define "NC_000913.fimB" "-" "<]" "[>" 0 602 @ NC_000913 4538980 1 "NC_000913.fimB" "" * orf 1.24 * 2007/12/07 18:55:43, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 TRIP2c_fimB 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 4538055.0 +1 "ir" "TRIP2c_fimB+" 3.984127 -1.211728 0.112808 @ NC_000913 4538058.0 +1 "orf" "2 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538046.0 +1 "sd" "" 9.659451 1.512569 0.065195 define "sd-(9)-ir 4538055 Gap" "-" "{}" "{}" 0.0 9.0 @ NC_000913 4538046.0 +1 "sd-(9)-ir 4538055 Gap" "2.3 bits" 2.279003 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538055 TRIP2c_fimB+ total 11.4" "-" "||" "||" -9.0 0.0 @ NC_000913 4538055.0 +1 "sd-ir 4538055 TRIP2c_fimB+ total 11.4" "bits" 11.364575 2.000000 4538058.000000 0.000000 -> [ir], [sd] @ NC_000913 4538057.0 +1 "ir" "TRIP2c_fimB+" 2.741482 -1.761739 0.039057 @ NC_000913 4538144.0 +1 "orf" "30 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538046.0 +1 "sd" "" 9.659451 1.512569 0.065195 define "sd-(11)-ir 4538057 Gap" "-" "{}" "{}" 0.0 11.0 @ NC_000913 4538046.0 +1 "sd-(11)-ir 4538057 Gap" "3.0 bits" 3.043105 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538057 TRIP2c_fimB+ total 9.4" "-" "||" "||" -11.0 0.0 @ NC_000913 4538057.0 +1 "sd-ir 4538057 TRIP2c_fimB+ total 9.4" "bits" 9.357828 30.000000 4538144.000000 1.000000 -> [ir], [sd] @ NC_000913 4538387.0 +1 "ir" "TRIP2c_fimB+" 6.172654 -0.243058 0.403980 @ NC_000913 4538420.0 +1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538375.0 +1 "sd" "" 4.749318 -0.412561 0.339964 define "sd-(12)-ir 4538387 Gap" "-" "{}" "{}" 0.0 12.0 @ NC_000913 4538375.0 +1 "sd-(12)-ir 4538387 Gap" "4.0 bits" 3.966064 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538387 TRIP2c_fimB+ total 7.0" "-" "||" "||" -12.0 0.0 @ NC_000913 4538387.0 +1 "sd-ir 4538387 TRIP2c_fimB+ total 7.0" "bits" 6.955908 12.000000 4538420.000000 1.000000 -> [ir], [sd] @ NC_000913 4538419.0 +1 "ir" "TRIP2c_fimB+" 8.195387 0.652230 0.257126 @ NC_000913 4538509.0 +1 "orf" "31 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538411.0 +1 "sd" "" 2.623226 -1.246144 0.106356 define "sd-(8)-ir 4538419 Gap" "-" "{}" "{}" 0.0 8.0 @ NC_000913 4538411.0 +1 "sd-(8)-ir 4538419 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538419 TRIP2c_fimB+ total 8.4" "-" "||" "||" -8.0 0.0 @ NC_000913 4538419.0 +1 "sd-ir 4538419 TRIP2c_fimB+ total 8.4" "bits" 8.372594 31.000000 4538509.000000 1.000000 -> [ir], [sd] @ NC_000913 4538468.0 +1 "ir" "TRIP2c_fimB+" 6.293359 -0.189632 0.424799 @ NC_000913 4538471.0 +1 "orf" "2 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538457.0 +1 "sd" "" 5.393112 -0.160146 0.436383 define "sd-(11)-ir 4538468 Gap" "-" "{}" "{}" 0.0 11.0 @ NC_000913 4538457.0 +1 "sd-(11)-ir 4538468 Gap" "3.0 bits" 3.043105 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538468 