> SSTRAND_ID=Bt_PrP; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GCCCCAUGGAGGUGGCUGGGGCCAGCCUCAUGGAGGUGGCUGGGG ...[[[[[[............((((((]]]]]]....)))))).. ((((((((..(.((((....)))).)..))))).)))........ ((((((((.(((((((....)))).)))))))).)))........ Energy of known structure: -11.64 Initial sens: 0.417, Initial ppv: 0.385, Initial F-measure: 0.400, Initial Energy: -12.27 New CC sens: 0.417, New CC ppv: 0.333, New CC F-measure: 0.370, New CC Energy: -14.04 ((([[[[[[....))).....((((((]]]]]]....)))))).. New CC sens: 1.000, New CC ppv: 0.800, New CC F-measure: 0.889, New CC Energy: -13.89 ((((((..[[[[[...))))))..]]]]].(((......)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.14 ((((((..........))))))(((((..........)))))... New CC sens: 0.417, New CC ppv: 0.455, New CC F-measure: 0.435, New CC Energy: -12.98 .(((((..........)))))((((((..........)))))).. New CC sens: 0.500, New CC ppv: 0.545, New CC F-measure: 0.522, New CC Energy: -12.98 ((((((((.(((((((....)))).))))))))....)))..... New CC sens: 0.417, New CC ppv: 0.333, New CC F-measure: 0.370, New CC Energy: -12.66 (((((((((.((((((....)))).))))))))....)))..... New CC sens: 0.500, New CC ppv: 0.400, New CC F-measure: 0.444, New CC Energy: -12.38 (((.....[[[[[)))...(((((]]]]].......))))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.76 (((((.....)).)))...(((((.((((...))))))))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.66 ...((((((............[[[[[[))))))....]]]]]].. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -11.64 ((([[[[[[....)))...(((((...]]]]]]...))))).... New CC sens: 0.500, New CC ppv: 0.429, New CC F-measure: 0.462, New CC Energy: -11.51 .(((((..((((((((....)))).))))...........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.99 ((((((..........))))))...(((((..........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.97 ...((((((.((((((....)))).))))))))............ New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -10.95 .(((((......((((....))))(((((...)))))...))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.92 .((((((....)))...))).((((((..........)))))).. New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -10.90 ((((((..........))))))..(((((...)))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.85 (((((((((...((((....))))...))))))....)))..... New CC sens: 0.500, New CC ppv: 0.462, New CC F-measure: 0.480, New CC Energy: -10.83 (((..........))).....((((((..........)))))).. New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -10.53 ..(((.(((......))).(((((.((((...))))))))).))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.50 New CC F-measure-avg: 0.327, New CC F-measure-best: 1.000, New CC best-subopt: 9, New CC num-subopt: 19 > SSTRAND_ID=BWYV; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCGCGGCACCGUCCGCGGAACAAACGG ..(((((..[[[[)))))......]]]] ..(((((..[[[[)))))......]]]] ..(((((..[[[[)))))......]]]] Energy of known structure: -8.79 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.79 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.79 ..(((((......))))).......... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -5.14 .(((.....[[[[.))).......]]]] New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -4.24 .........(((.[[[)))......]]] New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.14 ((.......))..(((.........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.03 .........(((....)))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.77 ((((......))))..((.......)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.67 .(((..........)))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.59 .........((((...........)))) New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -1.39 New CC F-measure-avg: 0.314, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 8 > SSTRAND_ID=Ec_PK1; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC [[[[[.((((((..]]]]].....)))))) (((((.[[[[[[..))))).....]]]]]] ((((([[[......)))))......]]].. Energy of known structure: -6.98 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.98 New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -6.99 (((((.[[[[[[..))))).....]]]]]] New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.98 ...((([[[[[[..))).......]]]]]] New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -5.73 ...(((((.....)))))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.08 ......((((((............)))))) New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -5.02 (((((.........)))))........... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -4.66 ((.....))..((((..........)))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.96 ......((((.[[[[.)))).....]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.38 .....(((((....)).........))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.92 ...(((........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.16 New CC F-measure-avg: 0.346, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 9 > SSTRAND_ID=Ec_PK4; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC ((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]] ((((((((((.(((........))).))))))))))................ ((((((((((.(((........))).))))))))))................ Energy of known structure: -12.24 Initial sens: 0.684, Initial ppv: 1.000, Initial F-measure: 0.812, Initial Energy: -11.01 New CC sens: 0.684, New CC ppv: 1.000, New CC F-measure: 0.812, New CC Energy: -11.01 ((((((((((((((....)))).[[[))))))))))...]]].......... New CC sens: 0.526, New CC ppv: 0.588, New CC F-measure: 0.556, New CC Energy: -9.04 ((((((((((((((....))))....))))))))))................ New CC sens: 0.526, New CC ppv: 0.714, New CC F-measure: 0.606, New CC Energy: -8.41 ((((((((((.[[[[...........))))))))))..]]]].......... New CC sens: 0.526, New CC ppv: 0.714, New CC F-measure: 0.606, New CC Energy: -7.52 New CC F-measure-avg: 0.645, New CC F-measure-best: 0.812, New CC best-subopt: 0, New CC num-subopt: 3 > SSTRAND_ID=EC_S15; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAA ((((.((((((.[[[[[[[))))))))))...............................]]]]]]] ((((.((((((.[[[[[[.)))))))))).............]]]]]]................... ((((.((((((..[[[[[.))))))))))....]]]]]......((((((...........)))))) Energy of known structure: -6.11 Initial sens: 0.588, Initial ppv: 0.625, Initial F-measure: 0.606, Initial Energy: -8.56 New CC sens: 0.588, New CC ppv: 0.476, New CC F-measure: 0.526, New CC Energy: -11.98 (((..((((((..[[[[[.))))))))).....]]]]]......((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.300, New CC F-measure: 0.324, New CC Energy: -10.90 ((((.((((((........))))))))))...............((((((...........)))))) New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -10.69 (((..((((((.[[[[[[.)))))))))..............]]]]]]................... New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -10.07 (((((((((((.[[[[[[.)))))).................]]]]]]...........)))))... New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -9.77 ((((.((((((........))))))))))...((((((.......))))))................ New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -9.38 (((((.(((((........))))))))))...............((((((...........)))))) New CC sens: 0.529, New CC ppv: 0.562, New CC F-measure: 0.545, New CC Energy: -9.33 (((..((((((........)))))))))................((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -9.31 ((((.((((((..[[[[[.))))))))))....]]]]]........(((...........))).... New CC sens: 0.588, New CC ppv: 0.556, New CC F-measure: 0.571, New CC Energy: -8.66 ((((.((((((.[[[[[[.)))))))))).............]]]]]]................... New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -8.56 .....((((((..[[[[[.))))))........]]]]]......((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -8.55 .....((((((.[[[[[[.)))))).................]]]]]]................... New CC sens: 0.353, New CC ppv: 0.500, New CC F-measure: 0.414, New CC Energy: -8.14 (((((((((((........)))))).......((((((.......))))))........)))))... New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -8.10 (((((.(((((........))))))))))...((((((.......))))))................ New CC sens: 0.529, New CC ppv: 0.562, New CC F-measure: 0.545, New CC Energy: -8.02 (((..((((((........)))))))))....((((((.......))))))................ New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -8.00 .....((((((........))))))...................((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.500, New CC F-measure: 0.414, New CC Energy: -7.89 (((((((((((........)))))).......))))).......((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -7.80 (((((...[[[[{{{{{{{{....)))))]]]].((((.......))))..........}}}}}}}} New CC sens: 0.647, New CC ppv: 0.524, New CC F-measure: 0.579, New CC Energy: -7.79 (((((..[[[[[{{{{{{{{....)))))..............]]]]]...........}}}}}}}} New CC sens: 0.647, New CC ppv: 0.611, New CC F-measure: 0.629, New CC Energy: -7.76 (((..((((((..[[[[[.))))))))).....]]]]]........(((...........))).... New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -7.58 New CC F-measure-avg: 0.463, New CC F-measure-best: 0.629, New CC best-subopt: 18, New CC num-subopt: 19 > SSTRAND_ID=HDV; TYPE=hepatitis delta virus ribozyme; EXT_SOURCE=Isambert and Siggia 2000; ggccggcatggtcccagcctcctcgctggcgccggctgggcaacauuccgaggggaccguccccucgguaauggcgaaugggaccca [[[[[[[..((((((((((........)))]]]]]]]......(((((((((((((...))))))))).)))).....))))))).. .((((((..[[[[[[[[[[[...{{{{...)))))).]]]]......(((((((((...)))))))))....}}}}..]]]]]]].. .((((((..[[[[[[[[[[[...{{{{{..)))))).]]]]......(((((((((...)))))))))...}}}}}..]]]]]]].. Energy of known structure: -27.20 Initial sens: 0.733, Initial ppv: 0.733, Initial F-measure: 0.733, Initial Energy: -30.58 New CC sens: 0.733, New CC ppv: 0.710, New CC F-measure: 0.721, New CC Energy: -31.20 .((((((..[[[[[[[[[[[..........)))))).]]]]..(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.867, New CC ppv: 0.867, New CC F-measure: 0.867, New CC Energy: -28.32 .((((((.....[[[[[[[.....))))))...]]]]]]]...(((((((((((((...))))))))).)))).............. New CC sens: 0.433, New CC ppv: 0.500, New CC F-measure: 0.464, New CC Energy: -28.18 (.(((((.((((.(((((......))))).))))))))).)..(((((((((((((...))))))))).)))).............. New CC sens: 0.433, New CC ppv: 0.464, New CC F-measure: 0.448, New CC Energy: -28.06 .((((((..[[[[[[[[[[[....)))))).......]]]]..(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.667, New CC ppv: 0.667, New CC F-measure: 0.667, New CC Energy: -28.02 .((((((..[[[[[[[.......[[[[[..))))))..(....)...(((((((((...)))))))))...]]]]]..]]]]]]].. New CC sens: 0.733, New CC ppv: 0.786, New CC F-measure: 0.759, New CC Energy: -27.33 .((((((......(((((......))))).))))))((((...(((((((((((((...)))))))))........))))...)))) New CC sens: 0.500, New CC ppv: 0.536, New CC F-measure: 0.517, New CC Energy: -26.91 ..(((((..(((.(((((......))))).))).)))))....(((((((((((((...))))))))).)))).............. New CC sens: 0.433, New CC ppv: 0.500, New CC F-measure: 0.464, New CC Energy: -26.45 ..(((((..[[[[[[[(((........)))....)))))....(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.767, New CC ppv: 0.821, New CC F-measure: 0.793, New CC Energy: -26.40 .((((((..[[[[[[[(((........)))))))))...((..(((((((((((((...))))))))).))))))...]]]]]]].. New CC sens: 0.967, New CC ppv: 0.935, New CC F-measure: 0.951, New CC Energy: -26.39 .((((((.....[[[[[[[.....))))))...]]]]]]].......(((((((((...)))))))))...(((..........))) New CC sens: 0.300, New CC ppv: 0.360, New CC F-measure: 0.327, New CC Energy: -26.26 (.(((((.((((.(((((......))))).))))))))).)......(((((((((...)))))))))...(((..........))) New CC sens: 0.300, New CC ppv: 0.333, New CC F-measure: 0.316, New CC Energy: -26.14 ..(((((..(((.(((((......))))).))).)))))((..(((((((((((((...))))))))).))))))............ New CC sens: 0.433, New CC ppv: 0.464, New CC F-measure: 0.448, New CC Energy: -26.08 ..(((((..[[[[[[[(((........)))....)))))((..(((((((((((((...))))))))).))))))...]]]]]]].. New CC sens: 0.767, New CC ppv: 0.767, New CC F-measure: 0.767, New CC Energy: -26.03 .((((((..[[[[[[[(((........))))))))).......(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.967, New CC ppv: 1.000, New CC F-measure: 0.983, New CC Energy: -25.68 .........(((((((((((((..((....)).))..))))..(((((((((((((...))))))))).)))).....))))))).. New CC sens: 0.667, New CC ppv: 0.714, New CC F-measure: 0.690, New CC Energy: -25.61 .((((((......(((((......))))).)))))).......(((((((((((((...))))))))).)))).............. New CC sens: 0.633, New CC ppv: 0.792, New CC F-measure: 0.704, New CC Energy: -25.58 .........(((((((((((....((((....)))).))))..(((((((((((((...))))))))).)))).....))))))).. New CC sens: 0.667, New CC ppv: 0.714, New CC F-measure: 0.690, New CC Energy: -25.38 .((((((..[[[[[[[[[[[..........)))))).]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.733, New CC ppv: 0.846, New CC F-measure: 0.786, New CC Energy: -25.23 .((((((..[[[[[[[[[[[....)))))).......]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -24.93 New CC F-measure-avg: 0.647, New CC F-measure-best: 0.983, New CC best-subopt: 14, New CC num-subopt: 19 > SSTRAND_ID=HDV_anti; TYPE=anti-genomic HDV; EXT_SOURCE=Ferre-D'Amareand et al 1998; GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCACGUCCACUCGGAUGGCUAAGGGAGAGCCACU .((((((........[[[[(((.......)))))))))....(((((((....((((....))))..)))))))......]]]]....... .........((((.(((((.((((((((..((((.....))))...)).))))))..((.(((((....)))))))....))))))))).. (((((((..[[[[.[[[[[.[[[[[[......)))))))...(((((((]]]]]]............)))))))......]]]]]]]]].. Energy of known structure: -14.38 Initial sens: 0.167, Initial ppv: 0.143, Initial F-measure: 0.154, Initial Energy: -23.91 New CC sens: 0.708, New CC ppv: 0.586, New CC F-measure: 0.642, New CC Energy: -26.51 (((((((..[[[[.[[[[[...[[[[[.....)))))))...(((((((..]]]]]...........)))))))......]]]]]]]]].. New CC sens: 0.708, New CC ppv: 0.607, New CC F-measure: 0.654, New CC Energy: -24.07 (((((((..[[[[.[[[[[.[[[[[[[[....))))))).......]].]]]]]]..((.(((((....)))))))....]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.323, New CC F-measure: 0.364, New CC Energy: -24.02 .........((((.(((((.((((((((..((((.....))))...)).))))))..((.(((((....)))))))....))))))))).. New CC sens: 0.167, New CC ppv: 0.143, New CC F-measure: 0.154, New CC Energy: -23.91 ((((((...[[[[.[[[[[.[[[[[[..))))))........(((((((]]]]]]............)))))))......]]]]]]]]].. New CC sens: 0.458, New CC ppv: 0.393, New CC F-measure: 0.423, New CC Energy: -23.16 ...((((..[[[[.[[[[[.[[[[[[....{{{{{{..{{{{{..))))]]]]]]......}}}}}.}}}}}}.......]]]]]]]]].. New CC sens: 0.167, New CC ppv: 0.133, New CC F-measure: 0.148, New CC Energy: -23.14 (((((((..[[[[.[[[[[.[[[[[[......)))))))((....))..]]]]]]..((.(((((....)))))))....]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.323, New CC F-measure: 0.364, New CC Energy: -22.31 .........((((.(((((.((((((((..((((.....))))...)).)))))).....(((((....)))))......))))))))).. New CC sens: 0.167, New CC ppv: 0.154, New CC F-measure: 0.160, New CC Energy: -22.29 (((((((.......[[[[[.[[[[[[......)))))))...(((((((]]]]]]............)))))))......]]]]]...... New CC sens: 0.708, New CC ppv: 0.680, New CC F-measure: 0.694, New CC Energy: -22.18 .........((((.(((((.((((((....(((((...)))))......))))))..((.(((((....)))))))....))))))))).. New CC sens: 0.167, New CC ppv: 0.148, New CC F-measure: 0.157, New CC Energy: -21.94 (((((((..[[[[.[[[[[.[[[[[[[[....))))))).......]].]]]]]].....(((((....)))))......]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.345, New CC F-measure: 0.377, New CC Energy: -21.91 (((((((..[[[[.[[[[[(((.......))))))))))((.(((((((....((((....))))..))))))).))...]]]]]]]]].. New CC sens: 1.000, New CC ppv: 0.750, New CC F-measure: 0.857, New CC Energy: -21.27 (((((((..[[[[.......[[[[[[......)))))))...(((((((]]]]]]............)))))))...........]]]].. New CC sens: 0.542, New CC ppv: 0.542, New CC F-measure: 0.542, New CC Energy: -21.11 (((((((..[[[[.[[[[[(((.......))))))))))...(((((((....((((....))))..)))))))......]]]]]]]]].. New CC sens: 1.000, New CC ppv: 0.800, New CC F-measure: 0.889, New CC Energy: -20.87 ((((((...[[[[.[[[[[.[[[[[[[[))))))............]].]]]]]]..((.(((((....)))))))....]]]]]]]]].. New CC sens: 0.167, New CC ppv: 0.133, New CC F-measure: 0.148, New CC Energy: -20.67 ((((((...[[[[.[[[[[.[[[[[[[[))))))....(((((...]].]]]]]]......)))))..............]]]]]]]]].. New CC sens: 0.167, New CC ppv: 0.143, New CC F-measure: 0.154, New CC Energy: -20.33 .........((((.(((((.((((((....(((((...)))))......)))))).....(((((....)))))......))))))))).. New CC sens: 0.167, New CC ppv: 0.160, New CC F-measure: 0.163, New CC Energy: -20.32 (((((((..[[[[.[[[[[.[[[[[[......)))))))((....))..]]]]]].....(((((....)))))......]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.345, New CC F-measure: 0.377, New CC Energy: -20.19 ((((((...[[[[.[[[[[.[[[[[[..))))))....(((((......]]]]]]......)))))