> SSTRAND_ID=Bt_PrP; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GCCCCAUGGAGGUGGCUGGGGCCAGCCUCAUGGAGGUGGCUGGGG ...[[[[[[............((((((]]]]]]....)))))).. ((((((((..(.((((....)))).)..))))).)))........ ((((((((..(.((((....)))).)..))))).)))........ Energy of known structure: -11.27 Initial sens: 0.417, Initial ppv: 0.385, Initial F-measure: 0.400, Initial Energy: -21.64 New CC sens: 0.417, New CC ppv: 0.385, New CC F-measure: 0.400, New CC Energy: -21.64 ((((((((..(.((((....)))).)..)))))....)))..... New CC sens: 0.417, New CC ppv: 0.385, New CC F-measure: 0.400, New CC Energy: -20.44 (((((.....)).)))...(((((.((((...))))))))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.60 (((((((((....(((((....)))))))))))....)))..... New CC sens: 0.500, New CC ppv: 0.429, New CC F-measure: 0.462, New CC Energy: -18.50 ((((((((.....(((((....))))).))))).)))........ New CC sens: 0.417, New CC ppv: 0.385, New CC F-measure: 0.400, New CC Energy: -18.30 .(((((..((((((((....)))).))))...........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.02 (((((.....)).))).....((((((..........)))))).. New CC sens: 0.500, New CC ppv: 0.545, New CC F-measure: 0.522, New CC Energy: -17.79 ((((((..........))))))(((((.(......).)))))... New CC sens: 0.417, New CC ppv: 0.417, New CC F-measure: 0.417, New CC Energy: -17.69 .(((((..((((((((....))).)))))...........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.62 New CC F-measure-avg: 0.289, New CC F-measure-best: 0.522, New CC best-subopt: 6, New CC num-subopt: 8 > SSTRAND_ID=BWYV; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCGCGGCACCGUCCGCGGAACAAACGG ..(((((..[[[[)))))......]]]] ..(((((..[[[[)))))......]]]] ..(((((..[[[[)))))......]]]] Energy of known structure: -13.69 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.69 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.69 .(((.....[[[[.))).......]]]] New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -10.54 ..(((((......))))).......... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -8.10 .(((.(((...))))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.30 .(((((....))..)))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.40 New CC F-measure-avg: 0.443, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=Ec_PK1; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; CGAGGGGCGGUUGGCCUCGUAAAAAGCCGC [[[[[.((((((..]]]]].....)))))) (((((.[[[[[[..))))).....]]]]]] (((((.[[[[[[..))))).....]]]]]] Energy of known structure: -14.19 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -14.19 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -14.19 ...(((((.....)))))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.20 ......((((((............)))))) New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -6.89 (((((.........)))))........... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -5.80 ((((([[[......)))))......]]].. New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -5.13 New CC F-measure-avg: 0.571, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=Ec_PK4; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; GUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC ((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]] ((((((((((.(((........))).))))))))))................ ((((((((((.(((........))).))))))))))................ Energy of known structure: -14.15 Initial sens: 0.684, Initial ppv: 1.000, Initial F-measure: 0.812, Initial Energy: -16.55 New CC sens: 0.684, New CC ppv: 1.000, New CC F-measure: 0.812, New CC Energy: -16.55 ((((((((((((((....))))....))))))))))................ New CC sens: 0.526, New CC ppv: 0.714, New CC F-measure: 0.606, New CC Energy: -14.10 New CC F-measure-avg: 0.709, New CC F-measure-best: 0.812, New CC best-subopt: 0, New CC num-subopt: 1 > SSTRAND_ID=EC_S15; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GGGAUCGCUGAAUUAGAGAUCGGCGUCCUUUCAUUCUAUAUACUUUGGAGUUUUAAAAUGUCUCUAA ((((.((((((.[[[[[[[))))))))))...............................]]]]]]] ((((.((((((.[[[[[[.)))))))))).............]]]]]]................... ((((.((((((.[[[[[[.)))))))))).............]]]]]]................... Energy of known structure: -16.80 Initial sens: 0.588, Initial ppv: 0.625, Initial F-measure: 0.606, Initial Energy: -16.84 New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -16.84 ((((.((((((.[[[[[[.))))))))))....(((((.......)))))]]]]]]........... New CC sens: 0.588, New CC ppv: 0.476, New CC F-measure: 0.526, New CC Energy: -16.11 (((((((((((.[[[[[[.)))))).................]]]]]]...........)))))... New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -16.04 ((((.((((((........))))))))))...............((((((...........)))))) New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -15.19 (((((((((((..[[[[[.))))))........]]]]].....................)))))... New CC sens: 0.353, New CC ppv: 0.375, New CC F-measure: 0.364, New CC Energy: -15.05 ((((.((((((........))))))))))...((((((.......))))))................ New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -14.60 (((..((((((.[[[[[[.)))))))))..............]]]]]]................... New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -13.78 (((((((((((.[[[[[[.))))))........(((((.......)))))]]]]]]...)))))... New CC sens: 0.353, New CC ppv: 0.273, New CC F-measure: 0.308, New CC Energy: -13.50 (((((.(((((........))))))))))...............((((((...........)))))) New CC sens: 0.529, New CC ppv: 0.562, New CC F-measure: 0.545, New CC Energy: -13.39 (((((((((((........)))))).......((((((.......))))))........)))))... New CC sens: 0.353, New CC ppv: 0.353, New CC F-measure: 0.353, New CC Energy: -13.00 ((((.((((((.[[[[[[.))))))))))...............((((((]]]]]].....)))))) New CC sens: 0.588, New CC ppv: 0.455, New CC F-measure: 0.513, New CC Energy: -12.91 (((((.(((((........))))))))))...((((((.......))))))................ New CC sens: 0.529, New CC ppv: 0.562, New CC F-measure: 0.545, New CC Energy: -12.80 (((((((((((.[[[[[[.))))))(((..................))).]]]]]]...)))))... New CC sens: 0.353, New CC ppv: 0.300, New CC F-measure: 0.324, New CC Energy: -12.36 ((((.((((((..[[[[[.))))))))))....]]]]]......((((((...........)))))) New CC sens: 0.588, New CC ppv: 0.476, New CC F-measure: 0.526, New CC Energy: -12.26 (((..((((((........)))))))))................((((((...........)))))) New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -12.09 (((..((((((.[[[[[[.))))))))).....(((((.......)))))]]]]]]........... New CC sens: 0.353, New CC ppv: 0.300, New CC F-measure: 0.324, New CC Energy: -11.95 (((((((((((.[[[[[[.))))))...(((((............)))))]]]]]]...)))))... New CC sens: 0.353, New CC ppv: 0.273, New CC F-measure: 0.308, New CC Energy: -11.89 (((..((((((........)))))))))....((((((.......))))))................ New CC sens: 0.353, New CC ppv: 0.400, New CC F-measure: 0.375, New CC Energy: -11.50 (((((((((((.[[[[[[.))))))[[[....))))).........]]].]]]]]]