TRIP2c_fimB+ total 8.6" "-" "||" "||" -11.0 0.0 @ NC_000913 4538468.0 +1 "sd-ir 4538468 TRIP2c_fimB+ total 8.6" "bits" 8.643366 2.000000 4538471.000000 0.000000 -> [ir], [sd] @ NC_000913 4538481.0 +1 "ir" "TRIP2c_fimB+" 4.894803 -0.808651 0.209358 @ NC_000913 4538487.0 +1 "orf" "3 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538466.0 +1 "sd" "" 8.627668 1.108035 0.133923 define "sd-(15)-ir 4538481 Gap" "-" "{}" "{}" 0.0 15.0 @ NC_000913 4538466.0 +1 "sd-(15)-ir 4538481 Gap" "6.0 bits" 6.001111 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538481 TRIP2c_fimB+ total 7.5" "-" "||" "||" -15.0 0.0 @ NC_000913 4538481.0 +1 "sd-ir 4538481 TRIP2c_fimB+ total 7.5" "bits" 7.521360 3.000000 4538487.000000 0.000000 -> [ir], [sd] @ NC_000913 4538535.0 +1 "ir" "TRIP2c_fimB+" 7.755400 0.457486 0.323661 @ NC_000913 4538574.0 +1 "orf" "14 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538520.0 +1 "sd" "" 3.632658 -0.850373 0.197559 define "sd-(15)-ir 4538535 Gap" "-" "{}" "{}" 0.0 15.0 @ NC_000913 4538520.0 +1 "sd-(15)-ir 4538535 Gap" "6.0 bits" 6.001111 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538535 TRIP2c_fimB+ total 5.4" "-" "||" "||" -15.0 0.0 @ NC_000913 4538535.0 +1 "sd-ir 4538535 TRIP2c_fimB+ total 5.4" "bits" 5.386947 14.000000 4538574.000000 1.000000 -> [ir], [sd] @ NC_000913 4538607.0 +1 "ir" "TRIP2c_fimB+" 6.237316 -0.214438 0.415103 @ NC_000913 4538694.0 +1 "orf" "30 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538594.0 +1 "sd" "" 5.990918 0.074237 0.470411 define "sd-(13)-ir 4538607 Gap" "-" "{}" "{}" 0.0 13.0 @ NC_000913 4538594.0 +1 "sd-(13)-ir 4538607 Gap" "4.6 bits" 4.637227 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538607 TRIP2c_fimB+ total 7.6" "-" "||" "||" -13.0 0.0 @ NC_000913 4538607.0 +1 "sd-ir 4538607 TRIP2c_fimB+ total 7.6" "bits" 7.591007 30.000000 4538694.000000 1.000000 -> [ir], [sd] @ NC_000913 4538661.0 +1 "ir" "TRIP2c_fimB+" 6.381195 -0.150755 0.440085 @ NC_000913 4538694.0 +1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538652.0 +1 "sd" "" 2.596386 -1.256667 0.104437 define "sd-(9)-ir 4538661 Gap" "-" "{}" "{}" 0.0 9.0 @ NC_000913 4538652.0 +1 "sd-(9)-ir 4538661 Gap" "2.3 bits" 2.279003 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538661 TRIP2c_fimB+ total 6.7" "-" "||" "||" -9.0 0.0 @ NC_000913 4538661.0 +1 "sd-ir 4538661 TRIP2c_fimB+ total 6.7" "bits" 6.698578 12.000000 4538694.000000 1.000000 -> [ir], [sd] @ NC_000913 4538693.0 +1 "ir" "TRIP2c_fimB+" 6.290382 -0.190950 0.424282 @ NC_000913 4538705.0 +1 "orf" "5 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538682.0 +1 "sd" "" 1.954244 -1.508433 0.065722 define "sd-(11)-ir 4538693 Gap" "-" "{}" "{}" 0.0 11.0 @ NC_000913 4538682.0 +1 "sd-(11)-ir 4538693 Gap" "3.0 bits" 3.043105 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538693 