..............]]]]]]]]].. New CC sens: 0.167, New CC ppv: 0.154, New CC F-measure: 0.160, New CC Energy: -19.94 .........((((.(((((.((...(((.....)))...)).(((((((....((((....))))..)))))))......))))))))).. New CC sens: 0.625, New CC ppv: 0.600, New CC F-measure: 0.612, New CC Energy: -19.91 New CC F-measure-avg: 0.402, New CC F-measure-best: 0.889, New CC best-subopt: 13, New CC num-subopt: 19 > SSTRAND_ID=HIVRT32; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGCUCAACGGGAAAAUGAGCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. .......(((((.[[[[[[.)))))...]]]]]]. Energy of known structure: -7.92 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.92 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.92 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -7.16 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -5.22 ...(((.[[[[[..)))...]]]]].......... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -3.81 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -2.60 .......((((...........))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.28 New CC F-measure-avg: 0.571, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 5 > SSTRAND_ID=HIVRT322; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGGGUAACGGGAAAAUGCCCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. .......(((((.[[[[[[.)))))...]]]]]]. Energy of known structure: -7.41 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.41 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.41 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -6.65 .........((....))....(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.71 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -4.65 .....(((((....)))))..(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.10 ....(((((((....))....[[[..)))))]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.73 .........((....))....(((.......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.66 ........(((...)))....(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.62 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -2.60 .....(((((....)))))..(((.......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.05 ....(((((.....[[[.........)))))]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.97 New CC F-measure-avg: 0.264, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 10 > SSTRAND_ID=HIVRT33; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGCUUGACGGGAAAAUAAGCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. ((((((.[[[[[..))))))]]]]].......... Energy of known structure: -6.09 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.09 New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -6.32 .......(((((.[[[[[[.)))))...]]]]]]. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.09 ((((((.[[[[...))))))..]]]]......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.87 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -5.33 ((((((........))))))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.94 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -2.84 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -2.60 .......((((...........))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.28 ...(((.(((((........)))))......))). New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -1.22 ...(((.((((...........)))).....))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.56 New CC F-measure-avg: 0.388, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 9 > SSTRAND_ID=Hs_Prp; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GCCUCAUGGUGGUGGCUGGGGGCAGCCUCAUGGUGGUGGCUGGGG ...((((((.............[[[[[))))))....]]]]]... (((((((.((((.(((((....))))))))).)))).)))..... (((((((.((((.(((((....))))))))).)))).)))..... Energy of known structure: -3.89 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -13.44 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.44 .((((.((((....))))))))(((((..........)))))... New CC sens: 0.455, New CC ppv: 0.385, New CC F-measure: 0.417, New CC Energy: -10.59 (((((.......[[[[[[))))).(((....)))..]]]]]]... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.37 .(((((..........))))).(((((..........)))))... New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -10.10 .((((((.((((.(((((....))))))))).)))......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.93 (((((..(((....))).)))))..(((((..........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.63 New CC F-measure-avg: 0.149, New CC F-measure-best: 0.476, New CC best-subopt: 3, New CC num-subopt: 5 > SSTRAND_ID=LP_PK1; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; CGAGAAGGAGAUCUCUCGUAAAUAAGACUC [[[[[..(((.((]]]]].......))))) .((((..[[[.))))............]]] (((((.(....).)))))............ Energy of known structure: -3.70 Initial sens: 0.300, Initial ppv: 0.429, Initial F-measure: 0.353, Initial Energy: -2.50 New CC sens: 0.500, New CC ppv: 0.833, New CC F-measure: 0.625, New CC Energy: -3.13 .((((......))))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.23 ......(((....))).............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: 0.38 New CC F-measure-avg: 0.208, New CC F-measure-best: 0.625, New CC best-subopt: 0, New CC num-subopt: 2 > SSTRAND_ID=minimalIBV; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGGGUAUCAGUCAGGCUCGGCUGGUACCCCUUGCAAAGCGAGCCU (((((((((((..[[[[[[)))))))))))........]]]]]]. ((((((((((((......))))))))))))............... ((((((((((((..[[[.))))))))))))......]]]...... Energy of known structure: -19.10 Initial sens: 0.647, Initial ppv: 0.917, Initial F-measure: 0.759, Initial Energy: -14.35 New CC sens: 0.647, New CC ppv: 0.733, New CC F-measure: 0.688, New CC Energy: -15.44 ((((((((((((......))))))))))))..((.......)).. New CC sens: 0.647, New CC ppv: 0.786, New CC F-measure: 0.710, New CC Energy: -14.65 .(((((((((((......)))))))))))(((((...)))))... New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -13.10 New CC F-measure-avg: 0.668, New CC F-measure-best: 0.710, New CC best-subopt: 1, New CC num-subopt: 2 > SSTRAND_ID=MMTV; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGGGCAGUCCCCUAGCCCCACUCAAAAGGGGGAU [[[[[..((((((.]]]]]........)))))). (((((.[[[[[[[.)))))........]]]]]]] (((((.[[[[[[[.)))))........]]]]]]] Energy of known structure: -16.25 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -15.15 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -15.15 (((((..[[[[[[.))))).......]]]]]].. New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -14.71 ((((....))))...((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.43 (((((....[[[[.))))).........]]]].. New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -9.40 (((((..[[[[...)))))........]]]]... New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -8.46 (((((.........))))).(((....))).... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -8.39 ((((....))))...((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.38 ((((.....))))..((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.49 .(((...[[[[[[...))).......]]]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.39 ((((....))))...(((.........))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.98 (((((.....[[[.)))))..........]]].. New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -6.96 (((...[[[[[[[..))).........]]]]]]] New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -6.92 .(((..[[[[[[[...)))........]]]]]]] New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -6.88 ((((...))))....((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.51 ((((.....))))..((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.44 ......(((((((..............))))))) New CC sens: 0.545, New CC ppv: 0.857, New CC F-measure: 0.667, New CC Energy: -6.41 ((((....))))....(((..........))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.28 .(((......)))..((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.69 ((((...))))....((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.46 New CC F-measure-avg: 0.278, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 18 > SSTRAND_ID=MMTV_vpk; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCGCAGUGGGUCAGCGCCACUCAAAAGGCCCAU [[[[[..((((((.]]]]]........)))))). (((((.[[[[[[[.)))))........]]]]]]] (((((.[[[[[[[.)))))........]]]]]]] Energy of known structure: -14.41 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -13.31 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -13.31 (((((..[[[[[..)))))]]]]].......... New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -8.02 (((((.........)))))............... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -6.54 (((....(((((.......)))))....)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.02 ......(((((((..............))))))) New CC sens: 0.545, New CC ppv: 0.857, New CC F-measure: 0.667, New CC Energy: -5.96 (((..(((((.......)))))......)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.21 .......(((((....[[[)))))...]]].... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.99 .....(((((.......)))))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.19 (((.......)))...(((........))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.40 (((......(((....))).........)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.67 New CC F-measure-avg: 0.272, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 9 > SSTRAND_ID=pKA_A; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCCGCCAGGCUCCAGCGGCCUUGCAAAAGGAGCCU [[[[[[..((((((.]]]]]]........)))))). ((((((.[[[[[[[.))))))........]]]]]]] ((((((.[[[[[[[.))))))........]]]]]]] Energy of known structure: -18.55 Initial sens: 1.000, Initial ppv: 0.923, Initial F-measure: 0.960, Initial Energy: -16.76 New CC sens: 1.000, New CC ppv: 0.923, New CC F-measure: 0.960, New CC Energy: -16.75 ....((([[[[[[[...))).........]]]]]]] New CC sens: 0.500, New CC ppv: 0.600, New CC F-measure: 0.545, New CC Energy: -9.26 ........((((((....((...))....)))))). New CC sens: 0.500, New CC ppv: 0.750, New CC F-measure: 0.600, New CC Energy: -8.84 ((((((.........))))))..((.......)).. New CC sens: 0.500, New CC ppv: 0.750, New CC F-measure: 0.600, New CC Energy: -8.82 ((((....))))...((..((((....)))).)).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.66 .......(((((((.((......))....))))))) New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -7.50 ((((....)))).....((((((....)))..))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.25 (((.((.((((.......)))).)).......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.96 ((((((.........))).((((....)))).))). New CC sens: 0.250, New CC ppv: 0.300, New CC F-measure: 0.273, New CC Energy: -6.27 ((((....)))).......((((....))))..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.02 (((([[[.)))).....]]](((....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.78 New CC F-measure-avg: 0.323, New CC F-measure-best: 0.960, New CC best-subopt: 0, New CC num-subopt: 10 > SSTRAND_ID=satRPV; TYPE=ribozyme; EXT_SOURCE=van Batenburg et al 2001; ACAGAGCGCGUACUGUCUGACGACGUAUCCGCGCGGACUAGAAGGCUGGUGCCUCGUCCAACAAAUAGAUACA ((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))). ((((.[[[[[..))))..(((((.{{{{{]]]]](((((((....))))).))))))).........}}}}}. .....(((((....(((....)))[[[[[)))))((((..((.(((....)))))))))........]]]]]. Energy of known structure: -13.06 Initial sens: 0.636, Initial ppv: 0.538, Initial F-measure: 0.583, Initial Energy: -13.47 New CC sens: 0.773, New CC ppv: 0.773, New CC F-measure: 0.773, New CC Energy: -14.14 .....(((((....(((....)))[[[[[)))))((((....((((....)))).))))........]]]]]. New CC sens: 0.818, New CC ppv: 0.857, New CC F-measure: 0.837, New CC Energy: -14.03 .(((([[[[[.....)))).....(((((]]]]]((((..((.(((....)))))))))........))))). New CC sens: 0.773, New CC ppv: 0.739, New CC F-measure: 0.756, New CC Energy: -13.92 .(((([[[[[.....)))).....(((((]]]]]((((....((((....)))).))))........))))). New CC sens: 0.818, New CC ppv: 0.818, New CC F-measure: 0.818, New CC Energy: -13.81 ((((.[[[[[..))))..(((((.{{{{{]]]]]..(((((....)))))...))))).........}}}}}. New CC sens: 0.636, New CC ppv: 0.583, New CC F-measure: 0.609, New CC Energy: -13.65 ((((.[[[[[..))))..(((((.{{{{{]]]]](((((((....))))).))))))).........}}}}}. New CC sens: 0.636, New CC ppv: 0.538, New CC F-measure: 0.583, New CC Energy: -13.47 ((((.[[[[[..))))........(((((]]]]]((((..((.(((....)))))))))........))))). New CC sens: 0.955, New CC ppv: 0.913, New CC F-measure: 0.933, New CC Energy: -13.17 ((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))). New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.06 .....((((((((.(((....))))))..)))))((((..((.(((....))))))))).............. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -13.04 ((((..[[[[[.))))..(((((.{{{{{.]]]]].(((((....)))))...))))).........}}}}}. New CC sens: 0.409, New CC ppv: 0.375, New CC F-measure: 0.391, New CC Energy: -13.03 .....((((((((.(((....))))))..)))))((((....((((....)))).)))).............. New CC sens: 0.591, New CC ppv: 0.684, New CC F-measure: 0.634, New CC Energy: -12.93 .....(((((....(((....))).....)))))((((..((.(((....))))))))).............. New CC sens: 0.545, New CC ppv: 0.706, New CC F-measure: 0.615, New CC Energy: -12.86 .....(((((....(((....))).....)))))((((....((((....)))).)))).............. New CC sens: 0.591, New CC ppv: 0.812, New CC F-measure: 0.684, New CC Energy: -12.75 .(((([[[[[.....))))..........]]]]]((((..((.(((....))))))))).............. New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -12.70 ((((..[[[[[.))))..............]]]]].......((((....))))................... New CC sens: 0.364, New CC ppv: 0.615, New CC F-measure: 0.457, New CC Energy: -12.69 .(((([[[[[.....))))..........]]]]]((((....((((....)))).)))).............. New CC sens: 0.591, New CC ppv: 0.765, New CC F-measure: 0.667, New CC Energy: -12.59 .....(((((....(((....)))[[[[[)))))........((((....)))).............]]]]]. New CC sens: 0.636, New CC ppv: 0.824, New CC F-measure: 0.718, New CC Energy: -12.56 .....(((((........[[[[[.{{{{{)))))..(((((....)))))...]]]]].........}}}}}. New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -12.46 ((((..[[[[[.))))..............]]]]].....((.(((....))))).................. New CC sens: 0.318, New CC ppv: 0.500, New CC F-measure: 0.389, New CC Energy: -12.33 .....(((((........[[[[[.{{{{{)))))(((((((....))))).))]]]]].........}}}}}. New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -12.28 New CC F-measure-avg: 0.648, New CC F-measure-best: 1.000, New CC best-subopt: 7, New CC num-subopt: 19 > SSTRAND_ID=SRV_1; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCA ((((((.[[[[[.)))))).............]]]]]. ((((((.[[[[[[))))))............]]]]]]. ((((((.[[[[[[))))))............]]]]]]. Energy of known structure: -18.89 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -16.78 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -16.78 ((((....))))..((((((...........)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.47 ((((((.......)))))).......((.......)). New CC sens: 0.545, New CC ppv: 0.750, New CC F-measure: 0.632, New CC Energy: -11.34 (((((([[[{{{.)))))).......]]]....}}}.. New CC sens: 0.545, New CC ppv: 0.500, New CC F-measure: 0.522, New CC Energy: -11.33 ((((((.......)))))).......((((...)))). New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -11.20 .(((..[[[)))..((((((......]]]..)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.63 ((((((...[[[.))))))..............]]].. New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -10.19 .......(((((((((..........)))..)))))). New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -10.03 (((((([[[....)))))).......]]]......... New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -9.63 .(((...[[[[[[...)))............]]]]]]. New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -9.29 .((((..[[[[[[.............)))).]]]]]]. New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -9.27 .(((.....)))..((((((...........)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.40 .((((.........[[[[[[......)))).]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.26 (((.....)))...((((((...........)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.24 New CC F-measure-avg: 0.383, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 13 > SSTRAND_ID=T2_gene32; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGC .[[[[[.(((((((]]]]].......))))))) .(((((.[[[[[[[))))).......]]]]]]] .(((((.[[[[[[[))))).......]]]]]]] Energy of known structure: -6.67 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.67 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.67 .......(((((((.(........).))))))) New CC sens: 0.583, New CC ppv: 0.875, New CC F-measure: 0.700, New CC Energy: -6.42 .(((((........))))).............. New CC sens: 0.417, New CC ppv: 1.000, New CC F-measure: 0.588, New CC Energy: -4.00 New CC F-measure-avg: 0.763, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 2 > SSTRAND_ID=T4_gene32; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; UGCCAGCUAUGAGGUAAAGUGUCAUAGC [[[[.