........... New CC sens: 0.353, New CC ppv: 0.300, New CC F-measure: 0.324, New CC Energy: -11.32 New CC F-measure-avg: 0.435, New CC F-measure-best: 0.606, New CC best-subopt: 0, New CC num-subopt: 18 > SSTRAND_ID=HDV; TYPE=hepatitis delta virus ribozyme; EXT_SOURCE=Isambert and Siggia 2000; ggccggcatggtcccagcctcctcgctggcgccggctgggcaacauuccgaggggaccguccccucgguaauggcgaaugggaccca [[[[[[[..((((((((((........)))]]]]]]]......(((((((((((((...))))))))).)))).....))))))).. .((((((..[[[[[[[[[[[...{{{{...)))))).]]]]......(((((((((...)))))))))....}}}}..]]]]]]].. .((((((..[[[[[[[[[[[...{{{{...)))))).]]]]......(((((((((...)))))))))....}}}}..]]]]]]].. Energy of known structure: -39.24 Initial sens: 0.733, Initial ppv: 0.733, Initial F-measure: 0.733, Initial Energy: -48.85 New CC sens: 0.733, New CC ppv: 0.733, New CC F-measure: 0.733, New CC Energy: -48.85 (.(((((.((((.(((((......))))).))))))))).)..((((((((((((.....)))))))).)))).............. New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -45.95 .........(((((((((((....((((....)))).))))..((((((((((((.....)))))))).)))).....))))))).. New CC sens: 0.633, New CC ppv: 0.704, New CC F-measure: 0.667, New CC Energy: -44.45 .((((....[[[[[[[((((....((((....)))).))))......(((((((((...)))))))))...))))...]]]]]]].. New CC sens: 0.533, New CC ppv: 0.571, New CC F-measure: 0.552, New CC Energy: -44.29 .((((((..[[[[[[[[[[[((.....)).)))))).]]]]..((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.833, New CC ppv: 0.806, New CC F-measure: 0.820, New CC Energy: -43.00 .((((((......(((((......))))).)))))).((((..((((((((((((.....)))))))).))))........).))). New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -42.59 .((((((..[[[[[[[[[[[....)))))).......]]]]..((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.633, New CC ppv: 0.655, New CC F-measure: 0.644, New CC Energy: -42.37 (.(((((.((((.(((((......))))).))))))))).)......(((((((((...)))))))))................... New CC sens: 0.300, New CC ppv: 0.375, New CC F-measure: 0.333, New CC Energy: -41.85 .........(((((((((((....((((....)))).))))......(((((((((...)))))))))..........))))))).. New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -40.35 .((((((..[[[[[[[(((........)))))))))...((..((((((((((((.....)))))))).))))))...]]]]]]].. New CC sens: 0.933, New CC ppv: 0.933, New CC F-measure: 0.933, New CC Energy: -40.23 ..(((((..(((.(((((......))))).))).)))))....((((((((((((.....)))))))).)))).............. New CC sens: 0.400, New CC ppv: 0.480, New CC F-measure: 0.436, New CC Energy: -39.95 .((((((......(((((......))))).)))))).......((((((((((((.....)))))))).)))).............. New CC sens: 0.600, New CC ppv: 0.783, New CC F-measure: 0.679, New CC Energy: -39.84 .((((((..[[[[[[[(((........))))))))).......((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.933, New CC ppv: 1.000, New CC F-measure: 0.966, New CC Energy: -39.73 ..(((((..(((.(((((......))))).))).)))))((..((((((((((((.....)))))))).))))))............ New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -39.15 ..(((((..[[[[[[[(((........)))....)))))....((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.733, New CC ppv: 0.815, New CC F-measure: 0.772, New CC Energy: -39.03 .((((((..[[[[[[[[[[[((.....)).)))))).]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.733, New CC ppv: 0.786, New CC F-measure: 0.759, New CC Energy: -38.90 .........(((((((((......))...(((((....(....)...(((((((((...)))))))))...)))))..))))))).. New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -38.50 .((((((..[[[[[[[[[[[....)))))).......]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -38.27 ..(((((..[[[[[[[(((........)))....)))))((..((((((((((((.....)))))))).))))))...]]]]]]].. New CC sens: 0.733, New CC ppv: 0.759, New CC F-measure: 0.746, New CC Energy: -38.23 .........(((((((((((.........[[[[[...))))......(((((((((...)))))))))...]]]]]..))))))).. New CC sens: 0.533, New CC ppv: 0.640, New CC F-measure: 0.582, New CC Energy: -38.19 New CC F-measure-avg: 0.643, New CC F-measure-best: 0.966, New CC best-subopt: 12, 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: -19.93 Initial sens: 0.167, Initial ppv: 0.143, Initial F-measure: 0.154, Initial Energy: -40.20 New CC sens: 0.167, New CC ppv: 0.143, New CC F-measure: 0.154, New CC Energy: -40.20 (((((((..[[[[.[[[[[.[[[[[[......)))))))...(((((((]]]]]]............)))))))......]]]]]]]]].. New CC sens: 0.708, New CC ppv: 0.586, New CC F-measure: 0.642, New CC Energy: -39.42 .........((((.(((((.((((((((..((((.....))))...)).)))))).....(((((....)))))......))))))))).. New CC sens: 0.167, New CC ppv: 0.154, New CC F-measure: 0.160, New CC Energy: -37.80 .........((((.(((((.((((((....(((((...)))))......))))))..((.(((((....)))))))....))))))))).. New CC sens: 0.167, New CC ppv: 0.148, New CC F-measure: 0.157, New CC Energy: -37.00 (((((((..[[[[.[[[[[.[[[[[[[[....))))))).......]].]]]]]]..((.(((((....)))))))....]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.323, New CC F-measure: 0.364, New CC Energy: -35.18 .........((((.(((((.((((((....(((((...)))))......)))))).....(((((....)))))......))))))))).. New CC sens: 0.167, New CC ppv: 0.160, New CC F-measure: 0.163, New CC Energy: -34.60 (((((((..[[[[.[[[[[.[[[[[[......)))))))((....))..]]]]]]..((.(((((....)))))))....]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.323, New CC F-measure: 0.364, New CC Energy: -34.45 ..(((.....))).(((((.((((((((..((((.....))))...)).))))))..((.(((((....)))))))....)))))...... New CC sens: 0.167, New CC ppv: 0.148, New CC F-measure: 0.157, New CC Energy: -34.30 .........((((.(((((.((...(((.....)))...)).(((((((....((((....))))..)))))))......))))))))).. New CC sens: 0.625, New CC ppv: 0.600, New CC F-measure: 0.612, New CC Energy: -32.90 (((((((..[[[[.[[[[[.[[[[[[[[....))))))).......]].]]]]]].....(((((....)))))......]]]]]]]]].. New CC sens: 0.417, New CC ppv: 0.345, New CC F-measure: 0.377, New CC Energy: -32.78 (((((((.((.((..............)).))))))))).....(((((.(..((((....)))).))))))(((((.......))))).. New CC sens: 0.625, New CC ppv: 0.577, New CC F-measure: 0.600, New CC Energy: -32.68 .........((((.......((((((((..((((.....))))...)).))))))..((.(((((....))))))).........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -32.40 (((((((..[[[[.[[[[[(((.......))))))))))((.(((((((.(..((((....)))).)))))))).))...]]]]]]]]].. New CC sens: 1.000, New CC ppv: 0.727, New CC F-measure: 0.842, New CC Energy: -32.37 .........((((.(((((...(((((...((((.....))))........))))).((.(((((....)))))))....))))))))).. New CC sens: 0.167, New CC ppv: 0.160, New CC F-measure: 0.163, New CC Energy: -32.25 New CC F-measure-avg: 0.340, New CC F-measure-best: 0.842, New CC best-subopt: 12, New CC num-subopt: 13 > SSTRAND_ID=HIVRT32; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGCUCAACGGGAAAAUGAGCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. .......(((((.[[[[[[.)))))...]]]]]]. Energy of known structure: -7.40 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.40 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.40 ((((((.[[[[[..)))...]]]]]...))).... New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -6.62 ...(((.[[[[[..)))...]]]]].......... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -6.52 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -6.50 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -5.92 (((....