TRIP2c_fimB+ total 5.2" "-" "||" "||" -11.0 0.0 @ NC_000913 4538693.0 +1 "sd-ir 4538693 TRIP2c_fimB+ total 5.2" "bits" 5.201521 5.000000 4538705.000000 0.000000 -> [ir], [sd] @ NC_000913 4538722.0 +1 "ir" "TRIP2c_fimB+" 6.969413 0.109598 0.456364 @ NC_000913 4538755.0 +1 "orf" "12 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538708.0 +1 "sd" "" 3.028684 -1.087175 0.138480 define "sd-(14)-ir 4538722 Gap" "-" "{}" "{}" 0.0 14.0 @ NC_000913 4538708.0 +1 "sd-(14)-ir 4538722 Gap" "4.9 bits" 4.898425 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538722 TRIP2c_fimB+ total 5.1" "-" "||" "||" -14.0 0.0 @ NC_000913 4538722.0 +1 "sd-ir 4538722 TRIP2c_fimB+ total 5.1" "bits" 5.099672 12.000000 4538755.000000 1.000000 -> [ir], [sd] @ NC_000913 4538725.0 +1 "ir" "TRIP2c_fimB+" 8.725503 0.886866 0.187575 @ NC_000913 4538755.0 +1 "orf" "11 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538708.0 +1 "sd" "" 3.028684 -1.087175 0.138480 define "sd-(17)-ir 4538725 Gap" "-" "{}" "{}" 0.0 17.0 @ NC_000913 4538708.0 +1 "sd-(17)-ir 4538725 Gap" "6.5 bits" 6.505583 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538725 TRIP2c_fimB+ total 5.2" "-" "||" "||" -17.0 0.0 @ NC_000913 4538725.0 +1 "sd-ir 4538725 TRIP2c_fimB+ total 5.2" "bits" 5.248604 11.000000 4538755.000000 1.000000 -> [ir], [sd] @ NC_000913 4538780.0 +1 "ir" "TRIP2c_fimB+" 5.613833 -0.490399 0.311926 @ NC_000913 4538816.0 +1 "orf" "13 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538771.0 +1 "sd" "" 8.043823 0.879125 0.189667 define "sd-(9)-ir 4538780 Gap" "-" "{}" "{}" 0.0 9.0 @ NC_000913 4538771.0 +1 "sd-(9)-ir 4538780 Gap" "2.3 bits" 2.279003 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538780 TRIP2c_fimB+ total 11.4" "-" "||" "||" -9.0 0.0 @ NC_000913 4538780.0 +1 "sd-ir 4538780 TRIP2c_fimB+ total 11.4" "bits" 11.378653 13.000000 4538816.000000 1.000000 -> [ir], [sd] @ NC_000913 4538801.0 +1 "ir" "TRIP2c_fimB+" 6.064036 -0.291134 0.385475 @ NC_000913 4538816.0 +1 "orf" "6 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538793.0 +1 "sd" "" 2.016349 -1.484084 0.068893 define "sd-(8)-ir 4538801 Gap" "-" "{}" "{}" 0.0 8.0 @ NC_000913 4538793.0 +1 "sd-(8)-ir 4538801 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538801 TRIP2c_fimB+ total 5.6" "-" "||" "||" -8.0 0.0 @ NC_000913 4538801.0 +1 "sd-ir 4538801 TRIP2c_fimB+ total 5.6" "bits" 5.634366 6.000000 4538816.000000 0.000000 -> [ir], [sd] @ NC_000913 4538919.0 +1 "ir" "TRIP2c_fimB+" 4.326485 -1.060196 0.144528 @ NC_000913 4538934.0 +1 "orf" "6 codons" R 1.000000 0.000000 0.000000 1.000000 @ NC_000913 4538912.0 +1 "sd" "" 9.914759 1.612669 0.053408 define "sd-(7)-ir 4538919 Gap" "-" "{}" "{}" 0.0 7.0 @ NC_000913 4538912.0 +1 "sd-(7)-ir 4538919 Gap" "3.7 bits" 3.703029 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538919 