define "NC_000913.ydaY" "-" "<]" "[>" 0 359 @ NC_000913 1423645 1 "NC_000913.ydaY" "" define "NC_000913.ynaA" "-" "<]" "[>" 0 1028 @ NC_000913 1424478 1 "NC_000913.ynaA" "" * orf 1.24 * 2007/12/07 21:10:06, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 ydaY_ynaA define "orf" "#" "<]" "[>" 0.0 2.0 * multiscan 3.94 define "ir" " w" " " " " -3.0 14.0 ribl "ir" * Ri 2.66 * * Ri(b,l) table is from: ** rseq 5.39 rsequence calculated from encoded sequences from: ** encode 1.40; encoding of sequences in ** * 2001/08/15 12:20:50, 1999/05/04 14:41:13, inst * * BOOK/INST sequences are from: * 2001/08/15 12:20:50, 1999/05/04 14:41:13, inst * title "inst"; * * PARAMETERS FOR Ri: * -3 14 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 -3 14 frombase, tobase 0.763679 -0.567865 -0.078059 -0.559121 -3 1656 658 924 662 0.060296 0.121401 -0.896385 0.412266 -2 1017 1061 524 1298 0.115951 0.077219 -0.700990 0.315744 -1 1057 1029 600 1214 1.864201 -9.929808 -1.710640 -4.285952 0 3551 1 298 50 -9.930548 -9.930548 -9.930548 1.999450 1 0 0 0 3900 -9.930548 -9.930548 1.999450 -9.930548 2 0 0 3900 0 0.980085 -0.684256 -0.271597 -0.797951 3 1924 607 808 561 0.577986 0.185235 -0.610136 -0.486865 4 1456 1109 639 696 0.421131 -0.371388 -0.649038 0.320490 5 1306 754 622 1218 0.761063 -0.222449 -0.164937 -0.850324 6 1653 836 870 541 0.760190 -0.361852 -0.990229 0.033088 7 1652 759 491 998 0.327579 -0.404288 -0.227636 0.181327 8 1224 737 833 1106 0.511061 -0.074940 -0.356161 -0.246814 9 1390 926 762 822 0.320490 -0.232841 -1.013929 0.489098 10 1218 830 483 1369 0.361362 -0.236321 -0.539639 0.235099 11 1253 828 671 1148 0.516241 -0.161624 -0.127292 -0.398427 12 1395 872 893 740 0.262484 -0.145174 -1.056364 0.499598 13 1170 882 469 1379 0.129536 -0.173252 -0.456103 0.365961 14 1067 865 711 1257 * 6.721797 bits = mean (Rsequence of selected region) 2.259310 bits = standard deviation * 13.926145 bits = Ri of consensus sequence from -3 to 14 -40.078734 bits = Ri of anticonsensus sequence from -3 to 14 * -18.663794 bits = average Ri for random sequence from -3 to 14 * 3900 n, number of sequences used to create the matrix * asymmetric 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 0.4 0.4 0.0 dashon, dashoff, dashoffset (in bases) 0.0 thickness: real; the thickness of the cosine wave. <=0 means default . * multiscan 3.94 define "sd" " w" " " " " -12.0 4.0 ribl "sd" * Ri 2.66 * * Ri(b,l) table is from: ** rseq 5.39 rsequence calculated from encoded sequences from: ** encode 1.40; encoding of sequences in ** * 2001/08/15 12:19:55, 1999/05/04 14:41:13, inst * * BOOK/INST sequences are from: * 2001/08/15 12:19:55, 1999/05/04 14:41:13, inst * title "inst"; * * PARAMETERS FOR Ri: * -12 4 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 -12 4 frombase, tobase 0.217397 -0.146810 -0.422014 0.246365 -12 1134 881 728 1157 0.214850 -0.225905 -0.493097 0.347479 -11 1132 834 693 1241 0.297808 -0.264472 -0.556943 0.329935 -10 1199 812 663 1226 0.335807 -0.201888 -0.667714 0.307402 -9 1231 848 614 1207 0.365961 -0.269813 -0.732592 0.354437 -8 1257 809 587 1247 0.390992 -0.260923 -0.644406 0.278426 -7 1279 814 624 1183 0.470004 -0.384844 -0.663022 0.282080 -6 1351 747 616 1186 0.534737 -0.443979 -0.628312 0.223744 -5 1413 717 631 1139 0.518308 -0.482725 -0.693794 0.301413 -4 1397 698 603 1202 0.728403 0.107739 0.058876 -2.168257 -3 1616 1051 1016 217 1.215487 -1.382914 -0.412139 -0.885414 -2 2265 374 733 528 -1.993170 -4.122453 1.824244 -2.749899 -1 245 56 3454 145 -9.930548 -9.930548 1.999450 -9.930548 0 0 0 3900 0 1.567045 -1.677143 -9.930548 -0.468329 1 2890 305 0 705 0.187835 -1.739984 0.884774 -0.486865 2 1111 292 1801 696 0.657969 -0.888149 -0.404288 0.169539 3 1539 527 737 1097 0.550982 -0.390650 -0.468329 0.067371 4 1429 744 705 1022 * 5.801573 bits = mean (Rsequence of selected region) 2.550546 bits = standard deviation * 12.967941 bits = Ri of consensus sequence from -12 to 4 -36.133077 bits = Ri of anticonsensus sequence from -12 to 4 * -13.026643 bits = average Ri for random sequence from -12 to 4 * 3900 n, number of sequences used to create the matrix * asymmetric 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 0.4 0.4 0.0 dashon, dashoff, dashoffset (in bases) 0.0 thickness: real; the thickness of the cosine wave. <=0 means default . @ NC_000913 1424212.0 +1 "ir" "ydaY_ynaA+" 7.691041 0.429000 0.333962 @ NC_000913 1424221.0 +1 "orf" "4 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 1424205.0 +1 "sd" "" 2.881701 -1.144803 0.126145 define "sd-(7)-ir 1424212 Gap" "-" "{}" "{}" 0.0 7.0 @ NC_000913 1424205.0 +1 "sd-(7)-ir 1424212 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424212 ydaY_ynaA+ total 6.9" "-" "||" "||" -7.0 0.0 @ NC_000913 1424212.0 +1 "sd-ir 1424212 ydaY_ynaA+ total 6.9" "bits" 6.869713 4.000000 1424221.000000 0.000000 -> [ir], [sd] @ NC_000913 1424303.0 +1 "ir" "ydaY_ynaA+" 2.661989 -1.796924 0.036174 @ NC_000913 1424345.0 +1 "orf" "15 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 1424298.0 +1 "sd" "" 8.531695 1.070407 0.142218 define "sd-(5)-ir 1424303 Gap" "-" "{}" "{}" 0.0 5.0 @ NC_000913 1424298.0 +1 "sd-(5)-ir 1424303 Gap" "5.4 bits" 5.408286 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424303 ydaY_ynaA+ total 5.8" "-" "||" "||" -5.0 0.0 @ NC_000913 1424303.0 +1 "sd-ir 1424303 ydaY_ynaA+ total 5.8" "bits" 5.785398 15.000000 1424345.000000 1.000000 -> [ir], [sd] @ NC_000913 1424305.0 +1 "ir" "ydaY_ynaA+" 0.303811 -2.840684 0.002251 @ NC_000913 1424317.0 +1 "orf" "5 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 1424298.0 +1 "sd" "" 8.531695 1.070407 0.142218 define "sd-(7)-ir 1424305 Gap" "-" "{}" "{}" 0.0 7.0 @ NC_000913 1424298.0 +1 "sd-(7)-ir 1424305 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424305 ydaY_ynaA+ total 5.1" "-" "||" "||" -7.0 0.0 @ NC_000913 1424305.0 +1 "sd-ir 1424305 ydaY_ynaA+ total 5.1" "bits" 5.132477 5.000000 1424317.000000 0.000000 -> [ir], [sd] @ NC_000913 1424307.0 +1 "ir" "ydaY_ynaA+" 1.220069 -2.435136 0.007443 @ NC_000913 1424310.0 +1 "orf" "2 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 1424298.0 +1 "sd" "" 8.531695 1.070407 0.142218 define "sd-(9)-ir 1424307 Gap" "-" "{}" "{}" 0.0 9.0 @ NC_000913 1424298.0 +1 "sd-(9)-ir 1424307 Gap" "2.3 bits" 2.279003 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424307 ydaY_ynaA+ total 7.5" "-" "||" "||" -9.0 0.0 @ NC_000913 1424307.0 +1 "sd-ir 1424307 ydaY_ynaA+ total 7.5" "bits" 7.472761 2.000000 1424310.000000 0.000000 -> [ir], [sd] @ NC_000913 1424347.0 +1 "ir" "ydaY_ynaA+" 5.043415 -0.742874 0.228779 @ NC_000913 1424431.0 +1 "orf" "29 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 1424339.0 +1 "sd" "" 2.510646 -1.290283 0.098476 define "sd-(8)-ir 1424347 Gap" "-" "{}" "{}" 0.0 8.0 @ NC_000913 1424339.0 +1 "sd-(8)-ir 1424347 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424347 ydaY_ynaA+ total 5.1" "-" "||" "||" -8.0 0.0 @ NC_000913 1424347.0 +1 "sd-ir 1424347 ydaY_ynaA+ total 5.1" "bits" 5.108042 29.000000 1424431.000000 