(((((........)))))...))).... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -4.84 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -4.60 ((((((.[[[[...))).....]]]]..))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.37 ...(((.[[[[...))).....]]]]......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.27 ...(((.(((((........)))))......))). New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -3.14 New CC F-measure-avg: 0.494, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 9 > SSTRAND_ID=HIVRT322; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGGGUAACGGGAAAAUGCCCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. .......(((((.[[[[[[.)))))...]]]]]]. Energy of known structure: -7.48 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.48 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.48 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -6.60 .........((....))....(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.30 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -6.00 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -4.60 .....(((((....)))))..(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.40 ....((((((((........)))...))))).... New CC sens: 0.273, New CC ppv: 0.375, New CC F-measure: 0.316, New CC Energy: -4.00 .........((....))....(((.......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.80 .......(((((..[[[...)))))......]]]. New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -3.66 ........(((...)))....(((......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.10 New CC F-measure-avg: 0.374, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 9 > SSTRAND_ID=HIVRT33; TYPE=HIV-1-RT ligand RNA; EXT_SOURCE=Turek et al 1992; UCAAGUAUUCCGAAGCUUGACGGGAAAAUAAGCUA .......[[[[[.((((((.]]]]]...)))))). .......(((((.[[[[[[.)))))...]]]]]]. .......(((((.[[[[[[.)))))...]]]]]]. Energy of known structure: -5.24 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -5.24 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -5.24 ((((((........))))))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.90 ((((((.[[[[[..))))))]]]]].......... New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -4.86 .......(((((........))))).......... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -4.60 .......((((..[[[[[[...))))..]]]]]]. New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -3.76 ((((((.[[[[...))))))..]]]]......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.48 .............((((((.........)))))). New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -3.40 ...(((.(((((........)))))......))). New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -3.14 .......((((...........))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.19 ...(((.((((...........)))).....))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.39 .....(((((((........)))...))))..... New CC sens: 0.273, New CC ppv: 0.429, New CC F-measure: 0.333, New CC Energy: -1.30 New CC F-measure-avg: 0.383, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 10 > SSTRAND_ID=Hs_Prp; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; GCCUCAUGGUGGUGGCUGGGGGCAGCCUCAUGGUGGUGGCUGGGG ...((((((.............[[[[[))))))....]]]]]... (((((((.((((.(((((....))))))))).)))).)))..... (((((((.((((.(((((....))))))))).)))).)))..... Energy of known structure: -9.11 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -21.60 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.60 New CC F-measure-avg: 0.000, New CC F-measure-best: 0.000, New CC best-subopt: 0, New CC num-subopt: 0 > SSTRAND_ID=LP_PK1; TYPE=tmRNA; EXT_SOURCE=van Batenburg et al 2001; CGAGAAGGAGAUCUCUCGUAAAUAAGACUC [[[[[..(((.((]]]]].......))))) .((((..[[[.))))............]]] .((((..[[[.))))............]]] Energy of known structure: -7.63 Initial sens: 0.300, Initial ppv: 0.429, Initial F-measure: 0.353, Initial Energy: -5.03 New CC sens: 0.300, New CC ppv: 0.429, New CC F-measure: 0.353, New CC Energy: -5.03 (((((........)))))............ New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -4.80 (((((..[[[...))))).........]]] New CC sens: 0.800, New CC ppv: 1.000, New CC F-measure: 0.889, New CC Energy: -3.68 .((((......))))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.10 .......(((....)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.70 New CC F-measure-avg: 0.382, New CC F-measure-best: 0.889, New CC best-subopt: 2, New CC num-subopt: 4 > SSTRAND_ID=minimalIBV; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGGGUAUCAGUCAGGCUCGGCUGGUACCCCUUGCAAAGCGAGCCU (((((((((((..[[[[[[)))))))))))........]]]]]]. ((((((((((((......))))))))))))............... ((((((((((((......))))))))))))............... Energy of known structure: -21.98 Initial sens: 0.647, Initial ppv: 0.917, Initial F-measure: 0.759, Initial Energy: -21.80 New CC sens: 0.647, New CC ppv: 0.917, New CC F-measure: 0.759, New CC Energy: -21.80 ((((((((((((......))))))))))))((((...)))).... New CC sens: 0.647, New CC ppv: 0.688, New CC F-measure: 0.667, New CC Energy: -21.30 .(((((((((((......)))))))))))(((((...)))))... New CC sens: 0.588, New CC ppv: 0.625, New CC F-measure: 0.606, New CC Energy: -20.20 New CC F-measure-avg: 0.677, New CC F-measure-best: 0.759, New CC best-subopt: 0, 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: -23.85 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -25.74 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -25.74 (((((..[[[[[[.))))).......]]]]]].. New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -23.03 (((((....[[[[.))))).........]]]].. New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -18.39 .(((..[[[[[[[...)))........]]]]]]] New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -15.46 (((((.....[[[.)))))..........]]].. New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -14.36 (((...[[[[[[[..))).........]]]]]]] New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -14.13 (((((..[[[[...)))))........]]]]... New CC sens: 0.455, New CC ppv: 0.556, New CC F-measure: 0.500, New CC Energy: -14.05 ((((....))))...((((.((....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.40 ((((....))))...((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.30 ((((...))))....((((.((....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.30 ((((....))))...((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.20 ((((...))))....((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.20 (((((((....)).))))).(((....))).... New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -11.60 ((((([[[.{{{{.)))))]]]......}}}}.. New CC sens: 0.455, New CC ppv: 0.417, New CC F-measure: 0.435, New CC Energy: -11.53 ((((.....))))..((((.((....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.40 ((((.....))))..((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.30 ((((.[[[))))...((((]]].....))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.20 ((((...))))....((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.10 ((((.[[[))))...