define "NC_000913.lrhA" "-" "<]" "[>" 0 938 @ NC_000913 2404663 -1 "NC_000913.lrhA" "" define "NC_000913.yfbQ" "-" "<]" "[>" 0 1217 @ NC_000913 2405583 1 "NC_000913.yfbQ" "" * orf 1.24 * 2007/12/07 19:07:27, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 lrhA_yfbQ 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 2405423.0 -1 "ir" "lrhA_yfbQ-" 4.950160 -0.784150 0.216476 @ NC_000913 2405390.0 -1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405432.0 -1 "sd" "" 4.725605 -0.421858 0.336564 define "sd-(9)-ir 2405423 Gap" "-" "}{" "}{" 0.0 -9.0 @ NC_000913 2405423.0 -1 "sd-(9)-ir 2405423 Gap" "2.3 bits" 2.279003 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405423 lrhA_yfbQ- total 7.4" "-" "||" "||" 0.0 9.0 @ NC_000913 2405432.0 -1 "sd-ir 2405423 lrhA_yfbQ- total 7.4" "bits" 7.396762 12.000000 2405390.000000 1.000000 -> [ir], [sd] @ NC_000913 2405412.0 -1 "ir" "lrhA_yfbQ-" 5.025883 -0.750634 0.226437 @ NC_000913 2405370.0 -1 "orf" "15 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405418.0 -1 "sd" "" 8.887219 1.209798 0.113178 define "sd-(6)-ir 2405412 Gap" "-" "}{" "}{" 0.0 -6.0 @ NC_000913 2405412.0 -1 "sd-(6)-ir 2405412 Gap" "4.3 bits" 4.339391 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405412 lrhA_yfbQ- total 9.6" "-" "||" "||" 0.0 6.0 @ NC_000913 2405418.0 -1 "sd-ir 2405412 lrhA_yfbQ- total 9.6" "bits" 9.573711 15.000000 2405370.000000 1.000000 -> [ir], [sd] @ NC_000913 2405403.0 -1 "ir" "lrhA_yfbQ-" 5.551280 -0.518086 0.302199 @ NC_000913 2405370.0 -1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405418.0 -1 "sd" "" 8.887219 1.209798 0.113178 define "sd-(15)-ir 2405403 Gap" "-" "}{" "}{" 0.0 -15.0 @ NC_000913 2405403.0 -1 "sd-(15)-ir 2405403 Gap" "6.0 bits" 6.001111 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405403 lrhA_yfbQ- total 8.4" "-" "||" "||" 0.0 15.0 @ NC_000913 2405418.0 -1 "sd-ir 2405403 lrhA_yfbQ- total 8.4" "bits" 8.437388 12.000000 2405370.000000 1.000000 -> [ir], [sd] @ NC_000913 2405325.0 -1 "ir" "lrhA_yfbQ-" 7.536623 0.360653 0.359180 @ NC_000913 2405304.0 -1 "orf" "8 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405333.0 -1 "sd" "" 0.562816 -2.053975 0.019989 define "sd-(8)-ir 2405325 Gap" "-" "}{" "}{" 0.0 -8.0 @ NC_000913 2405325.0 -1 "sd-(8)-ir 2405325 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405325 lrhA_yfbQ- total 5.7" "-" "||" "||" 0.0 8.0 @ NC_000913 2405333.0 -1 "sd-ir 2405325 lrhA_yfbQ- total 5.7" "bits" 5.653420 8.000000 2405304.000000 0.000000 -> [ir], [sd] @ NC_000913 2405302.0 -1 "ir" "lrhA_yfbQ-" 6.886270 0.072798 0.470983 @ NC_000913 2405263.0 -1 "orf" "14 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405312.0 -1 "sd" "" 1.420883 -1.717550 0.042939 define "sd-(10)-ir 2405302 Gap" "-" "}{" "}{" 0.0 -10.0 @ NC_000913 2405302.0 -1 "sd-(10)-ir 2405302 Gap" "2.7 bits" 2.719960 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405302 lrhA_yfbQ- total 5.6" "-" "||" "||" 0.0 10.0 @ NC_000913 2405312.0 -1 "sd-ir 2405302 lrhA_yfbQ- total 5.6" "bits" 5.587193 