(((((((]]]].....))))))) ((((.[[[[[[[)))).....]]]]]]] .....(((((((.........))))))) Energy of known structure: -1.71 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -1.71 New CC sens: 0.636, New CC ppv: 1.000, New CC F-measure: 0.778, New CC Energy: -5.48 ((((.[[[....)))).]]]........ New CC sens: 0.364, New CC ppv: 0.571, New CC F-measure: 0.444, New CC Energy: -2.15 ((((.[[[[[[[)))).....]]]]]]] New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -1.71 New CC F-measure-avg: 0.741, New CC F-measure-best: 1.000, New CC best-subopt: 2, New CC num-subopt: 2 > SSTRAND_ID=TMV.L; TYPE=viral RNA; EXT_SOURCE=van Belkum et al 1985; AUAAUAAAUAACGGAUUGUGUCCGUAAUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAAUCGAAGGG ............[[[.((((]]].....))))[[[.((((((]]]...))))))[[[[.....(((((]]]]......).)))) ................(((((.((((...[[[[{{{{))))..<<<<.)))))..]]]]....((((}}}}....>>>>.)))) ..........((((((...))))))....((((...((((((.[[[[.)))))).))))....((((........]]]].)))) Energy of known structure: -15.98 Initial sens: 0.160, Initial ppv: 0.160, Initial F-measure: 0.160, Initial Energy: -10.81 New CC sens: 0.520, New CC ppv: 0.542, New CC F-measure: 0.531, New CC Energy: -13.47 ..........((((((...))))))....(((([[[[(((((......)))))..))))....((((]]]].........)))) New CC sens: 0.480, New CC ppv: 0.522, New CC F-measure: 0.500, New CC Energy: -12.78 ..........(((...((((........))))))).((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.720, New CC ppv: 0.720, New CC F-measure: 0.720, New CC Energy: -12.58 ..........((((((...))))))...........((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.680, New CC ppv: 0.708, New CC F-measure: 0.694, New CC Energy: -12.45 ..........((((((...))))))....((((...((((((.[[[[.)))))).)))).....(((........]]]]..))) New CC sens: 0.360, New CC ppv: 0.391, New CC F-measure: 0.375, New CC Energy: -12.17 ..........((((((...))))))....((((...((((((......)))))).))))....((((.(.........).)))) New CC sens: 0.520, New CC ppv: 0.619, New CC F-measure: 0.565, New CC Energy: -12.06 ................((((........))))....((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.720, New CC ppv: 0.818, New CC F-measure: 0.766, New CC Energy: -12.03 ..........((((((...))))))........(((((((((......)))))..........[[[[)))).........]]]] New CC sens: 0.480, New CC ppv: 0.632, New CC F-measure: 0.545, New CC Energy: -11.53 ..........(((...((((........))))))).((((((.[[[[.))))))((((......{{{.))))...]]]]..}}} New CC sens: 0.560, New CC ppv: 0.583, New CC F-measure: 0.571, New CC Energy: -11.28 ..........((((((...))))))...........((((((.[[[[.))))))((((......{{{.))))...]]]]..}}} New CC sens: 0.520, New CC ppv: 0.565, New CC F-measure: 0.542, New CC Energy: -11.15 ..........(((...((((........))))))).((((((.[[[[.)))))).........((((........]]]].)))) New CC sens: 0.560, New CC ppv: 0.667, New CC F-measure: 0.609, New CC Energy: -11.06 ..........((((((...))))))....(((([[[[(((((......)))))..)))).....(((]]]]..........))) New CC sens: 0.320, New CC ppv: 0.364, New CC F-measure: 0.340, New CC Energy: -11.03 ..........((((((...))))))....(((([[[[......{{{{........))))....((((]]]]....}}}}.)))) New CC sens: 0.280, New CC ppv: 0.318, New CC F-measure: 0.298, New CC Energy: -10.95 ..........((((((...))))))...........((((((.[[[[.)))))).........((((........]]]].)))) New CC sens: 0.520, New CC ppv: 0.650, New CC F-measure: 0.578, New CC Energy: -10.93 ................((((........)))).(((((((((......)))))..........[[[[)))).........]]]] New CC sens: 0.520, New CC ppv: 0.765, New CC F-measure: 0.619, New CC Energy: -10.92 ..........((((((...))))))....(((([[[[(((((......)))))..))))........]]]]......(....). New CC sens: 0.320, New CC ppv: 0.400, New CC F-measure: 0.356, New CC Energy: -10.82 ................((((........))))....((((((.[[[[.))))))((((......{{{.))))...]]]]..}}} New CC sens: 0.560, New CC ppv: 0.667, New CC F-measure: 0.609, New CC Energy: -10.73 ................(((((........)))))..((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.560, New CC ppv: 0.609, New CC F-measure: 0.583, New CC Energy: -10.55 ................((((........))))....((((((.[[[[.)))))).........((((........]]]].)))) New CC sens: 0.560, New CC ppv: 0.778, New CC F-measure: 0.651, New CC Energy: -10.51 ..........(((...((((........))))))).((((((......))))))((((.....[[[[.))))........]]]] New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -10.47 New CC F-measure-avg: 0.562, New CC F-measure-best: 0.783, New CC best-subopt: 19, New CC num-subopt: 19 > SSTRAND_ID=Tt_LSU_P3P7; TYPE=ribozyme; EXT_SOURCE=van Batenburg et al 2001; AGACCGUCAAACACAGACUAAAUGUCGGUCGGGGAAGAUGUAUUCUUCUCAUAAGAUAUAGUCGG .(((((.((....[.[[[[[..)).))))).(((((((.....)))))))........]]]]]]. .(((((.((......[[[[[..)).))))).(((((((.....)))))))........]]]]].. .(((((.((.............)).))))).(((((((.....)))))))............... Energy of known structure: -11.87 Initial sens: 0.950, Initial ppv: 1.000, Initial F-measure: 0.974, Initial Energy: -12.29 New CC sens: 0.700, New CC ppv: 1.000, New CC F-measure: 0.824, New CC Energy: -12.98 .(((((.((......[[[[[..)).))))).(((((((.....)))))))........]]]]].. New CC sens: 0.950, New CC ppv: 1.000, New CC F-measure: 0.974, New CC Energy: -12.29 .(((((.((.............)).)))))((((((......))))))................. New CC sens: 0.350, New CC ppv: 0.538, New CC F-measure: 0.424, New CC Energy: -10.47 .(((((......(((.......)))))))).(((((((.....)))))))............... New CC sens: 0.600, New CC ppv: 0.800, New CC F-measure: 0.686, New CC Energy: -10.23 .(((((.........[[[[[.....))))).(((((((.....)))))))........]]]]].. New CC sens: 0.850, New CC ppv: 1.000, New CC F-measure: 0.919, New CC Energy: -10.21 .(((((.((.............)).)))))(((((...[[[[[[.)))))....]]]]]]..... New CC sens: 0.350, New CC ppv: 0.389, New CC F-measure: 0.368, New CC Energy: -10.14 ...(((.........((((..[[[[[)))).(((((((.....)))))))....]]]]]...))) New CC sens: 0.350, New CC ppv: 0.368, New CC F-measure: 0.359, New CC Energy: -10.06 ...............(((((...(((.....(((((((.....)))))))....))).))))).. New CC sens: 0.600, New CC ppv: 0.800, New CC F-measure: 0.686, New CC Energy: -9.79 .(((((.((......[[[[[..)).)))))((((((......))))))..........]]]]].. New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -9.78 ...............((((..[[[[[)))).(((((((.....)))))))....]]]]]...... New CC sens: 0.350, New CC ppv: 0.438, New CC F-measure: 0.389, New CC Energy: -9.44 .....(((.......)))...(((((.....(((((((.....)))))))....)))))...... New CC sens: 0.350, New CC ppv: 0.467, New CC F-measure: 0.400, New CC Energy: -9.06 New CC F-measure-avg: 0.605, New CC F-measure-best: 0.974, New CC best-subopt: 1, New CC num-subopt: 10 > SSTRAND_ID=TYMV; TYPE=viral RNA; EXT_SOURCE=Deiman et al 1997; UUAGCUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACCA ....(((((......)))))(((((((.......)))))))...((((.......))))[[[...((((((]]]...))))))... (((((([[[[)))))).((((((((((.......))))))......]]]].....[[[...))))((((((]]]...))))))... ....(((((......)))))(((((((.......)))))))....(((.......)))((((...[[[[[[))))..]]]]]]... Energy of known structure: -21.87 Initial sens: 0.480, Initial ppv: 0.414, Initial F-measure: 0.444, Initial Energy: -15.40 New CC sens: 0.960, New CC ppv: 0.960, New CC F-measure: 0.960, New CC Energy: -20.01 ....(((((......))))).((((((.......))))))....((((.......)))).(((((....)))))............ New CC sens: 0.600, New CC ppv: 0.750, New CC F-measure: 0.667, New CC Energy: -19.67 ....(((((......)))))((((((([[[....)))))))....]]]..........((((...[[[[[[))))..]]]]]]... New CC sens: 0.840, New CC ppv: 0.840, New CC F-measure: 0.840, New CC Energy: -19.02 ....(((((......)))))(((((((.......)))))))....(((.((.......)))))..((((((......))))))... New CC sens: 0.720, New CC ppv: 0.783, New CC F-measure: 0.750, New CC Energy: -18.94 ....(((((......)))))(((((((.......)))))))...((((.......))))......((((((......))))))... New CC sens: 0.880, New CC ppv: 1.000, New CC F-measure: 0.936, New CC Energy: -18.85 ....(((((......)))))((((((([[[....)))))))....(((.((.......)))))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.692, New CC F-measure: 0.706, New CC Energy: -18.84 ....(((((......)))))((((((([[[....)))))))....]]]......(((.(.(((((....))))).)...))).... New CC sens: 0.480, New CC ppv: 0.500, New CC F-measure: 0.490, New CC Energy: -18.67 ....(((((......)))))((((((([[[....)))))))...((((.......))))......((((((]]]...))))))... New CC sens: 0.880, New CC ppv: 0.880, New CC F-measure: 0.880, New CC Energy: -18.57 ....(((((......)))))(((((((.......)))))))....(((.......[[[..)))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.750, New CC F-measure: 0.735, New CC Energy: -18.54 ....(((((......)))))(((((((.......)))))))....(((((.......)))))...((((((......))))))... New CC sens: 0.720, New CC ppv: 0.783, New CC F-measure: 0.750, New CC Energy: -18.29 ....(((((......)))))((((((([[[....)))))))....(((((.......)))))...((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.692, New CC F-measure: 0.706, New CC Energy: -18.13 ....(((((......))))).......(((...............(((.((.......)))))..[[[[[[)))...]]]]]]... New CC sens: 0.440, New CC ppv: 0.579, New CC F-measure: 0.500, New CC Energy: -17.32 ....(((((......))))).......(((..............((((.......))))......[[[[[[)))...]]]]]]... New CC sens: 0.600, New CC ppv: 0.833, New CC F-measure: 0.698, New CC Energy: -17.23 ....(((((......)))))......(((................(((.((.......)))))..[[[[[[)))...]]]]]]... New CC sens: 0.440, New CC ppv: 0.579, New CC F-measure: 0.500, New CC Energy: -17.20 ....(((((......)))))......(((...............((((.......))))......[[[[[[)))...]]]]]]... New CC sens: 0.600, New CC ppv: 0.833, New CC F-measure: 0.698, New CC Energy: -17.11 ....(((((......)))))((((((([[[....)))))))....]]]............(((((....)))))............ New CC sens: 0.480, New CC ppv: 0.600, New CC F-measure: 0.533, New CC Energy: -17.07 ....(((((......)))))(((((((.......)))))))....(((............)))..((((((......))))))... New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -17.00 ....(((((......)))))((((((([[[....)))))))....(((............)))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.750, New CC F-measure: 0.735, New CC Energy: -16.90 ((((((....)))))).((((((((((.......))))))....((((.......))))..))))((((((......))))))... New CC sens: 0.640, New CC ppv: 0.615, New CC F-measure: 0.627, New CC Energy: -16.86 ....(((((......)))))((((((([[[....)))))))....]]].......(((.......[[[[[[)))...]]]]]]... New CC sens: 0.720, New CC ppv: 0.750, New CC F-measure: 0.735, New CC Energy: -16.85 New CC F-measure-avg: 0.711, New CC F-measure-best: 0.960, New CC best-subopt: 0, New CC num-subopt: 19 > AKV-MuLV GGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCACUGUCGGGGGGC ((((((((.[[[[[[[)))).))))..................]]]]]]] ...(((((.[[[[[[[)))))...(((((......)).)))..]]]]]]] ...(((((.[[[[[[[)))))...(((((......)).)))..]]]]]]] Energy of known structure: -14.37 Initial sens: 0.733, Initial ppv: 0.647, Initial F-measure: 0.688, Initial Energy: -17.79 New CC sens: 0.733, New CC ppv: 0.647, New CC F-measure: 0.688, New CC Energy: -17.79 ...(((((..[[[[[.)))))...(((((......)).)))..]]]]].. New CC sens: 0.267, New CC ppv: 0.267, New CC F-measure: 0.267, New CC Energy: -16.88 ((((((((.[[[[[[[)))).))))(((.....))).......]]]]]]] New CC sens: 1.000, New CC ppv: 0.833, New CC F-measure: 0.909, New CC Energy: -14.23 ((((((((........)))).)))).......(((((......))))).. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -13.45 ((((((((..[[[[[.)))).))))(((.....))).......]]]]].. New CC sens: 0.533, New CC ppv: 0.500, New CC F-measure: 0.516, New CC Energy: -13.32 ((((.....))))((((((((....(((.....))).....)))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.18 (((.......)))((((((((...(((((......)).))))))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.16 ((((((((........)))).)))).......(((((.......))))). New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -12.81 ((((.....[[[[[[[((((....))))...))))........]]]]]]] New CC sens: 0.467, New CC ppv: 0.467, New CC F-measure: 0.467, New CC Energy: -12.62 .........(((((((((((....))))...............))))))) New CC sens: 0.467, New CC ppv: 0.636, New CC F-measure: 0.538, New CC Energy: -12.22 ((((((((........)))).)))).......((((.......))))... New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -12.02 (((.(....).)))..((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.36 ((([[[[[.....)))]]]]]...........(((((......))))).. New CC sens: 0.267, New CC ppv: 0.308, New CC F-measure: 0.286, New CC Energy: -11.16 ((((.....))))...((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.15 (((.(....).)))..((((....))))....(((((.......))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.72 ((((((((........)))).))))........((((........)))). New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -10.67 ((([[[[[.....)))]]]]]...........(((((.......))))). New CC sens: 0.267, New CC ppv: 0.308, New CC F-measure: 0.286, New CC Energy: -10.52 ((((.....))))...((((....))))....(((((.......))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.51 (((..........)))((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.48 ((((.........[[[[[[[[))))(((.....))).....]]]]]]]]. New CC sens: 0.267, New CC ppv: 0.267, New CC F-measure: 0.267, New CC Energy: -10.01 New CC F-measure-avg: 0.328, New CC F-measure-best: 0.909, New CC best-subopt: 2, New CC num-subopt: 19 > BaEV GGGCUCUGGAGCCCCCCCCGAGCCCCGGCUAACUCUAUCUGUAGGGGGGC ((((((.((.[[[[[[[))))))))..................]]]]]]] ((((((......[[[[[[.))))))..................]]]]]]. ((((((...[[[[{{{{{{)))))).]]]].............}}}}}}. Energy of known structure: -14.61 Initial sens: 0.400, Initial ppv: 0.500, Initial F-measure: 0.444, Initial Energy: -14.45 New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -16.43 (((((([[[[[..{{{{{{)))))).......]]]]]......}}}}}}. New CC sens: 0.400, New CC ppv: 0.353, New CC F-measure: 0.375, New CC Energy: -15.93 (((((([[[[[.{{{{{{.)))))).......]]]]]......}}}}}}. New CC sens: 0.400, New CC ppv: 0.353, New CC F-measure: 0.375, New CC Energy: -15.76 ((((((......[[[[[[.))))))..................]]]]]]. New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -14.45 ((((((...[[[[.{{{{{)))))).]]]]..............}}}}}. New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -14.39 (((((([[[[[{{{{{...)))))).......]]]]]......}}}}}.. New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -14.35 ((((((....[[[[[[[..))))))..................]]]]]]] New CC sens: 0.867, New CC ppv: 1.000, New CC F-measure: 0.929, New CC Energy: -14.13 (((((....))))).......(((((..(((..........))).))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.07 (((((([[[[[...{{{{{)))))).......]]]]].......}}}}}. New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -13.88 ((((((.((.......)).))))))..(((..(((((....))))).))) New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -12.77 ((((((.......[[[[[[))))))..................]]]]]]. New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -12.59 ((((((...[[[[..{{{{)))))).]]]]...............}}}}. New CC sens: 0.400, New CC ppv: 0.429, New CC F-measure: 0.414, New CC Energy: -12.52 ((((([[[[)))))(((((.....]]]]................))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.23 .((((.[[[[[..{{{{{{.......))))..]]]]]......}}}}}}. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.86 ((((((...[[[[......)))))).]]]]..((((.......))))... New CC sens: 0.400, New CC ppv: 0.429, New CC F-measure: 0.414, New CC Energy: -11.80 .((((.[[[[[.{{{{{{........))))..]]]]]......}}}}}}. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.69 ((((((...[[[[......)))))).]]]]..(((((....))))).... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -11.64 ((((((.((.......)).)))))).......(((((....))))).... New CC sens: 0.400, New CC ppv: 0.462, New CC F-measure: 0.429, New CC Energy: -11.22 .((((....))))((((((.(((....))).............)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.06 (((((....)))))(((((.(((....)))..............))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.86 New CC F-measure-avg: 0.309, New CC F-measure-best: 0.929, New CC best-subopt: 6, New CC num-subopt: 19 > BLV GGGGGGACUUAGCGCCCCCCAAACCGU ((((((.....[[[))))))....]]] ((((((........))))))....... ((((((........))))))....... Energy of known structure: -6.45 Initial sens: 0.667, Initial ppv: 1.000, Initial F-measure: 0.800, Initial Energy: -9.98 New CC sens: 0.667, New CC ppv: 1.000, New CC F-measure: 0.800, New CC Energy: -9.98 .(((((.....[[[.)))))....]]] New CC sens: 0.333, New CC ppv: 0.375, New CC F-measure: 0.353, New CC Energy: -7.51 .(((((.........)))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.21 ((((((.....[[[))))))....]]] New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.45 (((((.........)))