1.000000 -> [ir], [sd] @ NC_000913 1424478.0 +1 "ir" "ydaY_ynaA+" 6.987340 0.117533 0.453219 @ NC_000913 1424466.0 +1 "sd" "" 8.567845 1.084580 0.139054 define "sd-(12)-ir 1424478 Gap" "-" "{}" "{}" 0.0 12.0 @ NC_000913 1424466.0 +1 "sd-(12)-ir 1424478 Gap" "4.0 bits" 3.966064 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 1424478 ydaY_ynaA+ total 11.6" "-" "||" "||" -12.0 0.0 @ NC_000913 1424478.0 +1 "sd-ir 1424478 ydaY_ynaA+ total 11.6" "bits" 11.589121 0.000000 0.000000 0.000000 -> [ir], [sd] * * 1 sequences are in the genomebook * 5 ORFs are in the genomebook * multiscan 3.94 * 2007/12/07 21:10:06, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 ydaY_ynaA define "p10" " w" " " " " -1.0 4.0 ribl "p10" * Ri 2.69 * * Ri(b,l) table is from: ** rseq 5.39 rsequence calculated from encoded sequences from: ** encode 1.41; encoding of sequences in ** * 2003/04/23 22:04:54, 1999/05/04 14:41:13, inst * * BOOK/INST sequences are from: * 2003/04/23 22:04:54, 1999/05/04 14:41:13, inst * title "inst"; * * PARAMETERS FOR Ri: * -1 4 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 -1 4 frombase, tobase -2.129296 -1.226594 -2.404931 1.650922 -1 23 43 19 316 1.890173 -6.660036 -5.067896 -2.009002 0 373 0 3 25 0.061387 -0.608464 -0.980433 0.830957 1 105 66 51 179 1.061387 -0.980433 -0.871499 -0.243467 2 210 51 55 85 1.061387 -0.052946 -1.443405 -0.819968 3 210 97 37 57 -6.660036 -2.404931 -3.193427 1.882417 4 0 19 11 371 * 4.783894 bits = mean (Rsequence of selected region) 2.128061 bits = standard deviation * 8.377244 bits = Ri of consensus sequence from -1 to 4 -19.129274 bits = Ri of anticonsensus sequence from -1 to 4 * -7.329533 bits = average Ri for random sequence from -1 to 4 * 401 n, number of sequences used to create the matrix * asymmetric 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 4.0 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 0.4 0.4 0.0 dashon, dashoff, dashoffset (in bases) 0.0 thickness: real; the thickness of the cosine wave. <=0 means default . * multiscan 3.94 * 2007/12/07 21:10:06, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 ydaY_ynaA define "p35" " w" " " " " -1.0 4.0 ribl "p35" * Ri 2.69 * * Ri(b,l) table is from: ** rseq 5.39 rsequence calculated from encoded sequences from: ** encode 1.41; encoding of sequences in ** * 2003/04/23 22:05:06, 1999/05/04 14:41:13, inst * * BOOK/INST sequences are from: * 2003/04/23 22:05:06, 1999/05/04 14:41:13, inst * title "inst"; * * PARAMETERS FOR Ri: * -1 4 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 -1 4 frombase, tobase -1.260541 -6.660036 -6.660036 1.834982 -1 42 0 0 359 -2.482933 -6.660036 -0.482933 1.627912 0 18 0 72 311 -2.482933 -4.067896 1.277879 0.402424 1 18 6 244 133 0.781770 0.423957 -6.660036 -0.113700 2 173 135 0 93 0.496889 0.476425 -1.330930 -0.349078 3 142 140 40 79 0.413231 -1.009002 -0.482933 0.527051 4 134 50 72 145 * 4.024391 bits = mean (Rsequence of selected region) 1.878152 bits = standard deviation * 6.546482 bits = Ri of consensus sequence from -1 to 4 -26.387937 bits = Ri of anticonsensus sequence from -1 to 4 * -8.110127 bits = average Ri for random sequence from -1 to 4 * 401 n, number of sequences used to create the matrix * asymmetric 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 * h extreme: char; h or l, the high or low extreme to be defined -1.0 wavelocation: real; the location in bases of the extreme 2.0 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 0.4 0.4 0.0 dashon, dashoff, dashoffset (in bases) 0.0 thickness: real; the thickness of the cosine wave. <=0 means default . @ NC_000913 1424210.0 +1 "p10" " 0.7 bits" 0.650474 -1.942341 0.026048 @ NC_000913 1424188.0 +1 "p35" " 6.2 bits" 6.168206 1.141449 0.126842 define "p35-(22)-p10 1424210 Gap" "-" "{}" "{}" 0.0 22 @ NC_000913 1424188.0 1 "p35-(22)-p10 1424210 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 1424210 total 4.5" "-" "||" "||" -22 0 @ NC_000913 1424210 1 "p35-p10 1424210 total 4.5" "bits" 4.484155 0.000000 0.000000 @ NC_000913 1424216.0 +1 "p10" " 2.7 bits" 2.715670 -0.971882 0.165555 @ NC_000913 1424193.0 +1 "p35" " 3.3 bits" 3.289008 -0.391546 0.347697 define "p35-(23)-p10 1424216 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 1424193.0 1 "p35-(23)-p10 1424216 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 1424216 total 4.6" "-" "||" "||" -23 0 @ NC_000913 1424216 1 "p35-p10 1424216 total 4.6" "bits" 4.567394 0.000000 0.000000 @ NC_000913 1424356.0 +1 "p10" " 4.5 bits" 4.478068 -0.143711 0.442864 @ NC_000913 1424333.0 +1 "p35" " 1.1 bits" 1.128660 -1.541798 0.061561 define "p35-(23)-p10 1424356 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 1424333.0 1 "p35-(23)-p10 1424356 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 1424356 total 4.2" "-" "||" "||" -23 0 @ NC_000913 1424356 1 "p35-p10 1424356 total 4.2" "bits" 4.169444 0.000000 0.000000 @ NC_000913 1424417.0 +1 "p10" " 5.6 bits" 5.632968 0.398990 0.344950 @ NC_000913 1424396.0 +1 "p35" " 4.1 bits" 4.057361 0.017554 0.492997 define "p35-(21)-p10 1424417 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 1424396.0 1 "p35-(21)-p10 1424417 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 1424417 total 6.4" "-" "||" "||" -21 0 @ NC_000913 1424417 1 "p35-p10 1424417 total 6.4" "bits" 6.391428 0.000000 0.000000 @ NC_000913 1424420.0 +1 "p10" " 7.1 bits" 7.072389 1.075390 0.141100 @ NC_000913 1424396.0 +1 "p35" " 4.1 bits" 4.057361 0.017554 0.492997 define "p35-(24)-p10 1424420 Gap" "-" "{}" "{}" 0.0 24 @ NC_000913 1424396.0 1 "p35-(24)-p10 1424420 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 1424420 total 8.7" "-" "||" "||" -24 0 @ NC_000913 1424420 1 "p35-p10 1424420 total 8.7" "bits" 8.702116 0.000000 0.000000 * petalfeatures: color rectangle features for the lister program * version = 2.16 of mkpetals 2007 Dec 07 * format: * el: integer; (* edgelinewidth: edge linewidth (integer) *) * c : char; (* color kind: how color is defined: r for RGB, h for HSB *) * (* ---------------------------------------------- *) * eh: real; (* edgeh: edge hue OR red *) * es: real; (* edges: edge saturation OR blue *) * eb: real; (* edgeb: edge brightness OR green *) * (* ---------------------------------------------- *) * fh: real; (* fillh: fill hue OR red *) * fs: real; (* fills: fill saturation OR blue *) * fb: real; (* fillb: fill brightness OR green *) * (* ---------------------------------------------- *) * spare: real; (* spare *) * "name" el c eh es eb fh fs fb spare * * Determine rgb for full saturation: * hsb is 0.000 1 1.0 * rgb is 1 0 0 petal "ir" -1 h 1.0 0.0 1.0 0.000 -1 1.0 0.0 * * Determine rgb for full saturation: * hsb is 0.250 1 1.0 * rgb is 0.499997914 1 0 petal "sd" -1 h 1.0 0.0 1.0 0.250 -1 1.0 0.0 * * Determine rgb for full saturation: * hsb is 0.500 1 1.0 * rgb is 0 1 1 petal "p10" -1 h 1.0 0.0 1.0 0.500 -1 1.0 0.0 * * Determine rgb for full saturation: * hsb is 0.750 1 1.0 * rgb is 0.499998093 0 1 petal "p35" -1 h 1.0 0.0 1.0 0.750 -1 1.0 0.0