14.000000 2405263.000000 1.000000 -> [ir], [sd] @ NC_000913 2405292.0 -1 "ir" "lrhA_yfbQ-" 6.707911 -0.006146 0.497548 @ NC_000913 2405190.0 -1 "orf" "35 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405300.0 -1 "sd" "" 4.034638 -0.692767 0.244228 define "sd-(8)-ir 2405292 Gap" "-" "}{" "}{" 0.0 -8.0 @ NC_000913 2405292.0 -1 "sd-(8)-ir 2405292 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405292 lrhA_yfbQ- total 8.3" "-" "||" "||" 0.0 8.0 @ NC_000913 2405300.0 -1 "sd-ir 2405292 lrhA_yfbQ- total 8.3" "bits" 8.296530 35.000000 2405190.000000 1.000000 -> [ir], [sd] @ NC_000913 2405289.0 -1 "ir" "lrhA_yfbQ-" 7.010637 0.127844 0.449136 @ NC_000913 2405190.0 -1 "orf" "34 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405300.0 -1 "sd" "" 4.034638 -0.692767 0.244228 define "sd-(11)-ir 2405289 Gap" "-" "}{" "}{" 0.0 -11.0 @ NC_000913 2405289.0 -1 "sd-(11)-ir 2405289 Gap" "3.0 bits" 3.043105 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405289 lrhA_yfbQ- total 8.0" "-" "||" "||" 0.0 11.0 @ NC_000913 2405300.0 -1 "sd-ir 2405289 lrhA_yfbQ- total 8.0" "bits" 8.002170 34.000000 2405190.000000 1.000000 -> [ir], [sd] @ NC_000913 2405233.0 -1 "ir" "lrhA_yfbQ-" 2.161076 -2.018634 0.021763 @ NC_000913 2405197.0 -1 "orf" "13 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405241.0 -1 "sd" "" 5.625370 -0.069084 0.472461 define "sd-(8)-ir 2405233 Gap" "-" "}{" "}{" 0.0 -8.0 @ NC_000913 2405233.0 -1 "sd-(8)-ir 2405233 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405233 lrhA_yfbQ- total 5.3" "-" "||" "||" 0.0 8.0 @ NC_000913 2405241.0 -1 "sd-ir 2405233 lrhA_yfbQ- total 5.3" "bits" 5.340427 13.000000 2405197.000000 1.000000 -> [ir], [sd] @ NC_000913 2405195.0 -1 "ir" "lrhA_yfbQ-" 8.778956 0.910525 0.181273 @ NC_000913 2405174.0 -1 "orf" "8 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405201.0 -1 "sd" "" 6.470957 0.262447 0.396488 define "sd-(6)-ir 2405195 Gap" "-" "}{" "}{" 0.0 -6.0 @ NC_000913 2405195.0 -1 "sd-(6)-ir 2405195 Gap" "4.3 bits" 4.339391 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405195 lrhA_yfbQ- total 10.9" "-" "||" "||" 0.0 6.0 @ NC_000913 2405201.0 -1 "sd-ir 2405195 lrhA_yfbQ- total 10.9" "bits" 10.910522 8.000000 2405174.000000 0.000000 -> [ir], [sd] @ NC_000913 2405191.0 -1 "ir" "lrhA_yfbQ-" 5.739002 -0.434998 0.331782 @ NC_000913 2405110.0 -1 "orf" "28 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405201.0 -1 "sd" "" 6.470957 0.262447 0.396488 define "sd-(10)-ir 2405191 Gap" "-" "}{" "}{" 0.0 -10.0 @ NC_000913 2405191.0 -1 "sd-(10)-ir 2405191 Gap" "2.7 bits" 2.719960 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405191 lrhA_yfbQ- total 9.5" "-" "||" "||" 0.0 10.0 @ NC_000913 2405201.0 -1 "sd-ir 2405191 lrhA_yfbQ- total 9.5" "bits" 9.489999 28.000000 2405110.000000 1.000000 -> [ir], [sd] @ NC_000913 2405185.0 -1 "ir" "lrhA_yfbQ-" 7.391749 0.296529 0.383413 @ NC_000913 2405110.0 -1 "orf" "26 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405201.0 -1 "sd" "" 6.470957 0.262447 0.396488 define "sd-(16)-ir 2405185 Gap" "-" "}{" "}{" 0.0 -16.0 @ NC_000913 2405185.0 -1 "sd-(16)-ir 2405185 Gap" "6.4 bits" 6.408286 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405185 lrhA_yfbQ- total 7.5" "-" "||" "||" 0.0 16.0 @ NC_000913 2405201.0 -1 "sd-ir 2405185 lrhA_yfbQ- total 7.5" "bits" 7.454420 26.000000 2405110.000000 1.000000 -> [ir], [sd] @ NC_000913 2405182.0 -1 "ir" "lrhA_yfbQ-" 7.860212 0.503877 0.307174 @ NC_000913 2405110.0 -1 "orf" "25 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405189.0 -1 "sd" "" 4.935383 -0.339610 0.367075 define "sd-(7)-ir 2405182 Gap" "-" "}{" "}{" 0.0 -7.0 @ NC_000913 2405182.0 -1 "sd-(7)-ir 2405182 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405182 lrhA_yfbQ- total 9.1" "-" "||" "||" 0.0 7.0 @ NC_000913 2405189.0 -1 "sd-ir 2405182 lrhA_yfbQ- total 9.1" "bits" 9.092566 25.000000 2405110.000000 1.000000 -> [ir], [sd] @ NC_000913 2405143.0 -1 "ir" "lrhA_yfbQ-" 4.495145 -0.985545 0.162178 @ NC_000913 2405110.0 -1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405149.0 -1 "sd" "" 7.835949 0.797624 0.212544 define "sd-(6)-ir 2405143 Gap" "-" "}{" "}{" 0.0 -6.0 @ NC_000913 2405143.0 -1 "sd-(6)-ir 2405143 Gap" "4.3 bits" 4.339391 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405143 lrhA_yfbQ- total 8.0" "-" "||" "||" 0.0 6.0 @ NC_000913 2405149.0 -1 "sd-ir 2405143 lrhA_yfbQ- total 8.0" "bits" 7.991703 12.000000 2405110.000000 1.000000 -> [ir], [sd] @ NC_000913 2405141.0 -1 "ir" "lrhA_yfbQ-" 4.922424 -0.796426 0.212892 @ NC_000913 2405105.0 -1 "orf" "13 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405149.0 -1 "sd" "" 7.835949 0.797624 0.212544 define "sd-(8)-ir 2405141 Gap" "-" "}{" "}{" 0.0 -8.0 @ NC_000913 2405141.0 -1 "sd-(8)-ir 2405141 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405141 lrhA_yfbQ- total 10.3" "-" "||" "||" 0.0 8.0 @ NC_000913 2405149.0 -1 "sd-ir 2405141 lrhA_yfbQ- total 10.3" "bits" 10.312354 13.000000 2405105.000000 1.000000 -> [ir], [sd] @ NC_000913 2405115.0 -1 "ir" "lrhA_yfbQ-" 3.714330 -1.331144 0.091571 @ NC_000913 2405100.0 -1 "orf" "6 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405122.0 -1 "sd" "" 6.266288 0.182202 0.427712 define "sd-(7)-ir 2405115 Gap" "-" "}{" "}{" 0.0 -7.0 @ NC_000913 2405115.0 -1 "sd-(7)-ir 2405115 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405115 lrhA_yfbQ- total 6.3" "-" "||" "||" 0.0 7.0 @ NC_000913 2405122.0 -1 "sd-ir 2405115 lrhA_yfbQ- total 6.3" "bits" 6.277589 6.000000 2405100.000000 0.000000 -> [ir], [sd] @ NC_000913 2405042.0 -1 "ir" "lrhA_yfbQ-" 5.427705 -0.572782 0.283396 @ NC_000913 2405033.0 -1 "orf" "4 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2405056.0 -1 "sd" "" 8.268335 0.967151 0.166734 define "sd-(14)-ir 2405042 Gap" "-" "}{" "}{" 0.0 -14.0 @ NC_000913 2405042.0 -1 "sd-(14)-ir 2405042 Gap" "4.9 bits" 4.898425 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2405042 lrhA_yfbQ- total 8.8" "-" "||" "||" 0.0 14.0 @ NC_000913 2405056.0 -1 "sd-ir 2405042 lrhA_yfbQ- total 8.8" "bits" 8.797615 