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.39 New CC F-measure-avg: 0.431, New CC F-measure-best: 1.000, New CC best-subopt: 3, New CC num-subopt: 4 > Bp_PK2 CCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCAACUUCCCAGGGGGCAACCCCGAACCGCAGCAGCGACAUUCACAAGGAAU .((((((..(((....[[[[[[..))).((((((((((....)))))).((((....))))...)))).)))))).......]]]]]].. .((((((.(((((((......)))))))((((((((((....)))))).((((....))))...)))).))))))............... .((((((.((((((((....))))))))((((((((((....)))))).((((....))))...)))).))))))............... Energy of known structure: -26.02 Initial sens: 0.793, Initial ppv: 0.852, Initial F-measure: 0.821, Initial Energy: -29.53 New CC sens: 0.793, New CC ppv: 0.821, New CC F-measure: 0.807, New CC Energy: -30.15 .((((((.((((((((....))))))))....((((((....)))))).((((....))))........))))))............... New CC sens: 0.655, New CC ppv: 0.792, New CC F-measure: 0.717, New CC Energy: -28.04 .((((((.((((((((....))))))))((((((((((....))))))..((((...))))...)))).))))))............... New CC sens: 0.655, New CC ppv: 0.679, New CC F-measure: 0.667, New CC Energy: -27.33 ..(((((.((((((((....))))))))....((((((....)))))).((((....)))).....)))))................... New CC sens: 0.448, New CC ppv: 0.565, New CC F-measure: 0.500, New CC Energy: -26.88 ...((((.((((((((....))))))))))))((((((....)))))).((((....))))....(((....)))............... New CC sens: 0.448, New CC ppv: 0.520, New CC F-measure: 0.481, New CC Energy: -25.74 .((((((.((((((((....))))))))....((((((....))))))..((((...))))........))))))............... New CC sens: 0.517, New CC ppv: 0.625, New CC F-measure: 0.566, New CC Energy: -25.22 ...((((.((((((((....))))))))))))((((((....)))))).((((....))))(((.(((....)))...)))......... New CC sens: 0.448, New CC ppv: 0.464, New CC F-measure: 0.456, New CC Energy: -24.89 New CC F-measure-avg: 0.599, New CC F-measure-best: 0.807, New CC best-subopt: 0, New CC num-subopt: 6 > BVDV_IRES GGGUAGCAACAGUGGUGAACAGCCUGAUAGGGUGCUGCAGAGGCCCACUGUAUUGCUACUAAAAAUCUCUGCU .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. Energy of known structure: -20.66 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -20.66 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -20.66 .((((((((((((((((....((((....))))....)).....)))))))..)))))))............. New CC sens: 0.720, New CC ppv: 0.900, New CC F-measure: 0.800, New CC Energy: -16.32 .((((((((((((((((....((((....))))....)).....))))))..))))))))............. New CC sens: 0.680, New CC ppv: 0.850, New CC F-measure: 0.756, New CC Energy: -16.21 .((((((((((((((....((((((....))..)))).......)))))))..)))))))............. New CC sens: 0.640, New CC ppv: 0.800, New CC F-measure: 0.711, New CC Energy: -15.75 .((((((((((((((......((((....))))(((.....))))))))))..)))))))............. New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -15.75 .((((((((((((((......((((...............)))))))))))..)))))))............. New CC sens: 0.560, New CC ppv: 0.778, New CC F-measure: 0.651, New CC Energy: -15.17 New CC F-measure-avg: 0.783, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 5 > BYDV-NY-RPV GGCGGCGGCGUCCGCCGUAACAAACGC (((((..[[[[))))).......]]]] (((((..[[[[))))).......]]]] (((((..[[[[))))).......]]]] Energy of known structure: -10.31 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -10.31 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -10.30 .(((((((...)))))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.22 (((((......)))))........... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -5.81 .((((((((....)))))......))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.17 ....(((((....)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.46 New CC F-measure-avg: 0.343, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > Cas-Br-E-MuLv GGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCAAAGUCGGGGGGC ((((((((.[[[[[[[)))).))))..................]]]]]]] ...(((((.[[[[[[[)))))....(((.....))).......]]]]]]] ...(((((.[[[[[[[)))))....(((.....))).......]]]]]]] Energy of known structure: -14.37 Initial sens: 0.733, Initial ppv: 0.733, Initial F-measure: 0.733, Initial Energy: -16.95 New CC sens: 0.733, New CC ppv: 0.733, New CC F-measure: 0.733, New CC Energy: -16.95 ...(((((..[[[[[.)))))....(((.....))).......]]]]].. New CC sens: 0.267, New CC ppv: 0.308, New CC F-measure: 0.286, New CC Energy: -16.04 ((((((((.[[[[[[[)))).))))(((.....))).......]]]]]]] New CC sens: 1.000, New CC ppv: 0.833, New CC F-measure: 0.909, New CC Energy: -14.23 ((((((((........)))).)))).......(((((......))))).. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -13.45 ((((((((..[[[[[.)))).))))(((.....))).......]]]]].. New CC sens: 0.533, New CC ppv: 0.500, New CC F-measure: 0.516, New CC Energy: -13.32 (((.......)))((((((((....(((.....))).....)))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.18 ((((((((........)))).)))).......(((((.......))))). New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -12.81 ((((.....[[[[[[[((((....))))...))))........]]]]]]] New CC sens: 0.467, New CC ppv: 0.467, New CC F-measure: 0.467, New CC Energy: -12.62 .........(((((((((((....))))...............))))))) New CC sens: 0.467, New CC ppv: 0.636, New CC F-measure: 0.538, New CC Energy: -12.22 ((((((((........)))).)))).......((((.......))))... New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -12.02 (((.(....).)))..((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.36 ((([[[[[.....)))]]]]]...........(((((......))))).. New CC sens: 0.267, New CC ppv: 0.308, New CC F-measure: 0.286, New CC Energy: -11.16 ((((.....))))...((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.15 (((.(....).)))..((((....))))....(((((.......))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.72 ((((((((........)))).))))........((((........)))). New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -10.67 ((([[[[[.....)))]]]]]...........(((((.......))))). New CC sens: 0.267, New CC ppv: 0.308, New CC F-measure: 0.286, New CC Energy: -10.52 ((((.....))))...((((....))))....(((((.......))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.51 (((..........)))((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.48 ((((.........[[[[[[[[))))(((.....))).....]]]]]]]]. New CC sens: 0.267, New CC ppv: 0.267, New CC F-measure: 0.267, New CC Energy: -10.01 (((.(....).)))..((((....))))....((((.......))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.93 New CC F-measure-avg: 0.331, New CC F-measure-best: 0.909, New CC best-subopt: 2, New CC num-subopt: 19 > CoxB3 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAAAAAA .((((((((((((.[[[[[[.........)))))))))))).....((.(((((.]]]]]]))))).)).... .((((((((((((................))))))))))))........(((((((...)))))))....... .((((((((((((................))))))))))))........(((((((...)))))))....... Energy of known structure: -19.70 Initial sens: 0.680, Initial ppv: 0.895, Initial F-measure: 0.773, Initial Energy: -18.06 New CC sens: 0.680, New CC ppv: 0.895, New CC F-measure: 0.773, New CC Energy: -18.06 .((((((((((((.[[[[[[.........)))))))))))).....((((.....]]]]]]..))))...... New CC sens: 0.720, New CC ppv: 0.818, New CC F-measure: 0.766, New CC Energy: -17.49 (((((((((((((................)))))))).)))))......(((((((...)))))))....... New CC sens: 0.520, New CC ppv: 0.650, New CC F-measure: 0.578, New CC Energy: -14.84 .((((((((((((................)))))))))))).....(((((((....)))...))))...... New CC sens: 0.480, New CC ppv: 0.632, New CC F-measure: 0.545, New CC Energy: -14.57 New CC F-measure-avg: 0.665, New CC F-measure-best: 0.773, New CC best-subopt: 0, New CC num-subopt: 3 > CSFV_IRES GACUAGCCGUAGUGGCGAACGACCUGAUAGGGUGCUGCAGAGGCCCACUAUUAGGCUAGUAUAAAAAUCUCUGCUG .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. Energy of known structure: -20.14 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -20.14 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -20.14 .((((((((((((((......((((....))))(((.....))))))))))..)))))))................ New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -15.35 ........(((((((......((((....))))[[[{{{{{{{.)))))))..]]]...........}}}}}}}.. New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -14.13 .....(((...((((((.....[[[[[[[[..))))))...)))...]]]]]]]]..((((..........)))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.97 .((((((((((((((............[[[[[.(((.....))))))))))..)))))))........]]]]]... New CC sens: 0.560, New CC ppv: 0.636, New CC F-measure: 0.596, New CC Energy: -13.14 .....(((.....)))......((((((((((.(((.....))))).))))))))..((((..........)))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.74 .....(((...(((((.....((((....)))))))))...))).........(((.((...........))))). New CC sens: 0.160, New CC ppv: 0.235, New CC F-measure: 0.190, New CC Energy: -12.73 .....(((.....))).....((((....))))...(((((((((........)))............)))))).. New CC sens: 0.400, New CC ppv: 0.625, New CC F-measure: 0.488, New CC Energy: -12.65 .....((((...)))).....((((....))))((([[[[[[[..........)))...........]]]]]]].. New CC sens: 0.440, New CC ppv: 0.611, New CC F-measure: 0.512, New CC Energy: -12.59 .(((((((.....((.......)).....((((.........)))).......)))))))................ New CC sens: 0.280, New CC ppv: 0.538, New CC F-measure: 0.368, New CC Energy: -12.14 .....(((...((((((.....(((....)))))))))...))).........(((.((...........))))). New CC sens: 0.120, New CC ppv: 0.176, New CC F-measure: 0.143, New CC Energy: -11.98 .....(((.....))).....((((....))))...(((((((...((((......)))).......))))))).. New CC sens: 0.440, New CC ppv: 0.611, New CC F-measure: 0.512, New CC Energy: -11.43 New CC F-measure-avg: 0.448, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 11 > EIAV GGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCC ((((((...[[[[))))))............]]]] (((((((....)).)))))................ ((((((.......))))))................ Energy of known structure: -9.22 Initial sens: 0.500, Initial ppv: 0.714, Initial F-measure: 0.588, Initial Energy: -6.80 New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -8.04 .(((.....[[[[[[.))).........]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.72 .(((.....[[[[[[.)))..........]]]]]] New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -6.94 (((.(((....))).)))................. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.37 (((......[[[[[[)))...........]]]]]] New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -5.18 (((......[[[[[.)))..........]]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.71 (((......[[[[[[)))..........]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.30 New CC F-measure-avg: 0.227, New CC F-measure-best: 0.750, New CC best-subopt: 0, New CC num-subopt: 6 > FeLV GGGCCAGGACCCCCCCCCCUGAGCCCAGGAUAACCUUAAGAAUAGGGGGG ((((((((...[[[[[[)))).))))..................]]]]]] ((((((((..[[[[[[.)))).))))(((....)))........]]]]]] ((((((((...[[[[[[)))).))))(((....)))........]]]]]] Energy of known structure: -15.15 Initial sens: 0.571, Initial ppv: 0.471, Initial F-measure: 0.516, Initial Energy: -14.28 New CC sens: 1.000, New CC ppv: 0.824, New CC F-measure: 0.903, New CC Energy: -15.05 ((((((((..[[[[[[.)))).))))(((....)))........]]]]]] New CC sens: 0.571, New CC ppv: 0.471, New CC F-measure: 0.516, New CC Energy: -14.28 ....((((...[[[[[[)))).....(((....)))........]]]]]] New CC sens: 0.714, New CC ppv: 0.769, New CC F-measure: 0.741, New CC Energy: -13.66 ((((.........[[[[[[[[.))))(((....)))......]]]]]]]] New CC sens: 0.286, New CC ppv: 0.267, New CC F-measure: 0.276, New CC Energy: -13.41 ....((((..[[[[[[.)))).....(((....)))........]]]]]] New CC sens: 0.286, New CC ppv: 0.308, New CC F-measure: 0.296, New CC Energy: -12.88 ((((((((.[[[[[[..)))).))))(((....)))........]]]]]] New CC sens: 0.571, New CC ppv: 0.471, New CC F-measure: 0.516, New CC Energy: -12.56 (((......))).(((((((...(..(((....)))...)...))))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.40 ((((((((.........)))).)))).......((((.......)))).. New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -12.17 ((((((((.........)))).)))).......(((((....)))))... New CC sens: 0.571, New CC ppv: 0.615, New CC F-measure: 0.593, New CC Energy: -12.13 (((......))).((((((((.....(((....)))......)))))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.09 ((((((((.........)))).)))).......((((........)))). New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -11.33 ....((((.[[[[[[..)))).....(((....)))........]]]]]] New CC sens: 0.286, New CC ppv: 0.308, New CC F-measure: 0.296, New CC Energy: -11.17 (((.[[[[.))).....]]]]..(((.......(((.......)))))). New CC sens: 0.286, New CC ppv: 0.308, New CC F-measure: 0.296, New CC Energy: -11.14 ((((((((.[[[[[...)))).))))(((....)))........]]]]]. New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -10.76 (((.[[[[.))).....]]]]............((((.......)))).. New CC sens: 0.286, New CC ppv: 0.364, New CC F-measure: 0.320, New CC Energy: -10.71 (((.[[[[.))).....]]]]............(((((....)))))... New CC sens: 0.286, New CC ppv: 0.333, New CC F-measure: 0.308, New CC Energy: -10.67 (((.[[[[.{{{{{)))]]]].....(((....)))........}}}}}. New CC sens: 0.286, New CC ppv: 0.267, New CC F-measure: 0.276, New CC Energy: -10.54 ((((((((.........)))).)))).......((((.........)))) New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -10.26 ((.......))((((((((((....))))...............)))))) New CC sens: 0.429, New CC ppv: 0.500, New CC F-measure: 0.462, New CC Energy: -9.99 (((......)))..((((((......(((....)))........)))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.92 New CC F-measure-avg: 0.409, New CC F-measure-best: 0.903, New CC best-subopt: 0, New CC num-subopt: 19 > FIV GGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC [[[[[..((((((]]]]]...........)))))) (((((..[[[[[[)))))...........]]]]]] (((((..[[[[[[)))))...........]]]]]] Energy of known structure: -13.15 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.15 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.15 (((....[[[[[[.)))............]]]]]] New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -10.74 (((((........)))))..((.........)).. New CC sens: 0.455, New CC ppv: 0.714, New CC F-measure: 0.556, New CC Energy: -7.62 (((((........))))).(((.......)))... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -7.36 .(((...[[[[[[..)))...........]]]]]] New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -7.09 .......((((((................)))))) New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -6.07 New CC F-measure-avg: 0.665, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 5 > HCV_229E CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAACAGUUAUGGACCACGAGCAGUCCAUG ((((((((((((...[[[[[)))))))))))).......(((((((..]]]]].))))))) ((((((((((((...[[[[[))))))))))))................]]]]]........ ((((((((((((...[[[[[)))))))))))).......(((((((..]]]]].))))))) Energy of known structure: -20.85 Initial sens: 0.708, Initial ppv: 1.000, Initial F-measure: 0.829, Initial Energy: -15.39 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -20.85 ((((((((((((........))))))))))))........((((((........)))))). New CC sens: 0.750, New CC ppv: 1.000, New CC F-measure: 0.857, New CC Energy: -19.51 New CC F-measure-avg: 0.929, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 1 > HCV_Ires CCUCCCGGGAGAACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAG (((((((((......(((......)))((.[[[[[[.))))))))))).]]]]]]. (((((((((.(.(((((((....)))).......))).))))))))))........ (((((((((.....(((((....))))).[[[[[[[...))))))))).]]]]]]] Energy of known structure: -14.63 Initial sens: 0.600, Initial ppv: 0.706, Initial F-measure: 0.649, Initial Energy: -16.09 New CC sens: 0.900, New CC ppv: 0.857, New CC F-measure: 0.878, New CC Energy: -17.34 (((((((((.(.(((((((....)))).......))).))))))))))........ New CC sens: 0.600, New CC ppv: 0.706, New CC F-measure: 0.649, New CC Energy: -16.09 (((((((((......((((....))))(((....)))..)))))))))........ New CC sens: 0.600, New CC ppv: 0.750, New CC F-measure: 0.667, New CC Energy: -15.47 (((((((((.......(((...)))(((((....))))))))))))))........ New CC sens: 0.450, New CC ppv: 0.529, New CC F-measure: 0.486, New CC Energy: -14.26 (((((((((.....(((((....)))))...........)))))))))........ New CC sens: 0.600, New CC ppv: 0.857, New CC F-measure: 0.706, New CC Energy: -13.92 (((((((((.......(((...)))....[[[[[[[...))))))))).]]]]]]] New CC sens: 0.750, New CC ppv: 0.789, New CC F-measure: 0.769, New CC Energy: -13.71 ........((((.((.((((...(((((((....))))))))))))).)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.56 ........((((....((((...(((((((....)))))))))))...)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.48 .....(((((...((.((((...(((((((....))))))))))))).)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.01 (((((((((.(.....(((...)))..(((....))).))))))))))........ New CC sens: 0.450, New CC ppv: 0.562, New CC F-measure: 0.500, New CC Energy: -12.76 .....(((((......((((...(((((((....)))))))))))...)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.49 .(((....)))....