* scan 3.42 * 2006/10/26 01:15:47, 2006/10/26 01:15:47, furoligos define "Fur-M9-24" " w" " " " " -9.0 9.0 ribl "Fur-M9-24" * Ri 2.77 * * Ri(b,l) table is from: ** rseq 5.41 rsequence calculated from encoded sequences from: ** encode 1.41; encoding of sequences in ** * 2006/08/28 17:47:40, 2004/10/11 17:24:49, fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28 * * BOOK/INST sequences are from: * 2006/08/28 17:47:40, 2004/10/11 17:24:49, fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28 * title 'fur sites version - 1.01 of Fur-M9-24.inst 2006 Aug 28'; * * PARAMETERS FOR Ri: * -9 9 from-to * 1 column of value file * -2147483647.000000 2147483647.000000 lowest to highest Ri selected * -2147483647.000000 2147483647.000000 lowest to highest Value selected * not printing sequences to sequ * printing sequences to rixyin * -: whole line printed when partial site * using Staden's Method: when f(b,l) = 0, replace with f(b,l) = 1/(n+t), t = 2 * * i alignmenttype first, book, instructions * Ri(a,l) Ri(c,l) Ri(g,l) Ri(t,l) l a c g t -9 9 frombase, tobase 1.539033 -3.689786 -3.630893 -0.171461 -9 36 0 1 11 1.578561 -3.689786 -2.045930 -0.630893 -8 37 0 3 8 -2.045930 -2.045930 -3.630893 1.726660 -7 3 3 1 41 -0.630893 -3.630893 1.654510 -3.689786 -6 8 1 39 0 1.726660 -2.045930 -3.630893 -2.045930 -5 41 3 1 3 -0.630893 -3.689786 -0.630893 1.369107 -4 8 0 8 32 1.860961 -3.689786 -3.689786 -2.045930 -3 45 0 0 3 1.617035 -1.630893 -2.630893 -1.630893 -2 38 4 2 4 -3.689786 -0.630893 -3.630893 1.654510 -1 0 8 1 39 -0.308964 0.176462 0.176462 -0.308964 0 10 14 14 10 1.654510 -3.630893 -0.630893 -3.689786 1 39 1 8 0 -1.630893 -2.630893 -1.630893 1.617035 2 4 2 4 38 -2.045930 -3.689786 -3.689786 1.860961 3 3 0 0 45 1.369107 -0.630893 -3.689786 -0.630893 4 32 8 0 8 -2.045930 -3.630893 -2.045930 1.726660 5 3 1 3 41 -3.689786 1.654510 -3.630893 -0.630893 6 0 39 1 8 1.726660 -3.630893 -2.045930 -2.045930 7 41 1 3 3 -0.630893 -2.045930 -3.689786 1.578561 8 8 3 0 37 -0.171461 -3.630893 -3.689786 1.539033 9 11 1 0 36 * 19.684195 bits = mean (Rsequence of selected region) 4.628724 bits = standard deviation * 29.630532 bits = Ri of consensus sequence from -9 to 9 -64.371754 bits = Ri of anticonsensus sequence from -9 to 9 * -25.441307 bits = average Ri for random sequence from -9 to 9 * 48 n, number of sequences used to create the matrix * odd symmetry of the matrix * -5000.000000 Ri bound: lower bound on Ri 100.000000 Z bound: lower bound on Z 1.000000 P bound: upper probability * l extreme: char; h or l, the high or low extreme to be defined 0.0 wavelocation: real; the location in bases of the extreme 1.0 wavebit: real; the location in bits of the extreme 0.5 waveamplitude: real; the amplitude of the wave in