((((]]]......)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.90 (((((.........))))).(((....))).... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -10.90 New CC F-measure-avg: 0.276, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 19 > SSTRAND_ID=MMTV_vpk; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCGCAGUGGGUCAGCGCCACUCAAAAGGCCCAU [[[[[..((((((.]]]]]........)))))). (((((.[[[[[[[.)))))........]]]]]]] (((((.[[[[[[[.)))))........]]]]]]] Energy of known structure: -21.35 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -23.24 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -23.24 (((..[[[[[)))....]]]]]............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.43 (((((.........)))))............... New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -9.30 ......(((((((..............))))))) New CC sens: 0.545, New CC ppv: 0.857, New CC F-measure: 0.667, New CC Energy: -8.53 ((((.((((((....).)))))).....)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.90 (((....(((((.......)))))....)))... 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: -7.74 (((((..[[[[[..)))))]]]]].......... New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -7.03 New CC F-measure-avg: 0.341, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 7 > SSTRAND_ID=pKA_A; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGCCGCCAGGCUCCAGCGGCCUUGCAAAAGGAGCCU [[[[[[..((((((.]]]]]]........)))))). ((((((.[[[[[[[.))))))........]]]]]]] ((((((.[[[[[[[.))))))........]]]]]]] Energy of known structure: -25.76 Initial sens: 1.000, Initial ppv: 0.923, Initial F-measure: 0.960, Initial Energy: -27.25 New CC sens: 1.000, New CC ppv: 0.923, New CC F-measure: 0.960, New CC Energy: -27.25 .......(((((((....((...))....))))))) New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -12.69 .......(((((((.(((....)))....))))))) New CC sens: 0.500, New CC ppv: 0.600, New CC F-measure: 0.545, New CC Energy: -12.10 ((((((.........))))))............... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -11.60 ((((....))))...((..((((....)))).)).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.10 (((.((.(((((.....))))).)).......))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.34 ((((....)))).....((((((....)))..))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.00 ((((((..(....).))).((((....)))).))). New CC sens: 0.250, New CC ppv: 0.273, New CC F-measure: 0.261, New CC Energy: -8.80 New CC F-measure-avg: 0.376, New CC F-measure-best: 0.960, New CC best-subopt: 0, New CC num-subopt: 7 > SSTRAND_ID=satRPV; TYPE=ribozyme; EXT_SOURCE=van Batenburg et al 2001; ACAGAGCGCGUACUGUCUGACGACGUAUCCGCGCGGACUAGAAGGCUGGUGCCUCGUCCAACAAAUAGAUACA ((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))). ((((.[[[[[..))))..(((((.{{{{{]]]]](((((((....))))).))))))).........}}}}}. ((((.[[[[[..))))..(((((.{{{{{]]]]](((((((....))))).))))))).........}}}}}. Energy of known structure: -20.80 Initial sens: 0.636, Initial ppv: 0.538, Initial F-measure: 0.583, Initial Energy: -23.65 New CC sens: 0.636, New CC ppv: 0.538, New CC F-measure: 0.583, New CC Energy: -23.65 ((((.[[[[[..))))..(((((.{{{{{]]]]]..(((((....)))))...))))).........}}}}}. New CC sens: 0.636, New CC ppv: 0.583, New CC F-measure: 0.609, New CC Energy: -23.55 .(((([[[[[.....)))).....(((((]]]]]((((....((((....)))).))))........))))). New CC sens: 0.818, New CC ppv: 0.818, New CC F-measure: 0.818, New CC Energy: -23.07 .....((((((((.(((....))))))..)))))((((....((((....)))).)))).............. New CC sens: 0.591, New CC ppv: 0.684, New CC F-measure: 0.634, New CC Energy: -21.85 ((((.[[[[[..))))........(((((]]]]]((((....((((....)))).))))........))))). New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -20.80 .....(((((....[[[[{{{{{.<<<<<)))))........]]]].......}}}}}.........>>>>>. New CC sens: 0.455, New CC ppv: 0.526, New CC F-measure: 0.488, New CC Energy: -20.60 ((((.[[[[[..)))).............]]]]]((((....((((....)))).)))).............. New CC sens: 0.773, New CC ppv: 1.000, New CC F-measure: 0.872, New CC Energy: -19.88 .....(((((........[[[[[.{{{{{)))))(((((((....))))).))]]]]].........}}}}}. New CC sens: 0.455, New CC ppv: 0.455, New CC F-measure: 0.455, New CC Energy: -18.84 .....(((((........[[[[[.{{{{{)))))..(((((....)))))...]]]]].........}}}}}. New CC sens: 0.455, New CC ppv: 0.500, New CC F-measure: 0.476, New CC Energy: -18.74 .....(((((....[[[[......{{{{{)))))((((....]]]].........))))........}}}}}. New CC sens: 0.636, New CC ppv: 0.778, New CC F-measure: 0.700, New CC Energy: -18.46 .....(((((....(((....)))[[[[[)))))((((....((((....)))).))))........]]]]]. New CC sens: 0.818, New CC ppv: 0.857, New CC F-measure: 0.837, New CC Energy: -18.20 .....((((((((.(((....))))))..)))))........((((....))))................... New CC sens: 0.409, New CC ppv: 0.600, New CC F-measure: 0.486, New CC Energy: -17.80 .(((([[[[[.....)))).....(((((]]]]]........((((....)))).............))))). New CC sens: 0.636, New CC ppv: 0.778, New CC F-measure: 0.700, New CC Energy: -17.72 New CC F-measure-avg: 0.666, New CC F-measure-best: 1.000, New CC best-subopt: 4, New CC num-subopt: 12 > SSTRAND_ID=SRV_1; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; GGGGCCAGCCCCAGGCCCCGAAACAAGCUUAUGGGGCA ((((((.[[[[[.)))))).............]]]]]. ((((((.[[[[[[))))))............]]]]]]. ((((((.[[[[[[))))))............]]]]]]. Energy of known structure: -28.13 Initial sens: 1.000, Initial ppv: 0.917, Initial F-measure: 0.957, Initial Energy: -28.69 New CC sens: 1.000, New CC ppv: 0.917, New CC F-measure: 0.957, New CC Energy: -28.69 ((((....))))..((((((.((.....)).)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.60 ((((....))))..((((((...........)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.99 ((((((...[[[.))))))..............]]].. New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -17.64 ((((((.......)))))).......(((.....))). New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -16.30 ((((((..[[[..)))))).............]]]... New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -15.01 New CC F-measure-avg: 0.459, New CC F-measure-best: 0.957, New CC best-subopt: 0, New CC num-subopt: 5 > SSTRAND_ID=T2_gene32; TYPE=viral ribosomal RNA frame-shifting signals; EXT_SOURCE=Giedroc et al 2000; CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGC .[[[[[.(((((((]]]]].......))))))) .(((((.[[[[[[[))))).......]]]]]]] .(((((.[[[[[[[))))).......]]]]]]] Energy of known structure: -16.32 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -16.32 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -16.32 .......(((((((.(........).))))))) New CC sens: 0.583, New CC ppv: 0.875, New CC F-measure: 0.700, New CC Energy: -9.55 .......((((((((((.....))).))))))) New CC sens: 0.583, New CC ppv: 0.700, New CC F-measure: 0.636, New CC Energy: -8.30 .(((((....[[[[)))))....]]]]...... New CC sens: 0.417, New CC ppv: 0.556, New CC F-measure: 0.476, New CC Energy: -6.48 .