((((....(((((((....)))))))[[[[))))]]]]... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.32 New CC F-measure-avg: 0.388, New CC F-measure-best: 0.878, New CC best-subopt: 0, New CC num-subopt: 11 > HDV-It_g UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCA .(((((((..[[[[[[[(((.[[.....))))))))))]]....(((((((((((((...))))))))).)))).....]]]]]]].. ((.(((((.((((.(((((......))))).))))))))).)).((((((((((((.....)))))))).)))).............. ((.(((((.((((.(((((......))))).))))))))).)).(((((((((((((...))))))))).)))).............. Energy of known structure: -28.96 Initial sens: 0.375, Initial ppv: 0.429, Initial F-measure: 0.400, Initial Energy: -26.97 New CC sens: 0.406, New CC ppv: 0.448, New CC F-measure: 0.426, New CC Energy: -28.41 ..((((((.....[[[[[[[.....))))))...]]]]]]]...(((((((((((((...))))))))).)))).............. New CC sens: 0.406, New CC ppv: 0.500, New CC F-measure: 0.448, New CC Energy: -28.18 ..((((((..[[[[[[[[[[[....)))))).......]]]]..(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.625, New CC ppv: 0.667, New CC F-measure: 0.645, New CC Energy: -28.02 ((((((((......(((((......))))).)))))))).((..(((((((((((((...))))))))).))))))............ New CC sens: 0.625, New CC ppv: 0.714, New CC F-measure: 0.667, New CC Energy: -28.00 ((((((((......(((((......))))).)))))))).....(((((((((((((...))))))))).)))).............. New CC sens: 0.625, New CC ppv: 0.769, New CC F-measure: 0.690, New CC Energy: -27.42 ((.(((((.((((.(((((......))))).))))))))).)).....(((((((((...)))))))))...(((..........))) New CC sens: 0.281, New CC ppv: 0.321, New CC F-measure: 0.300, New CC Energy: -26.58 ...(((((..(((.(((((......))))).))).)))))....(((((((((((((...))))))))).)))).............. New CC sens: 0.406, New CC ppv: 0.500, New CC F-measure: 0.448, New CC Energy: -26.45 ...(((((..[[[[[[[(((........)))....)))))....(((((((((((((...))))))))).)))).....]]]]]]].. New CC sens: 0.719, New CC ppv: 0.821, New CC F-measure: 0.767, New CC Energy: -26.40 ..((((((.....[[[[[[[.....))))))...]]]]]]].......(((((((((...)))))))))...(((..........))) New CC sens: 0.281, New CC ppv: 0.360, New CC F-measure: 0.316, New CC Energy: -26.26 ...(((((..(((.(((((......))))).))).)))))((..(((((((((((((...))))))))).))))))............ New CC sens: 0.406, New CC ppv: 0.464, New CC F-measure: 0.433, New CC Energy: -26.08 ...(((((..[[[[[[[(((........)))....)))))((..(((((((((((((...))))))))).))))))...]]]]]]].. New CC sens: 0.719, New CC ppv: 0.767, New CC F-measure: 0.742, New CC Energy: -26.03 ..........(((((((((((((..((....)).))..))))..(((((((((((((...))))))))).)))).....))))))).. New CC sens: 0.625, New CC ppv: 0.714, New CC F-measure: 0.667, New CC Energy: -25.61 ..........(((((((((((....((((....)))).))))..(((((((((((((...))))))))).)))).....))))))).. New CC sens: 0.625, New CC ppv: 0.714, New CC F-measure: 0.667, New CC Energy: -25.38 ..((((((......(((((......))))).))))))((((...(((((((((((((...))))))))).))))..........)))) New CC sens: 0.594, New CC ppv: 0.679, New CC F-measure: 0.633, New CC Energy: -25.25 ..((((((..[[[[[[[[[[[....)))))).......]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.500, New CC ppv: 0.615, New CC F-measure: 0.552, New CC Energy: -24.93 ...(((((..[[[[[[[......[[[[[[......)))))........(((((((((...)))))))))...]]]]]].]]]]]]].. New CC sens: 0.500, New CC ppv: 0.593, New CC F-measure: 0.542, New CC Energy: -24.85 ..........(((((((.........(((((....)))))....(((((((((((((...))))))))).)))).....))))))).. New CC sens: 0.625, New CC ppv: 0.800, New CC F-measure: 0.702, New CC Energy: -24.77 ((((((((......(((((......))))).))))))))(....)...(((((((((...)))))))))...(((..........))) New CC sens: 0.500, New CC ppv: 0.615, New CC F-measure: 0.552, New CC Energy: -24.53 ...(((((..(((.(((((......))))).))).)))))........(((((((((...)))))))))...(((..........))) New CC sens: 0.281, New CC ppv: 0.360, New CC F-measure: 0.316, New CC Energy: -24.53 ..........(((((((.........(((((....)))))((..(((((((((((((...))))))))).))))))...))))))).. New CC sens: 0.625, New CC ppv: 0.741, New CC F-measure: 0.678, New CC Energy: -24.52 New CC F-measure-avg: 0.559, New CC F-measure-best: 0.767, New CC best-subopt: 7, New CC num-subopt: 19 > HIV-1-RT-1-1 ucaagAAUUCCGUUUUCAGUCGGGAAAAACUGAACAa .......[[[[[..((((((]]]]]...))))))... .......(((((..[[[[[[)))))...]]]]]]... .......(((((..[[[[[[)))))...]]]]]]... Energy of known structure: -6.88 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.88 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.88 .......((((...[[[[[[..))))..]]]]]]... New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -5.80 .......(((((........)))))............ New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -3.56 ..............((((((........))))))... New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -3.35 ............(((((..[[[[))))).]]]].... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.97 ....(((.......)))..((((......)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.95 .......((((...........))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.28 ...........(((((.........)))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.01 ............(((((......)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.47 ............(((((....)))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.43 ............(((((.....))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: 0.33 New CC F-measure-avg: 0.264, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 10 > HIV-1-RT-1-3a gAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCaucu .......(((((..[[[[..)))))....]]]].... .......(((((..[[[[..)))))....]]]].... .......(((([[.[[[[....))))...]]]].]]. Energy of known structure: -3.71 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -3.71 New CC sens: 0.444, New CC ppv: 0.400, New CC F-measure: 0.421, New CC Energy: -6.34 ...........((.((((...........)))).)). New CC sens: 0.444, New CC ppv: 0.667, New CC F-measure: 0.533, New CC Energy: -4.82 ..............((((...........)))).... New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -4.39 .......(((((..[[[[..)))))....]]]].... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -3.71 ..............((((....[[[....)))).]]] New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -3.67 .....((((..[[.[[[[...))))....]]]].]]. New CC sens: 0.444, New CC ppv: 0.400, New CC F-measure: 0.421, New CC Energy: -3.04 .....(((([[[.........))))....]]]..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.67 .......((((...[[[[....))))...]]]].... New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -2.63 .......(((((........)))))............ New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -2.46 ....................(((.....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.17 .......((((...........))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.14 .........(((...((....))......)))..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.05 New CC F-measure-avg: 0.390, New CC F-measure-best: 1.000, New CC best-subopt: 3, New CC num-subopt: 11 > HIV-1-RT-1-6 gAAGAAGAUUACCCAAGCGCAGGGGAGAAGCGCaucu ...........[[[..((((.]]].....)))).... ...........(((..[[[[.))).....]]]].... ...........(((..[[[[.))).....]]]].... Energy of known structure: -9.24 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -9.24 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -9.24 .....((((..(((..[[[[.))).....]]]])))) New CC sens: 1.000, New CC ppv: 0.636, New CC F-measure: 0.778, New CC Energy: -8.32 ................((((.........)))).... New CC sens: 0.571, New CC ppv: 1.000, New CC F-measure: 0.727, New CC Energy: -4.70 ................((((...[[[...)))).]]] New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -3.79 .....((((.......((((.........)))))))) New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -3.56 ...........(((..[[[[..)))....]]]].... New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -3.52 ...........(((.......)))............. New CC sens: 0.429, New CC ppv: 1.000, New CC F-measure: 0.600, New CC Energy: -3.21 .....((((..(((..[[[[..)))....]]]])))) New CC sens: 0.571, New CC ppv: 0.364, New CC F-measure: 0.444, New CC Energy: -2.60 ...........(((........)))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.22 .....((((..(((.......))).........)))) New CC sens: 0.429, New CC ppv: 0.429, New CC F-measure: 0.429, New CC Energy: -1.33 New CC F-measure-avg: 0.565, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 9 > HIV-1-RT-1-7 agGAAUCGACCCAAGCCAAAGGGGAUAAUGCGGCauc .........[[[..(((...]]]........)))... .........(((..[[[...)))........]]]... .((.......))..(((..............)))... Energy of known structure: -1.09 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -1.09 New CC sens: 0.500, New CC ppv: 0.600, New CC F-measure: 0.545, New CC Energy: -3.71 .........(((........))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.15 .........(((.........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.10 .........(((..[[[...)))........]]]... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -1.08 .........(((..[[[....))).......]]]... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -0.94 New CC F-measure-avg: 0.542, New CC F-measure-best: 1.000, New CC best-subopt: 3, New CC num-subopt: 4 > HIV-1-RT-1-8 ucaagGAUUAACCGACGCCAACGGGAGAAUGGCAGGGau ...........[[[..((((.]]].....))))...... ...........(((..[[[[.))).....]]]]...... ...........(((..[[[[.))).....]]]]...... Energy of known structure: -8.04 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.04 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.04 ...........((...((((.........)))).))... New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -4.53 ....((.....))...((((.........))))...... New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -4.01 ...........(((.......)))............... New CC sens: 0.429, New CC ppv: 1.000, New CC F-measure: 0.600, New CC Energy: -2.08 New CC F-measure-avg: 0.708, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 3 > HIV-1-RT-1-9b gAGAGUAUCAUCCGUGCCGGCGGGAUAUCGGCGaucu ..........[[[[((((((]]]]...)))))).... ((..((....(((((....)))))......))..)). .........((((.[[[[[[..)))).]]]]]].... Energy of known structure: -6.63 Initial sens: 0.400, Initial ppv: 0.444, Initial F-measure: 0.421, Initial Energy: -4.37 New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -6.00 ..............((((((..[[[[.))))))]]]] New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -5.24 (...(((((..((((....)))))))))...)..... New CC sens: 0.300, New CC ppv: 0.300, New CC F-measure: 0.300, New CC Energy: -5.23 ..............((((((.......)))))).... New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -4.26 ..........(((((....)))))............. New CC sens: 0.400, New CC ppv: 0.800, New CC F-measure: 0.533, New CC Energy: -3.43 ....(((((..(((...)))...)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.77 ....(((((..[[[.........)))))]]]...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.35 ....(((((...[[[........)))))..]]].... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.14 ...........(((...)))(((....)))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.78 ...........(((..............)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.73 ............(((.......[[[[....)))]]]] New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.61 .........((((.........))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.45 ............(((.....(((....)))))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.38 New CC F-measure-avg: 0.214, New CC F-measure-best: 0.750, New CC best-subopt: 3, New CC num-subopt: 12 > HIV-1-RT-2-10 agUAAAUGAGUCCGUAGGAGGCGGGAUAUCUCCaAcu ..........[[[[..(((((]]]]...))))).... .............((.(((((.......))))).)). .........(((([[.[[[[[..)))).]]]]].]]. Energy of known structure: -6.66 Initial sens: 0.556, Initial ppv: 0.714, Initial F-measure: 0.625, Initial Energy: -4.67 New CC sens: 0.556, New CC ppv: 0.455, New CC F-measure: 0.500, New CC Energy: -6.57 .........((((...[[[[[..)))).]]]]].... New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -6.15 .............((.(((((.......))))).)). New CC sens: 0.556, New CC ppv: 0.714, New CC F-measure: 0.625, New CC Energy: -4.67 ................(((((.......))))).... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -4.31 ..........(((((.[[[.)))))...]]]...... New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -3.94 .........(((.......))).(((....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.14 ..........(((...)))....(((....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.01 .........((((...[[[....)))).]]]...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.87 ..........(((((.....)))))............ New CC sens: 0.444, New CC ppv: 0.800, New CC F-measure: 0.571, New CC Energy: -1.72 .........((((..........)))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.44 ..........(((...)))((.((....)).)).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.16 New CC F-measure-avg: 0.312, New CC F-measure-best: 0.714, New CC best-subopt: 3, New CC num-subopt: 10 > HIV-1-RT-2-11 gUCAUAUUACCGUUACUCCUCGGGAUAAAGGAGaucu .........[[[...(((((]]].....))))).... .........(((...[[[[[))).....]]]]].... .........(((...[[[[[))).....]]]]].... Energy of known structure: -8.63 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.63 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.63 ...............(((((..[[[[..)))))]]]] New CC sens: 0.625, New CC ppv: 0.556, New CC F-measure: 0.588, New CC Energy: -5.10 ...............(((((........))))).... New CC sens: 0.625, New CC ppv: 1.000, New CC F-measure: 0.769, New CC Energy: -3.81 .........(((........))).............. New CC sens: 0.375, New CC ppv: 1.000, New CC F-measure: 0.545, New CC Energy: -2.98 New CC F-measure-avg: 0.726, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 3 > HIV-1-RT-2-12 ucaagAAUAAUCCGACUCGCGGGAUAACGAGAAGaGc ..........[[[[.((((]]]]....))))...... ..........((((.[[[[))))....]]]]...... .........((((..[[[[..))))..]]]]...... Energy of known structure: -2.98 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -2.98 New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -4.57 ..........((((.[[[[))))....]]]]...... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -2.98 ..........((...((((........))))..)).. New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -2.73 ...............((((........))))...... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -2.63 ..........((((.....)))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -2.20 .........((((........))))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.82 New CC F-measure-avg: 0.567, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 5 > HIV-1-RT-2-1b caagAAUAUAUCCGAACUCGACGGGAUAACGAGAAGaGc ..........[[[[..((((.]]]]....))))...... ..........((((..[[[[.))))....]]]]...... ........(((((...[[[[...))))).]]]]...... Energy of known structure: -3.79 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -3.79 New CC sens: 0.500, New CC ppv: 0.444, New CC F-measure: 0.471, New CC Energy: -4.69 ..........((((..[[[[.))))....]]]]...... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -3.79 ........(((((..........)))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.18 ................((((.........))))...... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -2.18 ..........((((.......)))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -1.83 New CC F-measure-avg: 0.561, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 4 > HIV-1-RT-2-2b gacaaucaagUACCUAGGUGAUAAAAGGGAGAACACGUGUGa ............[[[..(((.....]]].....)))...... .....(((....(((..[[[.....))).....]]]...))) .(((........(((...........)))........))).. Energy of known structure: 0.82 Initial sens: 1.000, Initial ppv: 0.667, Initial F-measure: 0.800, Initial Energy: 2.07 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.87 ............(((..........))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -1.58 ............(((...........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.10 ....((((..........)))).................... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.43 ....((((....[[[...))))...]]].............. New CC sens: 0.500, New CC ppv: 0.429, New CC F-measure: 0.462, New CC Energy: 1.62 New CC F-measure-avg: 0.226, New CC F-measure-best: 0.667, New CC best-subopt: 1, New CC num-subopt: 4 > HIV-1-RT-2-3a gUUAAACAUAAUCCGUGAUCUUUCACACGGGAGaucuaugaaaga ...........[[[[[[.(((((((]]]]]].......))))))) ...........((((((.[[[[[[[)))))).......]]]]]]] ...........((((((.[[[[[[[)))))).......]]]]]]] Energy of known structure: -6.67 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.67 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.67 ...........((...((((((((....))))))))...)).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.30 ................((((((((....))))))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.87 ..............