bits 10.6 wavelength: real; the wave length of the wave in bases 0.2 0.2 0.0 dashon, dashoff, dashoffset (in bases) 0.0 thickness: real; the thickness of the cosine wave. <=0 means default . @ yoeA 19.0 +1 "Fur-M9-24" " 5.3 bits" 5.300838 -3.107413 0.000944 @ yoeA 25.0 +1 "Fur-M9-24" "27.1 bits" 27.145110 1.611873 0.053495 @ yoeA 28.0 +1 "Fur-M9-24" " 4.7 bits" 4.746056 -3.227269 0.000625 @ yoeA 31.0 +1 "Fur-M9-24" " 7.3 bits" 7.253309 -2.685597 0.003620 @ yoeA 37.0 +1 "Fur-M9-24" " 9.8 bits" 9.764625 -2.143046 0.016055 @ yoeA 43.0 +1 "Fur-M9-24" " 4.8 bits" 4.822012 -3.210860 0.000662 @ yoeA 85.0 +1 "Fur-M9-24" " 4.8 bits" 4.822012 -3.210860 0.000662 @ yoeA 91.0 +1 "Fur-M9-24" " 9.8 bits" 9.764625 -2.143046 0.016055 @ yoeA 97.0 +1 "Fur-M9-24" " 7.3 bits" 7.253309 -2.685597 0.003620 @ yoeA 100.0 +1 "Fur-M9-24" " 4.7 bits" 4.746056 -3.227269 0.000625 @ yoeA 103.0 +1 "Fur-M9-24" "27.1 bits" 27.145110 1.611873 0.053495 @ yoeA 109.0 +1 "Fur-M9-24" " 5.3 bits" 5.300838 -3.107413 0.000944 @ fepD-entS 25.0 +1 "Fur-M9-24" " 9.9 bits" 9.902602 -2.113237 0.017290 @ fepD-entS 31.0 +1 "Fur-M9-24" "20.1 bits" 20.124592 0.095144 0.462100 @ fepD-entS 37.0 +1 "Fur-M9-24" "13.0 bits" 12.961341 -1.452421 0.073192 @ fepD-entS 43.0 +1 "Fur-M9-24" " 3.6 bits" 3.551461 -3.485352 0.000246 @ fepD-entS 85.0 +1 "Fur-M9-24" " 3.6 bits" 3.551461 -3.485352 0.000246 @ fepD-entS 91.0 +1 "Fur-M9-24" "13.0 bits" 12.961341 -1.452421 0.073192 @ fepD-entS 97.0 +1 "Fur-M9-24" "20.1 bits" 20.124592 0.095144 0.462100 @ fepD-entS 103.0 +1 "Fur-M9-24" " 9.9 bits" 9.902602 -2.113237 0.017290 @ gpmA 19.0 +1 "Fur-M9-24" " 5.8 bits" 5.844609 -2.989935 0.001395 @ gpmA 22.0 +1 "Fur-M9-24" " 6.9 bits" 6.857734 -2.771058 0.002794 @ gpmA 25.0 +1 "Fur-M9-24" "27.1 bits" 27.145110 1.611873 0.053495 @ gpmA 31.0 +1 "Fur-M9-24" " 4.3 bits" 4.283622 -3.327175 0.000439 @ gpmA 73.0 +1 "Fur-M9-24" " 4.3 bits" 4.283622 -3.327175 0.000439 @ gpmA 79.0 +1 "Fur-M9-24" "27.1 bits" 27.145110 1.611873 0.053495 @ gpmA 82.0 +1 "Fur-M9-24" " 6.9 bits" 6.857734 -2.771058 0.002794 @ gpmA 85.0 +1 "Fur-M9-24" " 5.8 bits" 5.844609 -2.989935 0.001395 @ ryhB 19.0 +1 "Fur-M9-24" " 7.6 bits" 7.553426 -2.620759 0.004387 @ ryhB 25.0 +1 "Fur-M9-24" "25.3 bits" 25.345133 1.223002 0.110664 @ ryhB 31.0 +1 "Fur-M9-24" " 7.8 bits" 7.793233 -2.568950 0.005100 @ ryhB 73.0 +1 "Fur-M9-24" " 7.8 bits" 7.793233 -2.568950 0.005100 @ ryhB 79.0 +1 "Fur-M9-24" "25.3 bits" 25.345133 1.223002 0.110664 @ ryhB 85.0 +1 "Fur-M9-24" " 7.6 bits" 7.553426 -2.620759 0.004387 @ fhuA 25.0 +1 "Fur-M9-24" "10.6 bits" 10.562841 -1.970598 0.024385 @ fhuA 31.0 +1 "Fur-M9-24" "19.9 bits" 19.862049 0.038424 0.484675 @ fhuA 37.0 +1 "Fur-M9-24" " 5.4 bits" 5.359731 -3.094690 0.000985 @ fhuA 79.0 +1 "Fur-M9-24" " 