TRIP2c_fimB+ total 10.5" "-" "||" "||" -7.0 0.0 @ NC_000913 4538919.0 +1 "sd-ir 4538919 TRIP2c_fimB+ total 10.5" "bits" 10.538215 6.000000 4538934.000000 0.000000 -> [ir], [sd] @ NC_000913 4538980.0 +1 "ir" "TRIP2c_fimB+" 9.044211 1.027931 0.151991 @ NC_000913 4538972.0 +1 "sd" "" 9.507788 1.453107 0.073097 define "sd-(8)-ir 4538980 Gap" "-" "{}" "{}" 0.0 8.0 @ NC_000913 4538972.0 +1 "sd-(8)-ir 4538980 Gap" "2.4 bits" 2.446019 2.276413 9.344296 0.000000 -> [ir], [sd] define "sd-ir 4538980 TRIP2c_fimB+ total 16.1" "-" "||" "||" -8.0 0.0 @ NC_000913 4538980.0 +1 "sd-ir 4538980 TRIP2c_fimB+ total 16.1" "bits" 16.105980 0.000000 0.000000 0.000000 -> [ir], [sd] * * 1 sequences are in the genomebook * 15 ORFs are in the genomebook * multiscan 3.94 * 2007/12/07 18:55:43, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 TRIP2c_fimB 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 18:55:43, 2007/12/06 18:15:19, small proteins E.coli-K12 NC_000913 TRIP2c_fimB 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 4538105.0 +1 "p10" " 3.4 bits" 3.379644 -0.659873 0.254668 @ NC_000913 4538082.0 +1 "p35" " 3.5 bits" 3.519704 -0.268715 0.394075 define "p35-(23)-p10 4538105 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538082.0 1 "p35-(23)-p10 4538105 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538105 total 5.5" "-" "||" "||" -23 0 @ NC_000913 4538105 1 "p35-p10 4538105 total 5.5" "bits" 5.462064 0.000000 0.000000 @ NC_000913 4538129.0 +1 "p10" " 4.4 bits" 4.421464 -0.170310 0.432383 @ NC_000913 4538108.0 +1 "p35" " 4.1 bits" 4.134975 0.058879 0.476524 define "p35-(21)-p10 4538129 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 4538108.0 1 "p35-(21)-p10 4538129 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 4538129 total 5.3" "-" "||" "||" -21 0 @ NC_000913 4538129 1 "p35-p10 4538129 total 5.3" "bits" 5.257538 0.000000 0.000000 @ NC_000913 4538132.0 +1 "p10" " 2.6 bits" 2.596713 -1.027781 0.152026 @ NC_000913 4538108.0 +1 "p35" " 4.1 bits" 4.134975 0.058879 0.476524 define "p35-(24)-p10 4538132 Gap" "-" "{}" "{}" 0.0 24 @ NC_000913 4538108.0 1 "p35-(24)-p10 4538132 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 4538132 total 4.3" "-" "||" "||" -24 0 @ NC_000913 4538132 1 "p35-p10 4538132 total 4.3" "bits" 4.304054 0.000000 0.000000 @ NC_000913 4538186.0 +1 "p10" " 3.6 bits" 3.551820 -0.578966 0.281306 @ NC_000913 4538160.0 +1 "p35" " 6.1 bits" 6.074850 1.091743 0.137473 define "p35-(26)-p10 4538186 Gap" "-" "{}" "{}" 0.0 26 @ NC_000913 4538160.0 1 "p35-(26)-p10 4538186 Gap" "3.7 bits" 3.702256 1.428290 4.003602 define "p35-p10 4538186 total 5.9" "-" "||" "||" -26 0 @ NC_000913 4538186 1 "p35-p10 4538186 total 5.9" "bits" 5.924414 0.000000 0.000000 @ NC_000913 4538218.0 +1 "p10" " 5.5 bits" 5.499727 0.336378 0.368293 @ NC_000913 4538197.0 +1 "p35" " 4.1 bits" 4.114511 0.047983 0.480865 define "p35-(21)-p10 4538218 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 4538197.0 1 "p35-(21)-p10 4538218 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 4538218 total 6.3" "-" "||" "||" -21 0 @ NC_000913 4538218 1 "p35-p10 4538218 total 6.3" "bits" 6.315337 0.000000 0.000000 @ NC_000913 4538330.0 +1 "p10" " 3.4 bits" 3.379644 -0.659873 0.254668 @ NC_000913 4538309.0 +1 "p35" " 4.6 bits" 4.641274 0.328452 0.371285 define "p35-(21)-p10 4538330 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 4538309.0 1 "p35-(21)-p10 4538330 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 4538330 total 4.7" "-" "||" "||" -21 0 @ NC_000913 4538330 1 "p35-p10 4538330 total 4.7" "bits" 4.722017 0.000000 0.000000 @ NC_000913 4538399.0 +1 "p10" " 6.5 bits" 6.495888 0.804485 0.210558 @ NC_000913 4538377.0 +1 "p35" " 4.7 bits" 4.661044 0.338978 0.367313 define "p35-(22)-p10 4538399 Gap" "-" "{}" "{}" 0.0 22 @ NC_000913 4538377.0 1 "p35-(22)-p10 4538399 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 4538399 total 8.8" "-" "||" "||" -22 0 @ NC_000913 4538399 1 "p35-p10 4538399 total 8.8" "bits" 8.822407 0.000000 0.000000 @ NC_000913 4538424.0 +1 "p10" " 3.8 bits" 3.827455 -0.449442 0.326557 @ NC_000913 4538403.0 +1 "p35" " 4.1 bits" 4.114511 0.047983 0.480865 define "p35-(21)-p10 4538424 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 4538403.0 1 "p35-(21)-p10 4538424 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 4538424 total 4.6" "-" "||" "||" -21 0 @ NC_000913 4538424 1 "p35-p10 4538424 total 4.6" "bits" 4.643065 0.000000 0.000000 @ NC_000913 4538427.0 +1 "p10" " 2.6 bits" 2.555205 -1.047286 0.147484 @ NC_000913 4538403.0 +1 "p35" " 4.1 bits" 4.114511 0.047983 0.480865 define "p35-(24)-p10 4538427 Gap" "-" "{}" "{}" 0.0 24 @ NC_000913 4538403.0 1 "p35-(24)-p10 4538427 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 4538427 total 4.2" "-" "||" "||" -24 0 @ NC_000913 4538427 1 "p35-p10 4538427 total 4.2" "bits" 4.242082 0.000000 0.000000 @ NC_000913 4538488.0 +1 "p10" " 4.6 bits" 4.560454 -0.104997 0.458189 @ NC_000913 4538465.0 +1 "p35" " 1.3 bits" 1.340115 -1.429211 0.076472 define "p35-(23)-p10 4538488 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538465.0 1 "p35-(23)-p10 4538488 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538488 total 4.5" "-" "||" "||" -23 0 @ NC_000913 4538488 1 "p35-p10 4538488 total 4.5" "bits" 4.463285 0.000000 0.000000 @ NC_000913 4538604.0 +1 "p10" " 4.6 bits" 4.597025 -0.087812 0.465013 @ NC_000913 4538581.0 +1 "p35" " 2.9 bits" 2.947739 -0.573251 0.283237 define "p35-(23)-p10 4538604 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538581.0 1 "p35-(23)-p10 4538604 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538604 total 6.1" "-" "||" "||" -23 