(((([[[[))))..]]]]............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.92 ...........((((((........)))))).............. New CC sens: 0.462, New CC ppv: 1.000, New CC F-measure: 0.632, New CC Energy: -4.58 ..................(((((((...((....))..))))))) New CC sens: 0.538, New CC ppv: 0.778, New CC F-measure: 0.636, New CC Energy: -4.13 ...........(((((((....))))...)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.42 ..............((((....))))..((....))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.77 New CC F-measure-avg: 0.283, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 7 > HIV-1-RT-2-4a agUAGAUAUCCGAAGCUCAACGGGAUAAUGAGCaucu ........[[[[..(((((.]]]]....))))).... ........((((..[[[[[.))))....]]]]].... ......((((([[.[[[[[...))))).]]]]].]]. Energy of known structure: -6.25 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.25 New CC sens: 0.556, New CC ppv: 0.417, New CC F-measure: 0.476, New CC Energy: -7.71 ......(((((...[[[[[...))))).]]]]].... New CC sens: 0.556, New CC ppv: 0.500, New CC F-measure: 0.526, New CC Energy: -7.23 ........((((..[[[[[.))))....]]]]].... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.25 ..............(((((...[[[[..)))))]]]] New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -5.23 ...........((.(((((.........))))).)). New CC sens: 0.556, New CC ppv: 0.714, New CC F-measure: 0.625, New CC Energy: -5.16 ..............(((((.........))))).... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -4.73 ...((((.((((..[[[[[.))))....]]]]])))) New CC sens: 1.000, New CC ppv: 0.692, New CC F-measure: 0.818, New CC Energy: -4.64 ...((((.......(((((.........))))))))) New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -3.33 ......(((((...........))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.08 ........((((........))))............. New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -1.77 ((([[[[.[[[[..)))...]]]].........]]]] New CC sens: 0.444, New CC ppv: 0.364, New CC F-measure: 0.400, New CC Energy: -1.64 New CC F-measure-avg: 0.571, New CC F-measure-best: 1.000, New CC best-subopt: 2, New CC num-subopt: 10 > HIV-1-RT-2-5a ucaagAUAGUAUCCGUUCUUGAUCAUCGGGACAAAUGaucu ...........[[[[.....((((((]]]]....)))))). ...((((...(((.[[[[[.)))....]]]]].....)))) ..............(((((.[[[[[[.)))))..]]]]]]. Energy of known structure: -3.83 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -2.77 New CC sens: 0.600, New CC ppv: 0.545, New CC F-measure: 0.571, New CC Energy: -7.40 ((((((..........))))))..((((.......)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.74 ...........((((.....[[[[[[))))....]]]]]]. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -3.83 ..((((..........))))((((((........)))))). New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -3.55 ((((((..........))))))......(((.......))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.54 ...((((.......(((((........))))).....)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.42 ..............(((((........)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.41 ...........(((......[[[[[[..)))...]]]]]]. New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -2.92 ((((((.....[[[[.))))))....]]]]........... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -2.80 ...((((....((((...........)))).......)))) New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -2.47 ...........((((...........))))........... New CC sens: 0.400, New CC ppv: 1.000, New CC F-measure: 0.571, New CC Energy: -2.40 ................((((((...)))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.84 ...((((.........((((((...))))))......)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.13 ...((((....(((..............)))......)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.84 New CC F-measure-avg: 0.301, New CC F-measure-best: 1.000, New CC best-subopt: 2, New CC num-subopt: 13 > HIV-1-RT-2-6b agUGAAACUUAACCGUUAUCAUAGAUCGGGACAAaucuauga ............[[[...((((((((]]].....)))))))) ............(((...[[[[[[[[))).....]]]]]]]] ............(((...[[[[[[[[))).....]]]]]]]] Energy of known structure: -8.39 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.39 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.39 ..................((((((((........)))))))) New CC sens: 0.727, New CC ppv: 1.000, New CC F-measure: 0.842, New CC Energy: -4.33 ............(((...........)))............. New CC sens: 0.273, New CC ppv: 1.000, New CC F-measure: 0.429, New CC Energy: -2.65 .(((((((......))).))))......(((....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.41 .((((.............)))).....((......))..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.50 New CC F-measure-avg: 0.454, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > HIV-1-RT-2-7a agAUAUGAUCCGUAAGAGGACGGGAUAAACCUCAac ........[[[[...((((.]]]].....))))... ........(((((..[[[[))))).....]]]]... ........(((((..[[[[))))).....]]]]... Energy of known structure: -4.34 Initial sens: 1.000, Initial ppv: 0.889, Initial F-measure: 0.941, Initial Energy: -6.33 New CC sens: 1.000, New CC ppv: 0.889, New CC F-measure: 0.941, New CC Energy: -6.33 ...............((((..........))))... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.35 ........(((......))).(((......)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.69 ........(((((......)))))............ New CC sens: 0.500, New CC ppv: 0.800, New CC F-measure: 0.615, New CC Energy: -2.00 ........(((......))).(((.....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.95 .......((((...........)))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.23 .......((((....[[[[...))))...]]]]... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -0.62 New CC F-measure-avg: 0.389, New CC F-measure-best: 0.941, New CC best-subopt: 0, New CC num-subopt: 6 > HIV-1-RT-2-9 ucaagGUUUCCGAAAGAAAUCGGGAAAACUGucu .......(((((..[[[...)))))......]]] .((...(((((((......)))))))...))... ...((.(((((((......)))))))..)).... Energy of known structure: 3.33 Initial sens: 0.625, Initial ppv: 0.556, Initial F-measure: 0.588, Initial Energy: -4.89 New CC sens: 0.625, New CC ppv: 0.556, New CC F-measure: 0.588, New CC Energy: -4.96 ....(((((((((......))))..))))).... New CC sens: 0.375, New CC ppv: 0.333, New CC F-measure: 0.353, New CC Energy: -4.69 ......(((((((......)))))))........ New CC sens: 0.625, New CC ppv: 0.714, New CC F-measure: 0.667, New CC Energy: -4.12 ....((((((.....))))))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.03 ....((((((.....)))))).(((......))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.28 ......(((((...........)))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.85 ....(((((.............[[[))))).]]] New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.29 New CC F-measure-avg: 0.230, New CC F-measure-best: 0.667, New CC best-subopt: 2, New CC num-subopt: 6 > Hs_SRP_pkn GCCGGGCGCGGUGGCGCGUGCCUGUAGUCCCAGCUACUCGGGAGGCU (((.((((((.[[[[.)))))).....((((.]]]]...))))))). (((.((((((......)))))).....((((........))))))). ..((((((((......))))))))...(((([[[[....))))]]]] Energy of known structure: 0.13 Initial sens: 0.765, Initial ppv: 1.000, Initial F-measure: 0.867, Initial Energy: -11.71 New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -13.44 ..((((((((......))))))))...((((........)))).... New CC sens: 0.588, New CC ppv: 0.833, New CC F-measure: 0.690, New CC Energy: -12.15 ((((((((((......)))))))....((((........))))))). New CC sens: 0.765, New CC ppv: 0.929, New CC F-measure: 0.839, New CC Energy: -11.95 .....(((([[[[)))).]]]].....(((([[[[....))))]]]] New CC sens: 0.235, New CC ppv: 0.250, New CC F-measure: 0.242, New CC Energy: -11.50 (((..(((((....))))).((((((((....)))))..))).))). New CC sens: 0.176, New CC ppv: 0.188, New CC F-measure: 0.182, New CC Energy: -11.27 ((((((((((......)))))))(((((....)))))......))). New CC sens: 0.529, New CC ppv: 0.600, New CC F-measure: 0.562, New CC Energy: -11.14 (((..((((....))))...((((((((....)))))..))).))). New CC sens: 0.176, New CC ppv: 0.200, New CC F-measure: 0.188, New CC Energy: -10.81 (((..(((((....))))).((((((((....))))..)))).))). New CC sens: 0.176, New CC ppv: 0.188, New CC F-measure: 0.182, New CC Energy: -10.52 ...(((((((....)))).[[[[[[[[[))).]]]]].....]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.49 .....(((([[[[)))).]]]].((..((((........)))).)). New CC sens: 0.235, New CC ppv: 0.286, New CC F-measure: 0.258, New CC Energy: -10.47 ..((((((((......)))))))).......((((........)))) New CC sens: 0.353, New CC ppv: 0.500, New CC F-measure: 0.414, New CC Energy: -10.34 ..((((((((......)))))))).((((((........))..)))) New CC sens: 0.471, New CC ppv: 0.571, New CC F-measure: 0.516, New CC Energy: -10.26 .....(((([[[[)))).]]]].....((((........)))).... New CC sens: 0.235, New CC ppv: 0.333, New CC F-measure: 0.276, New CC Energy: -10.21 (((..(((((....)))))....(((((....)))))......))). New CC sens: 0.176, New CC ppv: 0.231, New CC F-measure: 0.200, New CC Energy: -10.06 (((..((((....))))...((((((((....))))..)))).))). New CC sens: 0.176, New CC ppv: 0.200, New CC F-measure: 0.188, New CC Energy: -10.06 (((..(((((....)))))........((((........))))))). New CC sens: 0.412, New CC ppv: 0.583, New CC F-measure: 0.483, New CC Energy: -9.96 .....((((....))))..((((.....(((........))))))). New CC sens: 0.176, New CC ppv: 0.273, New CC F-measure: 0.214, New CC Energy: -9.77 ...((((..[[[[[[....{{{{...))))..]]]]]]....}}}}. New CC sens: 0.235, New CC ppv: 0.286, New CC F-measure: 0.258, New CC Energy: -9.72 .....(((((....)))))........(((([[[[....))))]]]] New CC sens: 0.235, New CC ppv: 0.308, New CC F-measure: 0.267, New CC Energy: -9.67 ((((....))))(((....))).....(((([[[[....))))]]]] New CC sens: 0.235, New CC ppv: 0.267, New CC F-measure: 0.250, New CC Energy: -9.61 New CC F-measure-avg: 0.341, New CC F-measure-best: 0.839, New CC best-subopt: 2, New CC num-subopt: 19 > MMTVgag-pro GGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAU [[[[[.(((((((.]]]]]........))))))) (((((.[[[[[[[.)))))........]]]]]]] (((((.[[[[[[[.)))))........]]]]]]] Energy of known structure: -15.26 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -15.26 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -15.26 (((((..[[[[[[.))))).......]]]]]].. New CC sens: 0.417, New CC ppv: 0.455, New CC F-measure: 0.435, New CC Energy: -14.82 ((((....))))...((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.67 (((((....[[[[.))))).........]]]].. New CC sens: 0.417, New CC ppv: 0.556, New CC F-measure: 0.476, New CC Energy: -9.51 .(((..[[[[[[[[[[)))]]].....]]]]]]] New CC sens: 0.583, New CC ppv: 0.538, New CC F-measure: 0.560, New CC Energy: -9.15 (((((..[[[[...)))))........]]]]... New CC sens: 0.417, New CC ppv: 0.556, New CC F-measure: 0.476, New CC Energy: -8.57 (((((.........))))).(((....))).... New CC sens: 0.417, New CC ppv: 0.625, New CC F-measure: 0.500, New CC Energy: -8.50 ((((....))))...((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.42 ((((....)))).((([[[))).......]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.77 ((((.....))))..((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.73 .(((...[[[[[[[[[)))]]]....]]]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.70 .(((...[[[[[[...))).......]]]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.50 .((((..[[[[[[......))))...]]]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.29 (((((.....[[[.)))))..........]]].. New CC sens: 0.417, New CC ppv: 0.625, New CC F-measure: 0.500, New CC Energy: -7.08 .(((..[[[[[[[...)))........]]]]]]] New CC sens: 0.583, New CC ppv: 0.700, New CC F-measure: 0.636, New CC Energy: -6.99 ((((....))))...(((.........))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.98 (((...[[[[[[[..))).........]]]]]]] New CC sens: 0.583, New CC ppv: 0.700, New CC F-measure: 0.636, New CC Energy: -6.92 ((((...))))....((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.75 ((((.....))))..((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.48 ......(((((((..............))))))) New CC sens: 0.583, New CC ppv: 1.000, New CC F-measure: 0.737, New CC Energy: -6.41 New CC F-measure-avg: 0.298, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 19 > Ni_VS GGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUG ((((...[[[)))).....(((((((((.]]].))))))))) (((((....))))).....(((((((((.....))))))))) (((((....))))).....(((((((((.....))))))))) Energy of known structure: -9.40 Initial sens: 0.812, Initial ppv: 0.929, Initial F-measure: 0.867, Initial Energy: -11.09 New CC sens: 0.812, New CC ppv: 0.929, New CC F-measure: 0.867, New CC Energy: -11.09 (((....[[[[.)))....(((((((((]]]].))))))))) New CC sens: 0.750, New CC ppv: 0.750, New CC F-measure: 0.750, New CC Energy: -8.72 (((((....)))))......((((.......))))....... New CC sens: 0.250, New CC ppv: 0.444, New CC F-measure: 0.320, New CC Energy: -8.69 (((.[[[[....)))....(((((((((]]]].))))))))) New CC sens: 0.562, New CC ppv: 0.562, New CC F-measure: 0.562, New CC Energy: -8.53 (((((....)))))..(((((.......)))))......... New CC sens: 0.250, New CC ppv: 0.400, New CC F-measure: 0.308, New CC Energy: -8.00 New CC F-measure-avg: 0.561, New CC F-measure-best: 0.867, New CC best-subopt: 0, New CC num-subopt: 4 > PEMV UUCCGGUCGACUCCGGAGAAACAAAGUC ((((((..[[[[))))))......]]]] ((((((..[[[[))))))......]]]] ((((((..[[[[))))))......]]]] Energy of known structure: -6.04 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.04 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.04 .(((((......)))))........... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -5.74 New CC F-measure-avg: 0.833, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 1 > PLRV-S GCGGCACCGUCCGCCAAAACAAACGG [[[[..((((]]]]........)))) ((((..[[[[))))........]]]] ((((..[[[[))))........]]]] Energy of known structure: -7.35 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.35 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.35 ..(((.......)))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.13 ((((......))))............ New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -2.91 ..(((.[[[[..))).......]]]] New CC sens: 0.500, New CC ppv: 0.571, New CC F-measure: 0.533, New CC Energy: -2.83 ......((((............)))) New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -1.29 ..........(((..........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.09 (((....)))(((..........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.98 New CC F-measure-avg: 0.410, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > PRRSV-16244B GCCGCCAGCGGCUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAGACAGCGG ((((((.((((((....[[[[[[[))))))))))))...............]]]]]]] ((((((.((((((....[[[[[[[))))))))))))(..((....))..).]]]]]]] ((((((.((((((...........))))))))))))...((((((.....)))))).. Energy of known structure: -15.77 Initial sens: 1.000, Initial ppv: 0.864, Initial F-measure: 0.927, Initial Energy: -10.39 New CC sens: 0.632, New CC ppv: 0.667, New CC F-measure: 0.649, New CC Energy: -17.74 (((((([[[[[[[....{{{{{{{......))))))..]]]]]]]......}}}}}}} New CC sens: 0.684, New CC ppv: 0.650, New CC F-measure: 0.667, New CC Energy: -17.43 (((((.[[[[[[[....{{{{{{{....))))).....]]]]]]]......}}}}}}} New CC sens: 0.368, New CC ppv: 0.368, New CC F-measure: 0.368, New CC Energy: -15.51 (((((((((((......)))))).....)))))......((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.75 ((((....)))).(((((.[[[[[)))))..]]]]]...((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.62 ((((....)))).....((((((((((.(((((......))))).)))...))))))) New CC sens: 0.368, New CC ppv: 0.368, New CC F-measure: 0.368, New CC Energy: -14.55 (((((((((((......)))))).....)))))(.((((((....)))))).)..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.43 (((((............[[[[[[[....)))))..((((((....))))))]]]]]]] New CC sens: 0.368, New CC ppv: 0.389, New CC F-measure: 0.378, New CC Energy: -14.43 ((((....)))).....(((((((....)))))))((((((....))))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.28 ((((....)))).....(((((((....)))))))....((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.28 ((((((..(((((....[[[[[[[))))).))))))(((((....))))).]]]]]]] New CC sens: 0.947, New CC ppv: 0.783, New CC F-measure: 0.857, New CC Energy: -14.27 (((((([[[[[[[.((((......))))..))))))..]]]]]]].(((......))) New CC sens: 0.316, New CC ppv: 0.300, New CC F-measure: 0.308, New CC Energy: -14.17 (((((..(((((.......)))))....)))))......((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.04 ((((((.(((((.......)))))......))))))...((((((.....)))))).. New CC sens: 0.316, New CC ppv: 0.353, New CC F-measure: 0.333, New CC Energy: -13.86 New CC F-measure-avg: 0.281, New CC F-measure-best: 0.857, New CC best-subopt: 10, New CC num-subopt: 13 > PRRSV-LV GCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGG ((((((.((((((....[[[[[[[))))))))))))...............]]]]]]] ((((((.((((((....[[[[[[[)))))))))))).((((....))))..]]]]]]] ((((((.