(((((........))))).............. New CC sens: 0.417, New CC ppv: 1.000, New CC F-measure: 0.588, New CC Energy: -6.10 New CC F-measure-avg: 0.680, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=T4_gene32; TYPE=mRNA; EXT_SOURCE=van Batenburg et al 2001; UGCCAGCUAUGAGGUAAAGUGUCAUAGC [[[[.(((((((]]]].....))))))) ((((.[[[[[[[)))).....]]]]]]] ((((.[[[[[[[)))).....]]]]]]] Energy of known structure: -13.16 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.16 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.16 .....(((((((.(.....).))))))) New CC sens: 0.636, New CC ppv: 0.875, New CC F-measure: 0.737, New CC Energy: -7.80 New CC F-measure-avg: 0.868, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 1 > SSTRAND_ID=TMV.L; TYPE=viral RNA; EXT_SOURCE=van Belkum et al 1985; AUAAUAAAUAACGGAUUGUGUCCGUAAUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAAUCGAAGGG ............[[[.((((]]].....))))[[[.((((((]]]...))))))[[[[.....(((((]]]]......).)))) ................(((((.((((...[[[[{{{{))))..<<<<.)))))..]]]]....((((}}}}....>>>>.)))) ................(((((.((((...[[[[{{{{))))..<<<<.)))))..]]]]....((((}}}}....>>>>.)))) Energy of known structure: -24.15 Initial sens: 0.160, Initial ppv: 0.160, Initial F-measure: 0.160, Initial Energy: -25.22 New CC sens: 0.160, New CC ppv: 0.160, New CC F-measure: 0.160, New CC Energy: -25.22 ..........((((((...))))))...........((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.680, New CC ppv: 0.708, New CC F-measure: 0.694, New CC Energy: -20.98 ..............(((((((.((((.......[[[[))))..{{{{...)))))))......((((]]]]....}}}}.)))) New CC sens: 0.160, New CC ppv: 0.174, New CC F-measure: 0.167, New CC Energy: -20.89 ..........((((((...))))))...........((((((......))))))((((.....[[[[.))))........]]]] New CC sens: 0.680, New CC ppv: 0.850, New CC F-measure: 0.756, New CC Energy: -20.71 ................((((..[[[[..)))).((((]]]]..[[[[(((((...)))))...{{{{))))....]]]].}}}} New CC sens: 0.320, New CC ppv: 0.320, New CC F-measure: 0.320, New CC Energy: -19.93 ................(((((.((((.......[[[[))))..{{{{.)))))..........((((]]]]....}}}}.)))) New CC sens: 0.160, New CC ppv: 0.190, New CC F-measure: 0.174, New CC Energy: -19.63 ..........((((((...))))))....((((...((((((.[[[[.)))))).))))................]]]]..... New CC sens: 0.360, New CC ppv: 0.450, New CC F-measure: 0.400, New CC Energy: -19.58 ..........((((((...))))))....(((([[[[(((((......)))))..))))....((((]]]].........)))) New CC sens: 0.480, New CC ppv: 0.522, New CC F-measure: 0.500, New CC Energy: -19.42 ................(((((........[[[[{{{{......<<<<.)))))..]]]]....((((}}}}....>>>>.)))) New CC sens: 0.160, New CC ppv: 0.190, New CC F-measure: 0.174, New CC Energy: -19.13 ..........((((((...))))))........(((((((((......)))))..........[[[[)))).........]]]] New CC sens: 0.480, New CC ppv: 0.632, New CC F-measure: 0.545, New CC Energy: -19.01 ..........((((((...))))))....(((([[[[......{{{{........))))....((((]]]]....}}}}.)))) New CC sens: 0.280, New CC ppv: 0.318, New CC F-measure: 0.298, New CC Energy: -18.62 ..........((((((...))))))....((((...((((((.[[[[.)))))).))))....((((........]]]].)))) New CC sens: 0.520, New CC ppv: 0.542, New CC F-measure: 0.531, New CC Energy: -18.38 ..........((((((...))))))....((((...((((((......)))))).))))....((((.(.........).)))) New CC sens: 0.520, New CC ppv: 0.619, New CC F-measure: 0.565, New CC Energy: -18.30 ......................((((...[[[[{{{{))))..((((........]]]]....[[[[}}}}....)))).]]]] New CC sens: 0.160, New CC ppv: 0.200, New CC F-measure: 0.178, New CC Energy: -18.12 ................(((((........)))))..((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.560, New CC ppv: 0.609, New CC F-measure: 0.583, New CC Energy: -17.57 ................(((((.((((..(((.....)))..))))...))))).((((.....[[[[.))))........]]]] New CC sens: 0.320, New CC ppv: 0.400, New CC F-measure: 0.356, New CC Energy: -17.56 ................((((........))))....((((((.[[[[.))))))((((.....{{{{.))))...]]]].}}}} New CC sens: 0.720, New CC ppv: 0.818, New CC F-measure: 0.766, New CC Energy: -17.38 ................(((((........)))))..((((((......))))))((((.....[[[[.))))........]]]] New CC sens: 0.560, New CC ppv: 0.737, New CC F-measure: 0.636, New CC Energy: -17.31 ................((((........))))....((((((......))))))((((.....[[[[.))))........]]]] New CC sens: 0.720, New CC ppv: 1.000, New CC F-measure: 0.837, New CC Energy: -17.11 ..........((((((...))))))...........((((((.[[[[.))))))((((..........))))...]]]]..... New CC sens: 0.520, New CC ppv: 0.650, New CC F-measure: 0.578, New CC Energy: -16.54 New CC F-measure-avg: 0.461, New CC F-measure-best: 0.837, New CC best-subopt: 18, New CC num-subopt: 19 > SSTRAND_ID=Tt_LSU_P3P7; TYPE=ribozyme; EXT_SOURCE=van Batenburg et al 2001; AGACCGUCAAACACAGACUAAAUGUCGGUCGGGGAAGAUGUAUUCUUCUCAUAAGAUAUAGUCGG .(((((.((....[.[[[[[..)).))))).(((((((.....)))))))........]]]]]]. .(((((.((......[[[[[..)).))))).(((((((.....)))))))........]]]]].. .(((((.((......[[[[[..)).))))).(((((((.....)))))))........]]]]].. Energy of known structure: -16.60 Initial sens: 0.950, Initial ppv: 1.000, Initial F-measure: 0.974, Initial Energy: -17.66 New CC sens: 0.950, New CC ppv: 1.000, New CC F-measure: 0.974, New CC Energy: -17.66 .(((((.((.............)).))))).(((((((.....)))))))............... New CC sens: 0.700, New CC ppv: 1.000, New CC F-measure: 0.824, New CC Energy: -17.11 ...............(((((..((((.....(((((((.....)))))))....))))))))).. New CC sens: 0.600, New CC ppv: 0.750, New CC F-measure: 0.667, New CC Energy: -17.07 .(((.(((.......)))...(((((.....(((((((.....)))))))....))))).))).. New CC sens: 0.350, New CC ppv: 0.389, New CC F-measure: 0.368, New CC Energy: -16.67 ...(((.........((((..[[[[[)))).(((((((.....)))))))....]]]]]...))) New CC sens: 0.350, New CC ppv: 0.368, New CC F-measure: 0.359, New CC Energy: -16.42 .(((...........((((..[[[[[)))).(((((((.....)))))))....]]]]].))).. New CC sens: 0.350, New CC ppv: 0.368, New CC F-measure: 0.359, New CC Energy: -16.12 .(((((.........[[[[[.....))))).(((((((.....)))))))........]]]]].. New CC sens: 0.850, New CC ppv: 1.000, New CC F-measure: 0.919, New CC Energy: -15.92 .(((((...................))))).(((((((.....)))))))............... New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -15.10 .(((...........((((.......)))).(((((((.....)))))))..........))).. New CC sens: 0.350, New CC ppv: 0.500, New CC F-measure: 0.412, New CC Energy: -14.50 .(((...........(((.....))).....(((((((.....)))))))..........))).. New CC sens: 0.350, New CC ppv: 0.538, New CC F-measure: 0.424, New CC Energy: -14.40 .....(((.......)))...(((((.....(((((((.....)))))))....)))))...... New CC sens: 0.350, New CC ppv: 0.467, New CC F-measure: 0.400, New CC Energy: -14.07 ...(((.........((((.......)))).(((((((.....)))))))............))) New CC sens: 0.350, New CC ppv: 0.500, New CC F-measure: 0.412, New CC Energy: -13.90 ...(((.........(((.....))).....(((((((.....)))))))............))) New CC sens: 0.350, New CC ppv: 0.538, New CC F-measure: 0.424, New CC Energy: -13.80 ...............((((..[[[[[)))).(((((((.....)))))))....]]]]]...... New CC sens: 0.350, New CC ppv: 0.438, New CC F-measure: 0.389, New CC Energy: -13.72 ...