0 @ NC_000913 4538604 1 "p35-p10 4538604 total 6.1" "bits" 6.107480 0.000000 0.000000 @ NC_000913 4538606.0 +1 "p10" " 3.8 bits" 3.798027 -0.463270 0.321585 @ NC_000913 4538583.0 +1 "p35" " 2.8 bits" 2.813210 -0.644879 0.259503 define "p35-(23)-p10 4538606 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538583.0 1 "p35-(23)-p10 4538606 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538606 total 5.2" "-" "||" "||" -23 0 @ NC_000913 4538606 1 "p35-p10 4538606 total 5.2" "bits" 5.173953 0.000000 0.000000 @ NC_000913 4538670.0 +1 "p10" " 3.4 bits" 3.363735 -0.667349 0.252275 @ NC_000913 4538648.0 +1 "p35" " 4.3 bits" 4.332719 0.164166 0.434800 define "p35-(22)-p10 4538670 Gap" "-" "{}" "{}" 0.0 22 @ NC_000913 4538648.0 1 "p35-(22)-p10 4538670 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 4538670 total 5.4" "-" "||" "||" -22 0 @ NC_000913 4538670 1 "p35-p10 4538670 total 5.4" "bits" 5.361929 0.000000 0.000000 @ NC_000913 4538688.0 +1 "p10" " 2.0 bits" 2.048075 -1.285592 0.099293 @ NC_000913 4538665.0 +1 "p35" " 5.7 bits" 5.700516 0.892433 0.186080 define "p35-(23)-p10 4538688 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538665.0 1 "p35-(23)-p10 4538688 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538688 total 6.3" "-" "||" "||" -23 0 @ NC_000913 4538688 1 "p35-p10 4538688 total 6.3" "bits" 6.311307 0.000000 0.000000 @ NC_000913 4538693.0 +1 "p10" " 3.6 bits" 3.566841 -0.571907 0.283692 @ NC_000913 4538670.0 +1 "p35" " 5.7 bits" 5.650564 0.865837 0.193290 define "p35-(23)-p10 4538693 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538670.0 1 "p35-(23)-p10 4538693 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538693 total 7.8" "-" "||" "||" -23 0 @ NC_000913 4538693 1 "p35-p10 4538693 total 7.8" "bits" 7.780121 0.000000 0.000000 @ NC_000913 4538734.0 +1 "p10" " 7.1 bits" 7.072389 1.075390 0.141100 @ NC_000913 4538710.0 +1 "p35" " 0.7 bits" 0.747686 -1.744643 0.040524 define "p35-(24)-p10 4538734 Gap" "-" "{}" "{}" 0.0 24 @ NC_000913 4538710.0 1 "p35-(24)-p10 4538734 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 4538734 total 5.4" "-" "||" "||" -24 0 @ NC_000913 4538734 1 "p35-p10 4538734 total 5.4" "bits" 5.392441 0.000000 0.000000 @ NC_000913 4538737.0 +1 "p10" " 2.0 bits" 1.996545 -1.309807 0.095131 @ NC_000913 4538715.0 +1 "p35" " 6.2 bits" 6.188670 1.152345 0.124590 define "p35-(22)-p10 4538737 Gap" "-" "{}" "{}" 0.0 22 @ NC_000913 4538715.0 1 "p35-(22)-p10 4538737 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 4538737 total 5.9" "-" "||" "||" -22 0 @ NC_000913 4538737 1 "p35-p10 4538737 total 5.9" "bits" 5.850690 0.000000 0.000000 @ NC_000913 4538739.0 +1 "p10" " 1.8 bits" 1.775612 -1.413626 0.078736 @ NC_000913 4538715.0 +1 "p35" " 6.2 bits" 6.188670 1.152345 0.124590 define "p35-(24)-p10 4538739 Gap" "-" "{}" "{}" 