((((((...........))))))))))))...(((((.......))))).. Energy of known structure: -16.15 Initial sens: 1.000, Initial ppv: 0.826, Initial F-measure: 0.905, Initial Energy: -15.82 New CC sens: 0.632, New CC ppv: 0.706, New CC F-measure: 0.667, New CC Energy: -19.48 ((((((.(((((.......))))).[[[[.))))))................]]]].. New CC sens: 0.316, New CC ppv: 0.400, New CC F-measure: 0.353, New CC Energy: -16.67 ((((((..(((((....[[[[[[[))))).))))))...............]]]]]]] New CC sens: 0.947, New CC ppv: 1.000, New CC F-measure: 0.973, New CC Energy: -16.32 (((((((((((......)))))).....))))).(((..(((........)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -15.59 New CC F-measure-avg: 0.498, New CC F-measure-best: 0.973, New CC best-subopt: 2, New CC num-subopt: 3 > SARS-CoV UGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCU (((((((((((...[[[[[[[)))))))))))((((((((.........))).)))))...]].]]]]] (((((((((((...[[[[[..)))))))))))((((((((((....)).))).)))))......]]]]] (((((((((((...[[[[[..)))))))))))((((((((.........))).)))))......]]]]] Energy of known structure: -20.75 Initial sens: 0.923, Initial ppv: 0.923, Initial F-measure: 0.923, Initial Energy: -16.04 New CC sens: 0.923, New CC ppv: 1.000, New CC F-measure: 0.960, New CC Energy: -16.61 .((((((((((..........)))))))))).((((((((.........))).)))))........... New CC sens: 0.692, New CC ppv: 1.000, New CC F-measure: 0.818, New CC Energy: -16.33 (((((((((((..........))))))))))).(((((((.........))).))))((((...)))). New CC sens: 0.692, New CC ppv: 0.818, New CC F-measure: 0.750, New CC Energy: -15.74 (((((((((((....[[[...))))))))))).]]].(((.........))).....(((.....))). New CC sens: 0.538, New CC ppv: 0.700, New CC F-measure: 0.609, New CC Energy: -14.77 .((((((((((......[[[[))))))))))]]]]..(((.........))).....(((.....))). New CC sens: 0.500, New CC ppv: 0.650, New CC F-measure: 0.565, New CC Energy: -14.65 (((((((((((....[[[...))))))))))).......]]]....((.(((..........))).)). New CC sens: 0.423, New CC ppv: 0.579, New CC F-measure: 0.489, New CC Energy: -14.60 (((((((((((....[[[...))))))))))).]]]...((((..........))))((((...)))). New CC sens: 0.423, New CC ppv: 0.500, New CC F-measure: 0.458, New CC Energy: -14.51 .((((((((((....[[[...))))))))))((((((..]]]...........)))))).......... New CC sens: 0.577, New CC ppv: 0.789, New CC F-measure: 0.667, New CC Energy: -14.40 .((((((((((......[[[[))))))))))]]]]....((((..........))))((((...)))). New CC sens: 0.385, New CC ppv: 0.455, New CC F-measure: 0.417, New CC Energy: -14.30 (((((((((((....[[[...))))))))))).......]]]...............((((...)))). New CC sens: 0.423, New CC ppv: 0.611, New CC F-measure: 0.500, New CC Energy: -13.65 .((((((((((...[[[[[..))))))))))(((((((((.........))).)))))).....]]]]] New CC sens: 0.885, New CC ppv: 0.958, New CC F-measure: 0.920, New CC Energy: -13.51 (((((((((((....[[[...))))))))))).]]]..((((...............))))........ New CC sens: 0.423, New CC ppv: 0.611, New CC F-measure: 0.500, New CC Energy: -13.05 (((((((((((...[[[[[..)))))))))))......((((...............))))...]]]]] New CC sens: 0.615, New CC ppv: 0.800, New CC F-measure: 0.696, New CC Energy: -12.93 ...((((((((..........))))))))((((.......))))..((.(((..........))).)). New CC sens: 0.308, New CC ppv: 0.471, New CC F-measure: 0.372, New CC Energy: -12.84 .((((((((((......[[[[))))))))))]]]]...((((...............))))........ New CC sens: 0.385, New CC ppv: 0.556, New CC F-measure: 0.455, New CC Energy: -12.84 (((((((((((..........)))))))))))......((((...............))))........ New CC sens: 0.423, New CC ppv: 0.733, New CC F-measure: 0.537, New CC Energy: -12.36 New CC F-measure-avg: 0.607, New CC F-measure-best: 0.960, New CC best-subopt: 0, New CC num-subopt: 15 > SNV GGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC [[[[[[.[..(((((((].]]]]]]..................))))))) ((((((....[[[[[[[..))))))..................]]]]]]] (((....)))(((((((.....((...(((...)))...))..))))))) Energy of known structure: -13.48 Initial sens: 0.929, Initial ppv: 1.000, Initial F-measure: 0.963, Initial Energy: -11.29 New CC sens: 0.500, New CC ppv: 0.467, New CC F-measure: 0.483, New CC Energy: -11.96 ((((.[[[[[)))).......(((...(((...)))...)))..]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.69 ((((((....[[[[[[[..))))))..................]]]]]]] New CC sens: 0.929, New CC ppv: 1.000, New CC F-measure: 0.963, New CC Energy: -11.29 ((((((.[[[.[[[[....)))))).................]]]]]]]. New CC sens: 0.429, New CC ppv: 0.462, New CC F-measure: 0.444, New CC Energy: -10.03 (((....)))..(((((....(((...(((...)))...)))..))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.81 (((([[[[[[)))).......(((...(((...)))...))).]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.54 (((....))).((((((...(((...........)))..)).)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.32 ((((..[[[[)))).......(((...(((...)))...)))...]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.24 (((....))).(((((.....(((...(((...)))...))).))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.22 ((((......))))........(((..(((.........)))..)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.08 .......(((.((((((...(((...........)))..)).))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.04 (((((([[[[[[[......)))))).]]]................]]]]. New CC sens: 0.429, New CC ppv: 0.462, New CC F-measure: 0.444, New CC Energy: -8.44 ((((...[[[))))........(((..(((.........))).)))]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.03 (((....)))...((((....(((...(((...)))...)))...)))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.99 New CC F-measure-avg: 0.167, New CC F-measure-best: 0.963, New CC best-subopt: 2, New CC num-subopt: 13 > TMV-L GGGAUUCGAAUUCCCCCGGAACCCCCGGUUGGGGCCCA ...............[[[...((((]]]..)))).... (((........((((((((.....))))..))))))). ((((.......))))..((..((((.....)))).)). Energy of known structure: -6.90 Initial sens: 0.429, Initial ppv: 0.273, Initial F-measure: 0.333, Initial Energy: -8.32 New CC sens: 0.571, New CC ppv: 0.400, New CC F-measure: 0.471, New CC Energy: -9.99 ((((.......))))((((..[[[))))..]]]..... New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -9.94 (((........[[[[[[[[..)))]]]]..]]]].... New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -8.74 (((..........))).((..((((.....)))).)). New CC sens: 0.571, New CC ppv: 0.444, New CC F-measure: 0.500, New CC Energy: -8.48 (((........((((((((.....))))..))))))). New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -8.32 (((((....))))).((((..[[[))))..]]]..... New CC sens: 0.429, New CC ppv: 0.250, New CC F-measure: 0.316, New CC Energy: -8.25 (((...........)))((..((((.....)))).)). New CC sens: 0.571, New CC ppv: 0.444, New CC F-measure: 0.500, New CC Energy: -8.14 (((((....)))))...((..((((.....)))).)). New CC sens: 0.571, New CC ppv: 0.364, New CC F-measure: 0.444, New CC Energy: -8.06 (((.......[[[[)))]]]].((((....)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.01 (((.......[[[[.[[[[..)))]]]]..]]]].... New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -7.57 ((((.......)))).......((((....)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.50 ((((.......))))......((((.....)))).... New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -7.42 (((.......[[[[)))]]]]((((.....)))).... New CC sens: 0.571, New CC ppv: 0.364, New CC F-measure: 0.444, New CC Energy: -7.31 ((((.......))))....(((([[[)))).]]].... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.24 (((.........(((((((.....)))...))))))). New CC sens: 0.286, New CC ppv: 0.200, New CC F-measure: 0.235, New CC Energy: -7.23 ...........((((((((.....))))..)))).... New CC sens: 0.429, New CC ppv: 0.375, New CC F-measure: 0.400, New CC Energy: -7.20 (((.......((((.((((.....))))..))))))). New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -6.94 (((...........))).....((((....)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.82 (((...........)))....((((.....)))).... New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -6.74 ((((.......))))((((.....)))).......... New CC sens: 0.429, New CC ppv: 0.375, New CC F-measure: 0.400, New CC Energy: -6.59 New CC F-measure-avg: 0.324, New CC F-measure-best: 0.571, New CC best-subopt: 18, New CC num-subopt: 19 > BChV GCGGCGCCGACCGCCAAACAACCGGC [[[[.((((.]]]]........)))) ((((.[[[[.))))........]]]] ((((.[[[[.))))........]]]] Energy of known structure: -8.67 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.67 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.67 ((((......))))............ New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.49 ..((((.....))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.35 .....((((.............)))) New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.21 ............(((........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.20 .(((.................))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.46 ..........(((.........))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.05 New CC F-measure-avg: 0.333, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > CABYV GGCGGCGGCGACCGCCGAAACAACCGC (((((..[[[.)))))........]]] (((((..[[[.)))))........]]] (((((..[[[.)))))........]]] Energy of known structure: -8.62 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.62 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.62 (((((......)))))........... New CC sens: 0.625, New CC ppv: 1.000, New CC F-measure: 0.769, New CC Energy: -6.39 ..((((((...)))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.29 .((((((((....))))......)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.26 .....((((....)))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.53 ....((((...............)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.93 New CC F-measure-avg: 0.295, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 5 > GaLV GGGUUCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGG ((((((((..[[[[[[[)))))))).................]]]]]]] ((((((((..[[[[[[[)))))))).................]]]]]]] ((((((((..[[[[[[[)))))))).................]]]]]]] Energy of known structure: -13.89 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.89 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.89 ((((((((...[[[[..))))))))]]]]...(((.....)))...... New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -12.22 (((((((([[[[{{{{.)))))))).]]]]..(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.421, New CC F-measure: 0.471, New CC Energy: -11.94 (((((((([[[[.{{{{)))))))).]]]]..(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.421, New CC F-measure: 0.471, New CC Energy: -11.94 ((((((((..[[[{{{{)))))))).]]]...(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.444, New CC F-measure: 0.485, New CC Energy: -11.53 (((((((([[[[.....)))))))).]]]]..(((.....)))...... New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -11.08 ((((((((..[[[....)))))))).]]]...(((.....)))...... New CC sens: 0.533, New CC ppv: 0.571, New CC F-measure: 0.552, New CC Energy: -10.73 ((((((((.[[[.....)))))))).......(((.....)))..]]]. New CC sens: 0.533, New CC ppv: 0.571, New CC F-measure: 0.552, New CC Energy: -9.85 ((((((((.........)))))))).......(((.....)))...... New CC sens: 0.533, New CC ppv: 0.727, New CC F-measure: 0.615, New CC Energy: -9.23 (((........))).((((...(((((...........))).)).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.36 ..........(((((((((.......))..............))))))) New CC sens: 0.467, New CC ppv: 0.778, New CC F-measure: 0.583, New CC Energy: -8.30 ((((....))))...((((...(((((...........))).)).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.19 (((........[[[[))).......]]]]...(((.....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.07 ((((....))))(((((((.......)))...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.91 (((.......)))..((((...(((((...........))).)).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.81 .(((....)))(((([[[[......))))...(((.....)))..]]]] New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.74 .........((((...(((.......)))...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.51 (((.....[[[[{{{{))).......]]]]..(((.....)))..}}}} New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.99 (((........)))..(((.......)))...(((.....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.95 .........((((..(((........)))...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.90 New CC F-measure-avg: 0.290, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 19 > HIV-1-RT-1-17 agUAAUGACCAGAGGCCCAACUGGUAAACGGGCGGuc .......(((((..[[[[..)))))....]]]].... (((...[[[[....[[[[.))).......]]]]]]]] ......((((....((((...........)))))))) Energy of known structure: -5.50 Initial sens: 0.444, Initial ppv: 0.364, Initial F-measure: 0.400, Initial Energy: -6.97 New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -5.64 .......(((((..[[[[..)))))....]]]].... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -5.50 ..............((((...........)))).... New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -4.95 .............((((...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.00 .......(((((........)))))............ New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -3.69 .......(((((.[[[[...)))))........]]]] New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -3.43 ......((((....(((.....)))........)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.37 New CC F-measure-avg: 0.479, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 6 > PLRV-W GCGGCACCGCCCGCCAAAACAAACGG ((((..[[[.)))).........]]] ((((..[[[.)))).........]]] ((((..[[[.)))).........]]] Energy of known structure: -5.27 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -5.27 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -5.27 ..(((.[[[...)))........]]] New CC sens: 0.429, New CC ppv: 0.500, New CC F-measure: 0.462, New CC Energy: -3.92 ..(((.......)))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.13 ((((......))))............ New CC sens: 0.571, New CC ppv: 1.000, New CC F-measure: 0.727, New CC Energy: -2.89 (((....)))(((..........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.07 ..(((...)))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.06 ......(((..............))) New CC sens: 0.429, New CC ppv: 1.000, New CC F-measure: 0.600, New CC Energy: -0.81 New CC F-measure-avg: 0.398, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > SSTRAND_ID=PDB_00716; TYPE=Other Ribozyme; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=1SJF; ORGANISM=HOMO SAPIENS AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC ..(((((((...[[[[[[(((.{{.....))))))))))}}....((((..........)))).....]]]]]] .((.(((((.((((.(((((......))))).))))))))).)).((((((((.....))))))))........ .((.(((((.((((.(((((.[[[[.))))).))))))))).)).((((((((.....))))))))...]]]]. Energy of known structure: -17.44 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -21.37 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -22.16 .((.(((((.((((.(((((......))))).))))))))).)).(((((((.......)))))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.72 .((((((((......(((((.[[[[.))))).)))))))).....((((((((.....))))))))...]]]]. New CC sens: 0.318, New CC ppv: 0.280, New CC F-measure: 0.298, New CC Energy: -21.27 .((.(((((.((((.(((((......))))).))))))))).))...(((((.(((....)))...)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.65 .((((((((......(((((......))))).)))))))).....(((((((.......)))))))........ New CC sens: 0.318, New CC ppv: 0.350, New CC F-measure: 0.333, New CC Energy: -20.59 .((.(((((.((((.(((((.[[[[.))))).))))))))).)).((((..........))))......]]]]. New CC sens: 0.182, New CC ppv: 0.167, New CC F-measure: 0.174, New CC Energy: -19.78 .(((((((([[[[[.(((((.{{{{.))))).))))))))......]]]]]..(((....)))......}}}}. New CC sens: 0.318, New CC ppv: 0.280, New CC F-measure: 0.298, New CC Energy: -19.43 .((.(((((.((((.(((((.[[[[.))))).))))))))).))....((((((......))))))...]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.43 ....(((((..(((.(((((......))))).))).)))))....((((((((.....))))))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.27 .((.(((((.((((.(((((......))))).))))))))).)).((((..........))))........... New CC sens: 0.182, New CC ppv: 0.200, New CC F-measure: 0.190, New CC Energy: -19.17 ....(((((...[[[[[[(((........)))....)))))....((((((((.....))))))))..]]]]]] New CC sens: 0.409, New CC ppv: 0.409, New CC F-measure: 0.409, New CC Energy: -18.99 .((((((((......(((((.[[[[.))))).)))))))).....((((..........))))......]]]]. New CC sens: 0.500, New CC ppv: 0.524, New CC F-measure: 0.512, New CC Energy: -18.89 .((.(((((.((((.(((((......))))).))))))))).))....((((((......))))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.82 .(((((((([[[[[.(((((......))))).))))))))......]]]]]......(((........)))... New CC sens: 0.318, New CC ppv: 0.333, New CC F-measure: 0.326, New CC Energy: -18.60 ....(((((..(((.(((((......))))).))).)))))......(((((.(((....)))...)