(((..........((((..((((.....(((((((.....)))))))....))))))))))) New CC sens: 0.550, New CC ppv: 0.611, New CC F-measure: 0.579, New CC Energy: -13.52 New CC F-measure-avg: 0.551, New CC F-measure-best: 0.974, New CC best-subopt: 0, New CC num-subopt: 14 > SSTRAND_ID=TYMV; TYPE=viral RNA; EXT_SOURCE=Deiman et al 1997; UUAGCUCGCCAGUUAGCGAGGUCUGUCCCCACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUCUUCCGAGGGUCAUCGGAACCA ....(((((......)))))(((((((.......)))))))...((((.......))))[[[...((((((]]]...))))))... (((((([[[[)))))).((((((((((.......))))))......]]]].....[[[...))))((((((]]]...))))))... (((((([[[[)))))).((((((((((.......))))))......]]]].....[[[...))))((((((]]]...))))))... Energy of known structure: -31.08 Initial sens: 0.480, Initial ppv: 0.414, Initial F-measure: 0.444, Initial Energy: -28.18 New CC sens: 0.480, New CC ppv: 0.414, New CC F-measure: 0.444, New CC Energy: -28.18 ....(((((......)))))(((((((.......)))))))....(((.((....[[[)))))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.692, New CC F-measure: 0.706, New CC Energy: -27.73 ....(((((......)))))(((((((.......)))))))....(((.((.......)))))..((((((......))))))... New CC sens: 0.720, New CC ppv: 0.783, New CC F-measure: 0.750, New CC Energy: -27.50 ....(((((......)))))(((((((.......)))))))....(((((.......)))))...((((((......))))))... New CC sens: 0.720, New CC ppv: 0.783, New CC F-measure: 0.750, New CC Energy: -27.30 ....(((((......)))))((((((([[[....)))))))....(((.((.......)))))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.692, New CC F-measure: 0.706, New CC Energy: -27.20 ....(((((......)))))((((((([[[....)))))))....(((((.......)))))...((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.692, New CC F-measure: 0.706, New CC Energy: -26.90 ....(((((......)))))(((((((.......)))))))...((((.......)))).(((((....)))))............ New CC sens: 0.640, New CC ppv: 0.762, New CC F-measure: 0.696, New CC Energy: -26.50 ....(((((......)))))(((((((.......)))))))...((((.......))))......((((((......))))))... New CC sens: 0.880, New CC ppv: 1.000, New CC F-measure: 0.936, New CC Energy: -26.20 ....(((((......)))))((((((([[[....)))))))...((((.......))))......((((((]]]...))))))... New CC sens: 0.880, New CC ppv: 0.880, New CC F-measure: 0.880, New CC Energy: -25.60 (((((([[[[))))))....((((((({{{....))))))).....]]]]...............((((((}}}...))))))... New CC sens: 0.520, New CC ppv: 0.500, New CC F-measure: 0.510, New CC Energy: -25.27 ....(((((......)))))(((((((.......)))))))..............(((.......[[[[[[)))...]]]]]]... New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -25.25 ....(((((......)))))(((((((.......)))))))....(((.......[[[..)))..((((((]]]...))))))... New CC sens: 0.720, New CC ppv: 0.750, New CC F-measure: 0.735, New CC Energy: -24.82 ......((((......(((.(((((((.......)))))))..))))))).....(((.......[[[[[[)))...]]]]]]... New CC sens: 0.520, New CC ppv: 0.565, New CC F-measure: 0.542, New CC Energy: -23.85 ((((((....))))))....(((((((.......)))))))....(((.((....[[[)))))..((((((]]]...))))))... New CC sens: 0.520, New CC ppv: 0.481, New CC F-measure: 0.500, New CC Energy: -23.62 ....(((((......)))))(((((((.......)))))))....(((.((....[[[)))))........]]]............ New CC sens: 0.480, New CC ppv: 0.600, New CC F-measure: 0.533, New CC Energy: -23.62 ....(((((......))))).......(((...............(((.((.......)))))..[[[[[[)))...]]]]]]... New CC sens: 0.440, New CC ppv: 0.579, New CC F-measure: 0.500, New CC Energy: -23.45 ....(((((......)))))......(((................(((.((.......)))))..[[[[[[)))...]]]]]]... New CC sens: 0.440, New CC ppv: 0.579, New CC F-measure: 0.500, New CC Energy: -23.43 ((((((....))))))....(((((((.......)))))))....(((.((.......)))))..((((((......))))))... New CC sens: 0.520, New CC ppv: 0.542, New CC F-measure: 0.531, New CC Energy: -23.40 ((((((....)))))).((((((((((.......))))))....((((.......))))..))))((((((......))))))... New CC sens: 0.640, New CC ppv: 0.615, New CC F-measure: 0.627, New CC Energy: -23.40 ....(((((......)))))((((((([[[....)))))))....]]].......(((.......[[[[[[)))...]]]]]]... New CC sens: 0.720, New CC ppv: 0.750, New CC F-measure: 0.735, New CC Energy: -23.39 New CC F-measure-avg: 0.653, New CC F-measure-best: 0.936, New CC best-subopt: 7, New CC num-subopt: 19 > AKV-MuLV GGGUCAGGAGCCCCCCCCUGAACCCAGGAUAACCCUCACUGUCGGGGGGC ((((((((.[[[[[[[)))).))))..................]]]]]]] ...(((((.[[[[[[[)))))...(((((......)).)))..]]]]]]] ...(((((.[[[[[[[)))))...(((((......)).)))..]]]]]]] Energy of known structure: -29.80 Initial sens: 0.733, Initial ppv: 0.647, Initial F-measure: 0.688, Initial Energy: -25.23 New CC sens: 0.733, New CC ppv: 0.647, New CC F-measure: 0.688, New CC Energy: -25.23 ...(((((.[[[[[[[)))))....(((.....))).......]]]]]]] New CC sens: 0.733, New CC ppv: 0.733, New CC F-measure: 0.733, New CC Energy: -24.53 ((((.....[[[[[[[((((....))))...))))........]]]]]]] New CC sens: 0.467, New CC ppv: 0.467, New CC F-measure: 0.467, New CC Energy: -23.94 ((((.....))))((((((((....(((.....))).....)))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.37 ((((((((........)))).)))).......(((((......))))).. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -20.60 ((((.....))))((((((((...(((((......)).))))))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.50 ((((((((........)))).)))).......(((((.......))))). New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -19.10 ((((.....[[[[[[[.....))))(((.....))).......]]]]]]] New CC sens: 0.733, New CC ppv: 0.786, New CC F-measure: 0.759, New CC Energy: -18.25 ((((.........[[[[[[[[..........))))......]]]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.14 .........(((((((((((....))))...............))))))) New CC sens: 0.467, New CC ppv: 0.636, New CC F-measure: 0.538, New CC Energy: -18.12 ((((.........[[[[[[[[))))(((.....))).....]]]]]]]]. New CC sens: 0.267, New CC ppv: 0.267, New CC F-measure: 0.267, New CC Energy: -18.09 ((((.....))))...((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.20 ((((((((........)))).)))).......((((.......))))... New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -17.20 New CC F-measure-avg: 0.399, New CC F-measure-best: 0.759, New CC best-subopt: 7, New CC num-subopt: 12 > BaEV GGGCUCUGGAGCCCCCCCCGAGCCCCGGCUAACUCUAUCUGUAGGGGGGC ((((((.((.[[[[[[[))))))))..................]]]]]]] ((((((......[[[[[[.))))))..................]]]]]]. ((((((......[[[[[[.))))))..................]]]]]]. Energy of known structure: -30.40 Initial sens: 0.400, Initial ppv: 0.500, Initial F-measure: 0.444, Initial Energy: -23.86 New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -23.86 ((((((....[[[[[[[..))))))..................]]]]]]] New CC sens: 0.867, New CC ppv: 1.000, New CC F-measure: 0.929, New CC Energy: -23.63 ((((((.......[[[[[[))))))..................]]]]]]. New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -22.37 ((((((...[[[[{{{{{{)))))).]]]].............}}}}}}. New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -22.13 (((((([[[[[..{{{{{{)))))).......]]]]]......