0.0 24 @ NC_000913 4538715.0 1 "p35-(24)-p10 4538739 Gap" "2.4 bits" 2.427634 1.428290 4.003602 define "p35-p10 4538739 total 5.5" "-" "||" "||" -24 0 @ NC_000913 4538739 1 "p35-p10 4538739 total 5.5" "bits" 5.536648 0.000000 0.000000 @ NC_000913 4538740.0 +1 "p10" " 4.7 bits" 4.684498 -0.046707 0.481373 @ NC_000913 4538715.0 +1 "p35" " 6.2 bits" 6.188670 1.152345 0.124590 define "p35-(25)-p10 4538740 Gap" "-" "{}" "{}" 0.0 25 @ NC_000913 4538715.0 1 "p35-(25)-p10 4538740 Gap" "4.0 bits" 4.012597 1.428290 4.003602 define "p35-p10 4538740 total 6.9" "-" "||" "||" -25 0 @ NC_000913 4538740 1 "p35-p10 4538740 total 6.9" "bits" 6.860571 0.000000 0.000000 @ NC_000913 4538777.0 +1 "p10" " 4.5 bits" 4.524033 -0.122112 0.451405 @ NC_000913 4538755.0 +1 "p35" " 5.6 bits" 5.586696 0.831831 0.202752 define "p35-(22)-p10 4538777 Gap" "-" "{}" "{}" 0.0 22 @ NC_000913 4538755.0 1 "p35-(22)-p10 4538777 Gap" "2.3 bits" 2.334525 1.428290 4.003602 define "p35-p10 4538777 total 7.8" "-" "||" "||" -22 0 @ NC_000913 4538777 1 "p35-p10 4538777 total 7.8" "bits" 7.776204 0.000000 0.000000 @ NC_000913 4538815.0 +1 "p10" " 8.4 bits" 8.377243 1.688555 0.045652 @ NC_000913 4538792.0 +1 "p35" " 2.3 bits" 2.250006 -0.944750 0.172393 define "p35-(23)-p10 4538815 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538792.0 1 "p35-(23)-p10 4538815 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538815 total 9.2" "-" "||" "||" -23 0 @ NC_000913 4538815 1 "p35-p10 4538815 total 9.2" "bits" 9.189965 0.000000 0.000000 @ NC_000913 4538821.0 +1 "p10" " 0.5 bits" 0.490009 -2.017745 0.021809 @ NC_000913 4538798.0 +1 "p35" " 5.7 bits" 5.651013 0.866076 0.193224 define "p35-(23)-p10 4538821 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538798.0 1 "p35-(23)-p10 4538821 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538821 total 4.7" "-" "||" "||" -23 0 @ NC_000913 4538821 1 "p35-p10 4538821 total 4.7" "bits" 4.703738 0.000000 0.000000 @ NC_000913 4538916.0 +1 "p10" " 3.8 bits" 3.827455 -0.449442 0.326557 @ NC_000913 4538895.0 +1 "p35" " 4.8 bits" 4.775558 0.399950 0.344597 define "p35-(21)-p10 4538916 Gap" "-" "{}" "{}" 0.0 21 @ NC_000913 4538895.0 1 "p35-(21)-p10 4538916 Gap" "3.3 bits" 3.298901 1.428290 4.003602 define "p35-p10 4538916 total 5.3" "-" "||" "||" -21 0 @ NC_000913 4538916 1 "p35-p10 4538916 total 5.3" "bits" 5.304112 0.000000 0.000000 @ NC_000913 4538919.0 +1 "p10" " 0.8 bits" 0.782784 -1.880167 0.030043 @ NC_000913 4538896.0 +1 "p35" " 4.7 bits" 4.711241 0.365705 0.357293 define "p35-(23)-p10 4538919 Gap" "-" "{}" "{}" 0.0 23 @ NC_000913 4538896.0 1 "p35-(23)-p10 4538919 Gap" "1.4 bits" 1.437284 1.428290 4.003602 define "p35-p10 4538919 total 4.1" "-" "||" "||" -23 0 @ NC_000913 4538919 1 "p35-p10 4538919 total 4.1" "bits" 4.056741 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