5.4 bits" 5.359731 -3.094690 0.000985 @ fhuA 85.0 +1 "Fur-M9-24" "19.9 bits" 19.862049 0.038424 0.484675 @ fhuA 91.0 +1 "Fur-M9-24" "10.6 bits" 10.562841 -1.970598 0.024385 @ nohA 19.0 +1 "Fur-M9-24" "12.7 bits" 12.689814 -1.511082 0.065384 @ nohA 25.0 +1 "Fur-M9-24" "20.8 bits" 20.836119 0.248864 0.401733 @ nohA 79.0 +1 "Fur-M9-24" "20.8 bits" 20.836119 0.248864 0.401733 @ nohA 85.0 +1 "Fur-M9-24" "12.7 bits" 12.689814 -1.511082 0.065384 @ oppA 25.0 +1 "Fur-M9-24" " 9.6 bits" 9.564414 -2.186300 0.014397 @ oppA 31.0 +1 "Fur-M9-24" "21.2 bits" 21.163066 0.319499 0.374674 @ oppA 85.0 +1 "Fur-M9-24" "21.2 bits" 21.163066 0.319499 0.374674 @ oppA 91.0 +1 "Fur-M9-24" " 9.6 bits" 9.564414 -2.186300 0.014397 @ gspC 22.0 +1 "Fur-M9-24" " 3.5 bits" 3.519678 -3.492219 0.000240 @ gspC 28.0 +1 "Fur-M9-24" "14.3 bits" 14.304473 -1.162247 0.122568 @ gspC 76.0 +1 "Fur-M9-24" "14.3 bits" 14.304473 -1.162247 0.122568 @ gspC 82.0 +1 "Fur-M9-24" " 3.5 bits" 3.519678 -3.492219 0.000240 @ yhaU 22.0 +1 "Fur-M9-24" " 8.6 bits" 8.567583 -2.401658 0.008160 @ yhaU 25.0 +1 "Fur-M9-24" "11.0 bits" 11.041513 -1.867185 0.030938 @ yhaU 28.0 +1 "Fur-M9-24" "14.3 bits" 14.266622 -1.170425 0.120915 @ yhaU 31.0 +1 "Fur-M9-24" " 6.6 bits" 6.570278 -2.833160 0.002305 @ yhaU 79.0 +1 "Fur-M9-24" " 6.6 bits" 6.570278 -2.833160 0.002305 @ yhaU 82.0 +1 "Fur-M9-24" "14.3 bits" 14.266622 -1.170425 0.120915 @ yhaU 85.0 +1 "Fur-M9-24" "11.0 bits" 11.041513 -1.867185 0.030938 @ yhaU 88.0 +1 "Fur-M9-24" " 8.6 bits" 8.567583 -2.401658 0.008160 @ yahA 25.0 +1 "Fur-M9-24" "14.3 bits" 14.330667 -1.156588 0.123720 @ yahA 31.0 +1 "Fur-M9-24" "16.6 bits" 16.588191 -0.668868 0.251790 @ yahA 85.0 +1 "Fur-M9-24" "16.6 bits" 16.588191 -0.668868 0.251790 @ yahA 91.0 +1 "Fur-M9-24" "14.3 bits" 14.330667 -1.156588 0.123720 @ fadD 19.0 +1 "Fur-M9-24" " 3.8 bits" 3.779920 -3.435996 0.000295 @ fadD 25.0 +1 "Fur-M9-24" "23.0 bits" 22.961620 0.708062 0.239453 @ fadD 79.0 +1 "Fur-M9-24" "23.0 bits" 22.961620 0.708062 0.239453 @ fadD 85.0 +1 "Fur-M9-24" " 3.8 bits" 3.779920 -3.435996 0.000295 @ exbB 24.0 +1 "Fur-M9-24" "18.9 bits" 18.887751 -0.172066 0.431693 @ exbB 36.0 +1 "Fur-M9-24" " 3.2 bits" 3.205488 -3.560097 0.000185 @ exbB 76.0 +1 "Fur-M9-24" " 3.2 bits" 3.205488 -3.560097 0.000185 @ exbB 88.0 +1 "Fur-M9-24" "18.9 bits" 18.887751 -0.172066 0.431693 @ fhuF 16.0 +1 "Fur-M9-24" "22.1 bits" 22.090320 0.519825 0.301593 @ fhuF 33.0 +1 "Fur-M9-24" "22.4 bits" 22.386711 0.583858 0.279658 @ fhuF 39.0 +1 "Fur-M9-24" "15.9 bits" 15.947184 -0.807352 0.209732 @ fhuF 75.0 +1 "Fur-M9-24" "15.9 bits" 15.947184 -0.807352 0.209732 @ fhuF 81.0 +1 "Fur-M9-24" "22.4 bits" 22.386711 0.583858 0.279658 @ fhuF 98.0 +1 "Fur-M9-24" "22.1 bits" 22.090320 0.519825 0.301593