}}}}}}. New CC sens: 0.400, New CC ppv: 0.353, New CC F-measure: 0.375, New CC Energy: -21.74 (((((([[[[[.{{{{{{.)))))).......]]]]]......}}}}}}. New CC sens: 0.400, New CC ppv: 0.353, New CC F-measure: 0.375, New CC Energy: -21.64 (((((....)))))(((((.(((....))).((.......)).))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.80 (((((([[[[[{{{{{...)))))).......]]]]]......}}}}}.. New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -19.70 ((((((...[[[[.{{{{{)))))).]]]]..............}}}}}. New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -19.20 (((...[[[[[..{{{{{{.[[[))).]]]..]]]]]......}}}}}}. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.05 (((((([[[[[...{{{{{)))))).......]]]]].......}}}}}. New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -18.80 ((((((........[[[[[))))))...................]]]]]. New CC sens: 0.400, New CC ppv: 0.545, New CC F-measure: 0.462, New CC Energy: -18.61 (((((....)))))(((((.(((....))).............))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.44 .....((((.[[[[[[[.......))))...............]]]]]]] New CC sens: 0.467, New CC ppv: 0.636, New CC F-measure: 0.538, New CC Energy: -18.41 ((((((.....[[[[[...))))))..................]]]]].. New CC sens: 0.400, New CC ppv: 0.545, New CC F-measure: 0.462, New CC Energy: -18.16 ......(((((..[[[[[[.(((....)))..)))))......]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.69 ((((((.((.......)).)))))).......(((((....))))).... New CC sens: 0.400, New CC ppv: 0.462, New CC F-measure: 0.429, New CC Energy: -17.60 ((((((.((......))..))))))..(((..(((((....))))).))) New CC sens: 0.400, New CC ppv: 0.375, New CC F-measure: 0.387, New CC Energy: -17.55 .((((....))))((((((.(((....))).............)))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.54 (((((....)))))(((((.(((....)))..............))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.47 New CC F-measure-avg: 0.320, New CC F-measure-best: 0.929, New CC best-subopt: 1, New CC num-subopt: 19 > BLV GGGGGGACUUAGCGCCCCCCAAACCGU ((((((.....[[[))))))....]]] ((((((........))))))....... ((((((........))))))....... Energy of known structure: -11.44 Initial sens: 0.667, Initial ppv: 1.000, Initial F-measure: 0.800, Initial Energy: -13.90 New CC sens: 0.667, New CC ppv: 1.000, New CC F-measure: 0.800, New CC Energy: -13.90 ((((((.....[[[))))))....]]] New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -11.44 .(((((.....[[[.)))))....]]] New CC sens: 0.333, New CC ppv: 0.375, New CC F-measure: 0.353, New CC Energy: -11.44 .(((((.........)))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.00 New CC F-measure-avg: 0.538, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 3 > Bp_PK2 CCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCAACUUCCCAGGGGGCAACCCCGAACCGCAGCAGCGACAUUCACAAGGAAU .((((((..(((....[[[[[[..))).((((((((((....)))))).((((....))))...)))).)))))).......]]]]]].. .((((((.(((((((......)))))))((((((((((....)))))).((((....))))...)))).))))))............... .((((((.(((((((......)))))))((((((((((....)))))).((((....))))...)))).))))))............... Energy of known structure: -41.52 Initial sens: 0.793, Initial ppv: 0.852, Initial F-measure: 0.821, Initial Energy: -49.20 New CC sens: 0.793, New CC ppv: 0.852, New CC F-measure: 0.821, New CC Energy: -49.20 .((((((.(((((((......)))))))((((((((((....))))))..((((...))))...)))).))))))............... New CC sens: 0.655, New CC ppv: 0.704, New CC F-measure: 0.679, New CC Energy: -44.20 .((((((.(((((((......)))))))....((((((....)))))).((((....))))........))))))............... New CC sens: 0.655, New CC ppv: 0.826, New CC F-measure: 0.731, New CC Energy: -43.60 ..(((((.(((((((......)))))))....((((((....)))))).((((....)))).....)))))................... New CC sens: 0.448, New CC ppv: 0.591, New CC F-measure: 0.510, New CC Energy: -41.70 .((((((.........[[[[[[......((((((((((....)))))).((((....))))...)))).)))))).......]]]]]].. New CC sens: 0.897, New CC ppv: 1.000, New CC F-measure: 0.945, New CC Energy: -41.55 ...((((.(((((((......)))))))))))((((((....)))))).((((....))))....(((....)))............... New CC sens: 0.448, New CC ppv: 0.542, New CC F-measure: 0.491, New CC Energy: -40.30 New CC F-measure-avg: 0.696, New CC F-measure-best: 0.945, New CC best-subopt: 4, New CC num-subopt: 5 > BVDV_IRES GGGUAGCAACAGUGGUGAACAGCCUGAUAGGGUGCUGCAGAGGCCCACUGUAUUGCUACUAAAAAUCUCUGCU .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).....]]]]]]]. Energy of known structure: -24.51 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -24.51 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -24.51 .((((((((((((((.(..((((((.....)).))))......))))))))..)))))))............. New CC sens: 0.560, New CC ppv: 0.667, New CC F-measure: 0.609, New CC Energy: -24.19 .((((((((((((((......((((....))))(((.....))))))))))..)))))))............. New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -23.60 .((((((((((((((.(..((((((.....)).))))......)))))))..))))))))............. New CC sens: 0.520, New CC ppv: 0.619, New CC F-measure: 0.565, New CC Energy: -23.39 .((((((((((((((.(....((((....))))..........))))))))..)))))))............. New CC sens: 0.720, New CC ppv: 0.947, New CC F-measure: 0.818, New CC Energy: -22.24 .((((((((((((((......((((...............)))))))))))..)))))))............. New CC sens: 0.560, New CC ppv: 0.778, New CC F-measure: 0.651, New CC Energy: -22.15 .((((((((((((((....((((..........)))).......)))))))..)))))))............. New CC sens: 0.560, New CC ppv: 0.778, New CC F-measure: 0.651, New CC Energy: -21.74 New CC F-measure-avg: 0.725, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > BYDV-NY-RPV GGCGGCGGCGUCCGCCGUAACAAACGC (((((..[[[[))))).......]]]] (((((..[[[[))))).......]]]] (((((..[[[[))))).......]]]] Energy of known structure: -14.83 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -14.83 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -14.83 .(((((((...)))))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.20 (((((......)))))........... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -9.20 .((((((((....)))))......))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.90 ....(((((....)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.60 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: -29.80 Initial sens: 0.733, Initial ppv: 0.733, Initial F-measure: 0.733, Initial Energy: -24.53 New CC sens: 0.733, New CC ppv: 0.733, New CC F-measure: 0.733, New CC Energy: -24.53 ((((.....[[[[[[[((((....))))...))))........]]]]]]] New CC sens: 0.467, New CC ppv: 0.467, New CC F-measure: 0.467, New CC Energy: -23.94 ((((.....))))((((((((....(((.....))).....)))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.37 ((((((((........)))).)))).......(((((......))))).. New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -20.60 ((((((((........)))).)))).......(((((.......))))). New CC sens: 0.533, New CC ppv: 0.615, New CC F-measure: 0.571, New CC Energy: -19.10 ((((.....[[[[[[[.....))))(((.....))).......]]]]]]] New CC sens: 0.733, New CC ppv: 0.786, New CC F-measure: 0.759, New CC Energy: -18.25 ((((.........[[[[[[[[..........))))......]]]]]