4.000000 2405033.000000 0.000000 -> [ir], [sd] @ NC_000913 2404890.0 -1 "ir" "lrhA_yfbQ-" 5.827930 -0.395637 0.346186 @ NC_000913 2404815.0 -1 "orf" "26 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2404897.0 -1 "sd" "" 4.584739 -0.477088 0.316650 define "sd-(7)-ir 2404890 Gap" "-" "}{" "}{" 0.0 -7.0 @ NC_000913 2404890.0 -1 "sd-(7)-ir 2404890 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2404890 lrhA_yfbQ- total 6.7" "-" "||" "||" 0.0 7.0 @ NC_000913 2404897.0 -1 "sd-ir 2404890 lrhA_yfbQ- total 6.7" "bits" 6.709640 26.000000 2404815.000000 1.000000 -> [ir], [sd] @ NC_000913 2404818.0 -1 "ir" "lrhA_yfbQ-" 5.454268 -0.561025 0.287390 @ NC_000913 2404815.0 -1 "orf" "2 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2404823.0 -1 "sd" "" 5.588039 -0.083721 0.466639 define "sd-(5)-ir 2404818 Gap" "-" "}{" "}{" 0.0 -5.0 @ NC_000913 2404818.0 -1 "sd-(5)-ir 2404818 Gap" "5.4 bits" 5.408286 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2404818 lrhA_yfbQ- total 5.6" "-" "||" "||" 0.0 5.0 @ NC_000913 2404823.0 -1 "sd-ir 2404818 lrhA_yfbQ- total 5.6" "bits" 5.634021 2.000000 2404815.000000 0.000000 -> [ir], [sd] @ NC_000913 2404816.0 -1 "ir" "lrhA_yfbQ-" 3.445967 -1.449925 0.073540 @ NC_000913 2404759.0 -1 "orf" "20 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2404823.0 -1 "sd" "" 5.588039 -0.083721 0.466639 define "sd-(7)-ir 2404816 Gap" "-" "}{" "}{" 0.0 -7.0 @ NC_000913 2404816.0 -1 "sd-(7)-ir 2404816 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2404816 lrhA_yfbQ- total 5.3" "-" "||" "||" 0.0 7.0 @ NC_000913 2404823.0 -1 "sd-ir 2404816 lrhA_yfbQ- total 5.3" "bits" 5.330977 20.000000 2404759.000000 1.000000 -> [ir], [sd] @ NC_000913 2404732.0 -1 "ir" "lrhA_yfbQ-" 6.541655 -0.079733 0.468225 @ NC_000913 2404687.0 -1 "orf" "16 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 2404746.0 -1 "sd" "" 4.642177 -0.454568 0.324710 define "sd-(14)-ir 2404732 Gap" "-" "}{" "}{" 0.0 -14.0 @ NC_000913 2404732.0 -1 "sd-(14)-ir 2404732 Gap" "4.9 bits" 4.898425 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2404732 lrhA_yfbQ- total 6.3" "-" "||" "||" 0.0 14.0 @ NC_000913 2404746.0 -1 "sd-ir 2404732 lrhA_yfbQ- total 6.3" "bits" 6.285407 16.000000 2404687.000000 1.000000 -> [ir], [sd] @ NC_000913 2404663.0 -1 "ir" "lrhA_yfbQ-" 7.463578 0.328322 0.371334 @ NC_000913 2404671.0 -1 "sd" "" 0.923609 -1.912518 0.027905 define "sd-(8)-ir 2404663 Gap" "-" "}{" "}{" 0.0 -8.0 @ NC_000913 2404663.0 -1 "sd-(8)-ir 2404663 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 2404663 lrhA_yfbQ- total 5.9" "-" "||" "||" 0.0 8.0 @ NC_000913 2404671.0 -1 "sd-ir 2404663 lrhA_yfbQ- total 5.9" "bits" 5.941168 0.000000 0.000000 0.000000 -> [ir], [sd] * * 1 sequences are in the genomebook * 20 ORFs are in the genomebook * multiscan 3.94 * 2007/12/07 19:07:27, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 lrhA_yfbQ 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 19:07:27, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 lrhA_yfbQ 