ; meme.E-value 1.5e-07 ; pseudo 1 ; info.log.base 2.71828 ; min.prior 0.167 ; alphabet.size 4 ; max.bits 2 ; total.information 3.79039 ; information.per.column 0.473799 ; max.possible.info.per.col 1.78976 ; consensus.strict gCcaTtaa ; consensus.strict.rc ttaAtgGc ; consensus.IUPAC sCmaTtar ; consensus.IUPAC.rc ytaAtkGs ; consensus.regexp [cg]C[ac]aTta[ag] ; consensus.regexp.rc [ct]taAt[gt]G[cg] ; residues.content.crude.freq a:0.4160|c:0.1855|g:0.1055|t:0.2930 ; G+C.content.crude.freq 0.291016 ; residues.content.corrected.freq a:0.4147|c:0.1853|g:0.1064|t:0.2936 ; G+C.content.corrected.freq 0.291677 ; min(P(S|M)) 2.07004e-14 ; max(P(S|M)) 0.0254706 ; proba_range 0.0254706 ; Wmin -19 ; Wmax 7.3 ; Wrange 26.3 ; Job started 2007_12_10.132101 ; Job done 2007_12_10.132101