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.46 .((((((((......(((((......))))).))))))))(....).(((((.(((....)))...)))))... New CC sens: 0.318, New CC ppv: 0.318, New CC F-measure: 0.318, New CC Energy: -18.37 .((((((((......(((((......))))).)))))))).....((((..........))))........... New CC sens: 0.500, New CC ppv: 0.647, New CC F-measure: 0.564, New CC Energy: -18.04 New CC F-measure-avg: 0.201, New CC F-measure-best: 0.564, New CC best-subopt: 16, New CC num-subopt: 16 > SSTRAND_ID=PDB_00944; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2B57; ORGANISM=SYNTHETIC GACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC ((((((.....(((((..[..[[)))))..........((((((]]...].))))))..)))))) ((((((.....(((((.......)))))..........((((((.......))))))..)))))) ((((((.....(((((.......)))))..........((((((.......))))))..)))))) Energy of known structure: 1.82 Initial sens: 0.850, Initial ppv: 1.000, Initial F-measure: 0.919, Initial Energy: -12.89 New CC sens: 0.850, New CC ppv: 1.000, New CC F-measure: 0.919, New CC Energy: -12.89 ((((((.....(((.......((.((....)).))...[[[[[[.)))...]]]]]]..)))))) New CC sens: 0.600, New CC ppv: 0.632, New CC F-measure: 0.615, New CC Energy: -12.21 ..(((((....[[[[[.))))).]]]]]..........((((((.......))))))........ New CC sens: 0.550, New CC ppv: 0.688, New CC F-measure: 0.611, New CC Energy: -12.19 ...........(((((..[[[[[)))))..........((((((]]]]]..))))))........ New CC sens: 0.650, New CC ppv: 0.812, New CC F-measure: 0.722, New CC Energy: -11.37 ...........(((((.......)))))..........((((((.......))))))........ New CC sens: 0.550, New CC ppv: 1.000, New CC F-measure: 0.710, New CC Energy: -11.08 ...........((((([[[[[[[)))))..........((((((.......)))))).]]]]]]] New CC sens: 0.550, New CC ppv: 0.611, New CC F-measure: 0.579, New CC Energy: -10.62 ((((((.....(((((..[[[[[)))))..(((.......))).]]]]]..........)))))) New CC sens: 0.650, New CC ppv: 0.684, New CC F-measure: 0.667, New CC Energy: -10.47 ...........(((.......((.((....)).))...[[[[[[.)))...]]]]]]........ New CC sens: 0.300, New CC ppv: 0.462, New CC F-measure: 0.364, New CC Energy: -10.17 (((((......(((((..[[[[[)))))..(((.......))).]]]]].))))).......... New CC sens: 0.350, New CC ppv: 0.389, New CC F-measure: 0.368, New CC Energy: -9.69 New CC F-measure-avg: 0.617, New CC F-measure-best: 0.919, New CC best-subopt: 0, New CC num-subopt: 8 > SSTRAND_ID=PDB_01009; TYPE=Other RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2DU3; ORGANISM=ARCHAEOGLOBUS FULGIDUS GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC ((((((([.(((.].......)))..((((.......))))......(((((.......)))))))))))) (((((((....((((.((.(((((((....))))))).)).))))..(((((.......)))))))))))) (((((((..((((((...)))))).(((((.......))))).....(((((.......)))))))))))) Energy of known structure: -6.53 Initial sens: 0.600, Initial ppv: 0.480, Initial F-measure: 0.533, Initial Energy: -23.22 New CC sens: 0.950, New CC ppv: 0.826, New CC F-measure: 0.884, New CC Energy: -24.04 ((((((((((.((((.((.(((((((....))))))).)).)))).))((((.......)))))))))))) New CC sens: 0.550, New CC ppv: 0.407, New CC F-measure: 0.468, New CC Energy: -22.99 ((((((((.((((((...))))))((((((.......)))))).....((((.......)))))))))))) New CC sens: 0.900, New CC ppv: 0.750, New CC F-measure: 0.818, New CC Energy: -22.63 (((((((..((((...........[[[[[[))))...]]]]]]....(((((.......)))))))))))) New CC sens: 0.800, New CC ppv: 0.727, New CC F-measure: 0.762, New CC Energy: -22.03 (((((((.......((((((((((((....)))))))...)))))..(((((.......)))))))))))) New CC sens: 0.600, New CC ppv: 0.500, New CC F-measure: 0.545, New CC Energy: -21.80 ((((((((......((((......((((((.......))))))...))))((.......))..)))))))) New CC sens: 0.650, New CC ppv: 0.650, New CC F-measure: 0.650, New CC Energy: -21.46 (((((((..((((....(((....)))...)))).............(((((.......)))))))))))) New CC sens: 0.600, New CC ppv: 0.632, New CC F-measure: 0.615, New CC Energy: -21.33 ((((((((......((((((((((((....)))))))...)))))...((((.......)))))))))))) New CC sens: 0.550, New CC ppv: 0.458, New CC F-measure: 0.500, New CC Energy: -21.03 ((((((((.((((....(((....)))...))))..............((((.......)))))))))))) New CC sens: 0.550, New CC ppv: 0.579, New CC F-measure: 0.564, New CC Energy: -20.43 ((((((((......((((....((((............))))....))))((.......))..)))))))) New CC sens: 0.450, New CC ppv: 0.500, New CC F-measure: 0.474, New CC Energy: -20.36 ((((((((.((((...........[[[[[[))))...]]]]]].....((((.......)))))))))))) New CC sens: 0.750, New CC ppv: 0.682, New CC F-measure: 0.714, New CC Energy: -20.27 (((((((..((((.[[[[[...........))))......]]]]]..(((((.......)))))))))))) New CC sens: 0.600, New CC ppv: 0.571, New CC F-measure: 0.585, New CC Energy: -20.11 ((((((((.((((((...))))))..((((.....((.(((........))).))...)))).)))))))) New CC sens: 0.500, New CC ppv: 0.435, New CC F-measure: 0.465, New CC Energy: -19.84 New CC F-measure-avg: 0.619, New CC F-measure-best: 0.884, New CC best-subopt: 0, New CC num-subopt: 12 > SSTRAND_ID=PDB_01021; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2EET; ORGANISM=SYNTHETIC GGACAUGUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACCAUGUCCa .((((((...(.(((((..[..[[))))).)........((((((]]...].))))))..)))))).. (((((((.....(((((.......)))))..........((((((.......))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). Energy of known structure: 0.90 Initial sens: 0.810, Initial ppv: 0.944, Initial F-measure: 0.872, Initial Energy: -17.43 New CC sens: 0.810, New CC ppv: 0.944, New CC F-measure: 0.872, New CC Energy: -17.43 (((((((.....(((.......((.((....)).))...[[[[[[.)))...]]]]]]..))))))). New CC sens: 0.571, New CC ppv: 0.600, New CC F-measure: 0.585, New CC Energy: -16.75 (((((((.....(((((..[[[[[)))))..(((.......))).]]]]]..........))))))). New CC sens: 0.619, New CC ppv: 0.650, New CC F-measure: 0.634, New CC Energy: -15.02 New CC F-measure-avg: 0.697, New CC F-measure-best: 0.872, New CC best-subopt: 0, New CC num-subopt: 2 > SSTRAND_ID=PDB_01023; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2EEV; ORGANISM=SYNTHETIC GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa (((((((...(.(((((..[..[[))))).)........((((((]]...].))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). Energy of known structure: -0.53 Initial sens: 0.818, Initial ppv: 1.000, Initial F-measure: 0.900, Initial Energy: -16.20 New CC sens: 0.818, New CC ppv: 1.000, New CC F-measure: 0.900, New CC Energy: -16.20 (((((((.....(((............(((......)))[[[[[[.)))...]]]]]]..))))))). New CC sens: 0.591, New CC ppv: 0.684, New CC F-measure: 0.634, New CC Energy: -14.33 (((((((.....(((((..[[[[[)))))..(((.......))).]]]]]..........))))))). New CC sens: 0.636, New CC ppv: 0.700, New CC F-measure: 0.667, New CC Energy: -13.79 (((((((.....(((((..[[[[[))))).......(((...)))]]]]]..........))))))). New CC sens: 0.636, New CC ppv: 0.700, New CC F-measure: 0.667, New CC Energy: -13.30 (((((((.......(((((......((....)).)))))((((((.......))))))..))))))). New CC sens: 0.591, New CC ppv: 0.650, New CC F-measure: 0.619, New CC Energy: -12.51 New CC F-measure-avg: 0.697, New CC F-measure-best: 0.900, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=RFA_00632; TYPE=Hepatitis Delta Virus Ribozyme; EXT_SOURCE=Rfam Database; EXT_ID=RF00094 AB037947.1/775-685; ORGANISM=Hepatitis delta virus GUGGCCGGCAUGGCCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACGAUCCGAGGGGACUGUCCCUCUCGAGAAUCGGCAAAUGGGGCCCC ...[[[[[[...(((((((((........)))]]]]]].......(((((.(((((((...).))))))..).)))).....))))))... .((.(((((.((((.(((((......))))).))))))))).)).((((((((((((......))))))).).))))......((....)) .((.(((((.((((.(((((......))))).))))))))).))....(((((((((......))))))).))...(((.......))).. Energy of known structure: -17.19 Initial sens: 0.407, Initial ppv: 0.367, Initial F-measure: 0.386, Initial Energy: -25.19 New CC sens: 0.259, New CC ppv: 0.250, New CC F-measure: 0.255, New CC Energy: -26.00 .((.(((((.((((.(((((......))))).))))))))).))......(((((((......)))))))......(((.......))).. New CC sens: 0.222, New CC ppv: 0.231, New CC F-measure: 0.226, New CC Energy: -25.93 ..(((((((.((((.(((((......))))).)))))))..((..((((((((((((......))))))).).))))))......)))).. New CC sens: 0.407, New CC ppv: 0.367, New CC F-measure: 0.386, New CC Energy: -25.23 ...((((((.....[[[[[[[.....))))))...]]]]]]]......(((((((((......))))))).))...(((.......))).. New CC sens: 0.259, New CC ppv: 0.280, New CC F-measure: 0.269, New CC Energy: -25.08 ...((((((.....[[[[[[[.....))))))...]]]]]]]........(((((((......)))))))......(((.......))).. New CC sens: 0.222, New CC ppv: 0.261, New CC F-measure: 0.240, New CC Energy: -25.01 ...(((((...[[[[[[[((((((..((....)).))..)))).....(((((((((......))))))).)).)))))...]]]]]]].. New CC sens: 0.481, New CC ppv: 0.448, New CC F-measure: 0.464, New CC Energy: -24.99 ..(((((((......(((((......))))).)))))))((((..((((((((((((......))))))).).)))).........)))). New CC sens: 0.630, New CC ppv: 0.607, New CC F-measure: 0.618, New CC Energy: -24.95 ...(((((...[[[[[[[((((((..((....)).))..)))).......(((((((......)))))))....)))))...]]]]]]].. New CC sens: 0.444, New CC ppv: 0.444, New CC F-measure: 0.444, New CC Energy: -24.94 .((((((((......(((((......))))).)))))))).((..((((((((((((......))))))).).))))))............ New CC sens: 0.630, New CC ppv: 0.630, New CC F-measure: 0.630, New CC Energy: -24.39 ..(((((((......(((((......))))).)))))))((((.....(((((((((......))))))).)).(((.....))).)))). New CC sens: 0.481, New CC ppv: 0.464, New CC F-measure: 0.473, New CC Energy: -24.38 .((.(((((.((((.(((((......))))).))))))))).)).......((((((....)))))).........(((.......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -24.22 ..(((((((......(((((......))))).)))))))((((.......(((((((......)))))))....(((.....))).)))). New CC sens: 0.444, New CC ppv: 0.462, New CC F-measure: 0.453, New CC Energy: -24.21 ....(((((..(((.(((((......))))).))).))))).......(((((((((......))))))).))...(((.......))).. New CC sens: 0.259, New CC ppv: 0.280, New CC F-measure: 0.269, New CC Energy: -23.95 ....(((((..(((.(((((......))))).))).))))).........(((((((......)))))))......(((.......))).. New CC sens: 0.222, New CC ppv: 0.261, New CC F-measure: 0.240, New CC Energy: -23.88 ....(((((..[[[[[[[(((........)))....)))))((..((((((((((((......))))))).).))))))...]]]]]]].. New CC sens: 0.741, New CC ppv: 0.690, New CC F-measure: 0.714, New CC Energy: -23.87 ...........(((((((((((((..((....)).))..))))..((((((((((((......))))))).).)))).....))))))).. New CC sens: 0.630, New CC ppv: 0.630, New CC F-measure: 0.630, New CC Energy: -23.72 .((((((((......(((((......))))).))))))))(....)..(((((((((......))))))).))...(((.......))).. New CC sens: 0.481, New CC ppv: 0.500, New CC F-measure: 0.491, New CC Energy: -23.30 ...((((((.....[[[[[[[.....))))))...]]]]]]].........((((((....)))))).........(((.......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.30 ....(((((..(((.(((((......))))).))).)))))((..((((((((((((......))))))).).))))))............ New CC sens: 0.407, New CC ppv: 0.407, New CC F-measure: 0.407, New CC Energy: -23.23 .((((((((......(((((......))))).))))))))(....)....(((((((......)))))))......(((.......))).. New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -23.23 New CC F-measure-avg: 0.384, New CC F-measure-best: 0.714, New CC best-subopt: 14, New CC num-subopt: 19 > SSTRAND_ID=RFA_00636; TYPE=Hepatitis Delta Virus Ribozyme; EXT_SOURCE=Rfam Database; EXT_ID=RF00094 M84917.1/773-684; ORGANISM=Hepatitis delta virus GUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCUCCUCGGUAAUGGCGAAUGGGACCCA ...[[[[[[...(((((((((........)))]]]]]].......(((((((((((((...).)))))))).)))).....))))))... .((.(((((.((((.(((((......))))).))))))))).)).((((((((((((......)))))))).)))).............. .((.(((((.((((.(((((......))))).))))))))).)).((((((((((((......)))))))).)))).............. Energy of known structure: -20.27 Initial sens: 0.429, Initial ppv: 0.429, Initial F-measure: 0.429, Initial Energy: -27.01 New CC sens: 0.429, New CC ppv: 0.429, New CC F-measure: 0.429, New CC Energy: -27.01 ...((((((.....[[[[[[[.....))))))...]]]]]]]...((((((((((((......)))))))).)))).............. New CC sens: 0.429, New CC ppv: 0.480, New CC F-measure: 0.453, New CC Energy: -26.78 .((((((((......(((((......))))).)))))))).((..((((((((((((......)))))))).))))))............ New CC sens: 0.643, New CC ppv: 0.667, New CC F-measure: 0.655, New CC Energy: -26.60 .((((((((......(((((......))))).)))))))).....((((((((((((......)))))))).)))).............. New CC sens: 0.643, New CC ppv: 0.720, New CC F-measure: 0.679, New CC Energy: -26.02 .((.(((((.((((.(((((......))))).))))))))).)).....((((((((......))))))))...(((..........))) New CC sens: 0.286, New CC ppv: 0.296, New CC F-measure: 0.291, New CC Energy: -25.18 ....(((((..(((.(((((......))))).))).)))))....((((((((((((......)))))))).)))).............. New CC sens: 0.429, New CC ppv: 0.480, New CC F-measure: 0.453, New CC Energy: -25.05 ....(((((..[[[[[[[(((........)))....)))))....((((((((((((......)))))))).)))).....]]]]]]].. New CC sens: 0.750, New CC ppv: 0.778, New CC F-measure: 0.764, New CC Energy: -24.92 ...((((((.....[[[[[[[.....))))))...]]]]]]].......((((((((......))))))))...(((..........))) New CC sens: 0.286, New CC ppv: 0.333, New CC F-measure: 0.308, New CC Energy: -24.86 ....(((((..(((.(((((......))))).))).)))))((..((((((((((((......)))))))).))))))............ New CC sens: 0.429, New CC ppv: 0.444, New CC F-measure: 0.436, New CC Energy: -24.68 ....(((((..[[[[[[[(((........)))....)))))((..((((((((((((......)))))))).))))))...]]]]]]].. New CC sens: 0.750, New CC ppv: 0.724, New CC F-measure: 0.737, New CC Energy: -24.55 ...........(((((((((((((..((....)).))..))))..((((((((((((......)))))))).)))).....))))))).. New CC sens: 0.643, New CC ppv: 0.667, New CC F-measure: 0.655, New CC Energy: -24.21 ....(((((..[[[[[[[......[[[[[[......)))))........((((((((......))))))))...]]]]]].]]]]]]].. New CC sens: 0.500, New CC ppv: 0.538, New CC F-measure: 0.519, New CC Energy: -23.45 ...........(((((((.........(((((....)))))....((((((((((((......)))))))).)))).....))))))).. New CC sens: 0.643, New CC ppv: 0.750, New CC F-measure: 0.692, New CC Energy: -23.37 ...((((((.....[[[[[[[{{{{{))))))...]]]]]]]...........}}}}}..(((((..(((.......)))..)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.35 .((.(((((.((((.(((((.[[[[[))))).))))))))).)).........]]]]]..(((((..(((.......)))..)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.15 ....(((((..(((.(((((......))))).))).)))))........((((((((......))))))))...(((..........))) New CC sens: 0.286, New CC ppv: 0.333, New CC F-measure: 0.308, New CC Energy: -23.13 .((((((((......(((((......))))).))))))))(....)...((((((((......))))))))...(((..........))) New CC sens: 0.500, New CC ppv: 0.560, New CC F-measure: 0.528, New CC Energy: -23.13 ...........(((((((.........(((((....)))))((..((((((((((((......)))))))).))))))...))))))).. New CC sens: 0.643, New CC ppv: 0.692, New CC F-measure: 0.667, New CC Energy: -23.12 ....(((((..[[[[[[[(((........)))....)))))........((((((((......))))))))..........]]]]]]].. New CC sens: 0.607, New CC ppv: 0.739, New CC F-measure: 0.667, New CC Energy: -22.91 ....(((((......(((((......))))).....)))))....((((((((((((......)))))))).)))).............. New CC sens: 0.429, New CC ppv: 0.545, New CC F-measure: 0.480, New CC Energy: -22.62 New CC F-measure-avg: 0.486, New CC F-measure-best: 0.764, New CC best-subopt: 6, New CC num-subopt: 19 > SSTRAND_ID=TMR_00007; TYPE=Transfer Messenger RNA; EXT_SOURCE=tmRNA Database; EXT_ID=Acid.caps._TRW-240015_1-352; ORGANISM=NULL CGGGGGGUGGGCACCCGUAAUCGCUCGCA [[[[..((((((.]]]].....)))))). ..(((.[[[[[[.)))......]]]]]]. ..(((.[[[[[[.)))......]]]]]]. Energy of known structure: -9.75 Initial sens: 0.600, Initial ppv: 0.667, Initial F-measure: 0.632, Initial Energy: -11.40 New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -11.40 ((((..[[[[[[.)))).....]]]]]]. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -9.75 ...((([[[[[[.)))......]]]]]]. New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -8.05 (((([[[[[[...))))...]]]]]]... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -7.94 ..(.((((((..........)))))).). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.43 ......((((((..........)))))). New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -5.41 ((((.........))))............ New CC sens: 0.400, New CC ppv: 1.000, New CC F-measure: 0.571, New CC Energy: -4.29 ((((((((....)))).......)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.00 ...(((.......)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.52 ....((((....))))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.51 ..(((........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.46 ((((..((((....)))).....)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.52 New CC F-measure-avg: 0.332, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 11