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 2405426.0 -1 "p10" " 4.6 bits" 4.597025 -0.087812 0.465013 @ NC_000913 2405449.0 -1 "p35" " 2.6 bits" 2.550893 -0.784547 0.216360 define "p35-(23)-p10 2405426 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2405426.0 -1 "p35-(23)-p10 2405426 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2405426 total 5.7" "-" "||" "||" 0 23 @ NC_000913 2405449 -1 "p35-p10 2405426 total 5.7" "bits" 5.710634 0.000000 0.000000 @ NC_000913 2405412.0 -1 "p10" " 5.3 bits" 5.330024 0.256633 0.398731 @ NC_000913 2405433.0 -1 "p35" " 3.3 bits" 3.316676 -0.376815 0.353156 define "p35-(21)-p10 2405412 Gap" "-" "}{" "}{" 0.0 -21 @ NC_000913 2405412.0 -1 "p35-(21)-p10 2405412 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 2405412 total 5.3" "-" "||" "||" 0 21 @ NC_000913 2405433 -1 "p35-p10 2405412 total 5.3" "bits" 5.347799 0.000000 0.000000 @ NC_000913 2405391.0 -1 "p10" " 5.9 bits" 5.872451 0.511525 0.304492 @ NC_000913 2405416.0 -1 "p35" " 2.6 bits" 2.600396 -0.758189 0.224169 define "p35-(25)-p10 2405391 Gap" "-" "}{" "}{" 0.0 -25 @ NC_000913 2405391.0 -1 "p35-(25)-p10 2405391 Gap" "4.0 bits" 4.012597 1.428290 4.003602 define "p35-p10 2405391 total 4.5" "-" "||" "||" 0 25 @ NC_000913 2405416 -1 "p35-p10 2405391 total 4.5" "bits" 4.460250 0.000000 0.000000 @ NC_000913 2405384.0 -1 "p10" " 0.8 bits" 0.787379 -1.878008 0.030190 @ NC_000913 2405407.0 -1 "p35" " 5.5 bits" 5.536744 0.805235 0.210342 define "p35-(23)-p10 2405384 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2405384.0 -1 "p35-(23)-p10 2405384 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2405384 total 4.9" "-" "||" "||" 0 23 @ NC_000913 2405407 -1 "p35-p10 2405384 total 4.9" "bits" 4.886839 0.000000 0.000000 @ NC_000913 2405342.0 -1 "p10" " 5.7 bits" 5.674787 0.418641 0.337739 @ NC_000913 2405366.0 -1 "p35" " 5.5 bits" 5.537193 0.805474 0.210273 define "p35-(24)-p10 2405342 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2405342.0 -1 "p35-(24)-p10 2405342 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2405342 total 8.8" "-" "||" "||" 0 24 @ NC_000913 2405366 -1 "p35-p10 2405342 total 8.8" "bits" 8.784346 0.000000 0.000000 @ NC_000913 2405328.0 -1 "p10" " 3.6 bits" 3.551820 -0.578966 0.281306 @ NC_000913 2405351.0 -1 "p35" " 4.8 bits" 4.775558 0.399950 0.344597 define "p35-(23)-p10 2405328 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2405328.0 -1 "p35-(23)-p10 2405328 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2405328 total 6.9" "-" "||" "||" 0 23 @ NC_000913 2405351 -1 "p35-p10 2405328 total 6.9" "bits" 6.890094 0.000000 0.000000 @ NC_000913 2405292.0 -1 "p10" " 2.4 bits" 2.388504 -1.125621 0.130163 @ NC_000913 2405316.0 -1 "p35" " 4.7 bits" 4.661044 0.338978 0.367313 define "p35-(24)-p10 2405292 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2405292.0 -1 "p35-(24)-p10 2405292 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2405292 total 4.6" "-" "||" "||" 0 24 @ NC_000913 2405316 -1 "p35-p10 2405292 total 4.6" "bits" 4.621914 0.000000 0.000000 @ NC_000913 2405172.0 -1 "p10" " 3.3 bits" 3.292171 -0.700978 0.241659 @ NC_000913 2405194.0 -1 "p35" " 3.5 bits" 3.450960 -0.305317 0.380063 define "p35-(22)-p10 2405172 Gap" "-" "}{" "}{" 0.0 -22 @ NC_000913 2405172.0 -1 "p35-(22)-p10 2405172 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 2405172 total 4.4" "-" "||" "||" 0 22 @ NC_000913 2405194 -1 "p35-p10 2405172 total 4.4" "bits" 4.408606 0.000000 0.000000 @ NC_000913 2405169.0 -1 "p10" " 7.1 bits" 7.072389 1.075390 0.141100 @ NC_000913 2405194.0 -1 "p35" " 3.5 bits" 3.450960 -0.305317 0.380063 define "p35-(25)-p10 2405169 Gap" "-" "}{" "}{" 0.0 -25 @ NC_000913 2405169.0 -1 "p35-(25)-p10 2405169 Gap" "4.0 bits" 4.012597 1.428290 4.003602 define "p35-p10 2405169 total 6.5" "-" "||" "||" 0 25 @ NC_000913 2405194 -1 "p35-p10 2405169 total 6.5" "bits" 6.510752 0.000000 0.000000 @ NC_000913 2405162.0 -1 "p10" " 6.3 bits" 6.302819 0.713760 0.237688 @ NC_000913 2405184.0 -1 "p35" " 1.6 bits" 1.595009 -1.293496 0.097920 define "p35-(22)-p10 2405162 Gap" "-" "}{" "}{" 0.0 -22 @ NC_000913 2405162.0 -1 "p35-(22)-p10 2405162 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 2405162 total 5.6" "-" "||" "||" 0 22 @ NC_000913 2405184 -1 "p35-p10 2405162 total 5.6" "bits" 5.563303 0.000000 0.000000 @ NC_000913 2405109.0 -1 "p10" " 5.6 bits" 5.565853 0.367451 0.356641 @ NC_000913 2405133.0 -1 "p35" " 1.8 bits" 1.825884 -1.170569 0.120886 define "p35-(24)-p10 2405109 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2405109.0 -1 "p35-(24)-p10 2405109 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2405109 total 5.0" "-" "||" "||" 0 24 @ NC_000913 2405133 -1 "p35-p10 2405109 total 5.0" "bits" 4.964103 0.000000 0.000000 @ NC_000913 2405104.0 -1 "p10" " 5.6 bits" 5.565853 0.367451 0.356641 @ NC_000913 2405126.0 -1 "p35" " 1.4 bits" 1.425654 -1.383667 0.083230 define "p35-(22)-p10 2405104 Gap" "-" "}{" "}{" 0.0 -22 @ NC_000913 2405104.0 -1 "p35-(22)-p10 2405104 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 2405104 total 4.7" "-" "||" "||" 0 22 @ NC_000913 2405126 -1 "p35-p10 2405104 total 4.7" "bits" 4.656982 0.000000 0.000000 @ NC_000913 2405045.0 -1 "p10" " 7.6 bits" 7.607673 1.326926 0.092267 @ NC_000913 2405068.0 -1 "p35" " 1.8 bits" 1.776381 -1.196927 0.115668 define "p35-(23)-p10 2405045 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2405045.0 -1 "p35-(23)-p10 2405045 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2405045 total 7.9" "-" "||" "||" 0 23 @ NC_000913 2405068 -1 "p35-p10 2405045 total 7.9" "bits" 7.946770 0.000000 0.000000 @ NC_000913 2404973.0 -1 "p10" " 2.2 bits" 2.157009 -1.234403 0.108526 @ NC_000913 2404995.0 -1 "p35" " 4.3 bits" 4.332719 0.164166 0.434800 define "p35-(22)-p10 2404973 Gap" "-" "}{" "}{" 0.0 -22 @ NC_000913 2404973.0 -1 "p35-(22)-p10 2404973 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 2404973 total 4.2" "-" "||" "||" 0 22 @ NC_000913 2404995 -1 "p35-p10 2404973 total 4.2" "bits" 4.155203 0.000000 0.000000 @ NC_000913 2404884.0 -1 "p10" " 3.7 bits" 3.684498 -0.516619 0.302711 @ NC_000913 2404907.0 -1 "p35" " 3.2 bits" 3.202370 -0.437675 0.330811 define "p35-(23)-p10 2404884 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2404884.0 -1 "p35-(23)-p10 2404884 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2404884 total 5.4" "-" "||" "||" 0 23 @ NC_000913 2404907 -1 "p35-p10 2404884 total 5.4" "bits" 5.449584 0.000000 0.000000 @ NC_000913 2404855.0 -1 "p10" " 6.5 bits" 6.495888 0.804485 0.210558 @ NC_000913 2404876.0 -1 "p35" " 1.5 bits" 1.475851 -1.356940 0.087400 define "p35-(21)-p10 2404855 Gap" "-" "}{" "}{" 0.0 -21 @ NC_000913 2404855.0 -1 "p35-(21)-p10 2404855 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 2404855 total 4.7" "-" "||" "||" 0 21 @ NC_000913 2404876 -1 "p35-p10 2404855 total 4.7" "bits" 4.672838 0.000000 0.000000 @ NC_000913 2404853.0 -1 "p10" " 6.0 bits" 5.958056 0.551752 0.290559 @ NC_000913 2404876.0 -1 "p35" " 1.5 bits" 1.475851 -1.356940 0.087400 define "p35-(23)-p10 2404853 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2404853.0 -1 "p35-(23)-p10 2404853 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2404853 total 6.0" "-" "||" "||" 0 23 @ NC_000913 2404876 -1 "p35-p10 2404853 total 6.0" "bits" 5.996623 0.000000 0.000000 @ NC_000913 2404781.0 -1 "p10" " 3.4 bits" 3.363735 -0.667349 0.252275 @ NC_000913 2404804.0 -1 "p35" " 3.8 bits" 3.765574 -0.137804 0.445198 define "p35-(23)-p10 2404781 Gap" "-" "}{" "}{" 0.0 -23 @ NC_000913 2404781.0 -1 "p35-(23)-p10 2404781 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 2404781 total 5.7" "-" "||" "||" 0 23 @ NC_000913 2404804 -1 "p35-p10 2404781 total 5.7" "bits" 5.692025 0.000000 0.000000 @ NC_000913 2404779.0 -1 "p10" " 3.8 bits" 3.751613 -0.485081 0.313810 @ NC_000913 2404803.0 -1 "p35" " 3.8 bits" 3.843209 -0.096468 0.461574 define "p35-(24)-p10 2404779 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2404779.0 -1 "p35-(24)-p10 2404779 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2404779 total 5.2" "-" "||" "||" 0 24 @ NC_000913 2404803 -1 "p35-p10 2404779 total 5.2" "bits" 5.167188 0.000000 0.000000 @ NC_000913 2404757.0 -1 "p10" " 2.4 bits" 2.437487 -1.102603 0.135100 @ NC_000913 2404781.0 -1 "p35" " 5.7 bits" 5.650564 0.865837 0.193290 define "p35-(24)-p10 2404757 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2404757.0 -1 "p35-(24)-p10 2404757 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2404757 total 5.7" "-" "||" "||" 0 24 @ NC_000913 2404781 -1 "p35-p10 2404757 total 5.7" "bits" 5.660417 0.000000 0.000000 @ NC_000913 2404663.0 -1 "p10" " 6.4 bits" 6.444357 0.780270 0.217616 @ NC_000913 2404687.0 -1 "p35" " 0.1 bits" 0.087088 -2.096371 0.018025 define "p35-(24)-p10 2404663 Gap" "-" "}{" "}{" 0.0 -24 @ NC_000913 2404663.0 -1 "p35-(24)-p10 2404663 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 2404663 total 4.1" "-" "||" "||" 0 24 @ NC_000913 2404687 -1 "p35-p10 2404663 total 4.1" "bits" 4.103811 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