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.14 .........(((((((((((....))))...............))))))) New CC sens: 0.467, New CC ppv: 0.636, New CC F-measure: 0.538, New CC Energy: -18.12 ((((.........[[[[[[[[))))(((.....))).....]]]]]]]]. New CC sens: 0.267, New CC ppv: 0.267, New CC F-measure: 0.267, New CC Energy: -18.09 ((((.....))))...((((....))))....(((((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -17.20 ((((((((........)))).)))).......((((.......))))... New CC sens: 0.533, New CC ppv: 0.667, New CC F-measure: 0.593, New CC Energy: -17.20 New CC F-measure-avg: 0.409, New CC F-measure-best: 0.759, New CC best-subopt: 5, New CC num-subopt: 10 > CoxB3 ACCCUACUGUGCUAACCGAACCAGAUAACGGUACAGUAGGGGUAAAUUCUCCGCAUUCGGUGCGGAAAAAAAA .((((((((((((.[[[[[[.........)))))))))))).....((.(((((.]]]]]]))))).)).... .((((((((((((................))))))))))))........(((((((...)))))))....... .((((((((((((................))))))))))))........(((((((...)))))))....... Energy of known structure: -28.36 Initial sens: 0.680, Initial ppv: 0.895, Initial F-measure: 0.773, Initial Energy: -28.48 New CC sens: 0.680, New CC ppv: 0.895, New CC F-measure: 0.773, New CC Energy: -28.48 .((((((((((((.[[[[[[.........))))))))))))..............]]]]]]............ New CC sens: 0.720, New CC ppv: 1.000, New CC F-measure: 0.837, New CC Energy: -27.25 (((((((((((((................)))))))).)))))......(((((((...)))))))....... New CC sens: 0.520, New CC ppv: 0.650, New CC F-measure: 0.578, New CC Energy: -24.98 New CC F-measure-avg: 0.729, New CC F-measure-best: 0.837, New CC best-subopt: 1, New CC num-subopt: 2 > CSFV_IRES GACUAGCCGUAGUGGCGAACGACCUGAUAGGGUGCUGCAGAGGCCCACUAUUAGGCUAGUAUAAAAAUCUCUGCUG .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. .((((((((((((((......((((....))))...[[[[[[[.)))))))..))))))).......]]]]]]].. Energy of known structure: -24.19 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -24.19 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -24.19 .((((((((((((((......((((....))))(((.....))))))))))..)))))))................ New CC sens: 0.720, New CC ppv: 0.857, New CC F-measure: 0.783, New CC Energy: -23.30 .(((((((.[[[[[[.........((((((((.(((.....))))).)))))))))))))..........]]]]]] New CC sens: 0.280, New CC ppv: 0.292, New CC F-measure: 0.286, New CC Energy: -21.75 .((((((((((((((......((((....))))...........)))))))..)))))))................ New CC sens: 0.720, New CC ppv: 1.000, New CC F-measure: 0.837, New CC Energy: -20.63 .....((((...))))..((..((((((((((.(((.....))))).))))))))...))................ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.50 .....(((.....)))......((((((((((.(((.....))))).))))))))..................... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.20 .....((((...))))......((((((((((.(((.....))))).)))))))).(((((..........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.79 .....(((.....)))......((((((((......[[[[[[[....))))))))............]]]]]]].. New CC sens: 0.280, New CC ppv: 0.389, New CC F-measure: 0.326, New CC Energy: -19.61 .(((((((....[[[[[.......((((((((.(((.....))))).)))))))))))))...........]]]]] New CC sens: 0.280, New CC ppv: 0.304, New CC F-measure: 0.292, New CC Energy: -19.24 ...(((((((....))).((..((((((((((.(((.....))))).))))))))...))............)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -18.90 New CC F-measure-avg: 0.352, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 9 > EIAV GGGGCUCAAGGGAGGCCCCAGAAACAAACUUUCCC ((((((...[[[[))))))............]]]] (((((((....)).)))))................ (((((((....)).)))))................ Energy of known structure: -16.73 Initial sens: 0.500, Initial ppv: 0.714, Initial F-measure: 0.588, Initial Energy: -11.50 New CC sens: 0.500, New CC ppv: 0.714, New CC F-measure: 0.588, New CC Energy: -11.50 ((((((.......))))))................ New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -11.40 (((((((....)).))))).((((.....)))).. New CC sens: 0.500, New CC ppv: 0.455, New CC F-measure: 0.476, New CC Energy: -11.10 ((((((.......)))))).((((.....)))).. New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -11.00 (((......[[[[[[)))...........]]]]]] New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -10.16 ((((((.[[[[..)))))).........]]]]... New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -9.82 (((.(((....))).)))................. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.80 (((.(((....))).)))..((((.....)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.60 New CC F-measure-avg: 0.429, New CC F-measure-best: 0.750, New CC best-subopt: 1, New CC num-subopt: 7 > FeLV GGGCCAGGACCCCCCCCCCUGAGCCCAGGAUAACCUUAAGAAUAGGGGGG ((((((((...[[[[[[)))).))))..................]]]]]] ((((((((..[[[[[[.)))).))))(((....)))........]]]]]] ((((((((..[[[[[[.)))).))))(((....)))........]]]]]] Energy of known structure: -27.06 Initial sens: 0.571, Initial ppv: 0.471, Initial F-measure: 0.516, Initial Energy: -26.50 New CC sens: 0.571, New CC ppv: 0.471, New CC F-measure: 0.516, New CC Energy: -26.50 ((((((((...[[[[[[)))).))))(((....)))........]]]]]] New CC sens: 1.000, New CC ppv: 0.824, New CC F-measure: 0.903, New CC Energy: -25.86 ((((((((.[[[[[[..)))).))))(((....)))........]]]]]] New CC sens: 0.571, New CC ppv: 0.471, New CC F-measure: 0.516, New CC Energy: -24.00 ((((((((.[[[[[...)))).))))(((....)))........]]]]]. New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -22.00 ((((.........[[[[[[[[.))))(((....)))......]]]]]]]] New CC sens: 0.286, New CC ppv: 0.267, New CC F-measure: 0.276, New CC Energy: -21.79 (((......))).((((((((..(..(((....)))...)..)))))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.90 ((((((((.........)))).)))).......(((((....)))))... New CC sens: 0.571, New CC ppv: 0.615, New CC F-measure: 0.593, New CC Energy: -17.60 ((((((((.[[[[....)))).))))(((....)))........]]]].. New CC sens: 0.571, New CC ppv: 0.533, New CC F-measure: 0.552, New CC Energy: -17.40 (((........)))(((((((..(..(((....)))...)..))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -16.50 ((((.....[[[[[[.......))))(((....)))........]]]]]] New CC sens: 0.286, New CC ppv: 0.308, New CC F-measure: 0.296, New CC Energy: -16.07 New CC F-measure-avg: 0.419, New CC F-measure-best: 0.903, New CC best-subopt: 1, New CC num-subopt: 9 > FIV GGGGCGAGCUGCAGCCCCAGUGAAUCAAAUGCAGC [[[[[..((((((]]]]]...........)))))) (((((..[[[[[[)))))...........]]]]]] (((((..[[[[[[)))))...........]]]]]] Energy of known structure: -20.91 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -20.91 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -20.91 (((....[[[[[[.)))............]]]]]] New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -14.53 .(((...[[[[[[..)))...........]]]]]] New CC sens: 0.545, New CC ppv: 0.667, New CC F-measure: 0.600, New CC Energy: -12.60 (((((........)))))................. New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -11.60 New CC F-measure-avg: 0.706, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 3 > HCV_229E CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAACAGUUAUGGACCACGAGCAGUCCAUG ((((((((((((...[[[[[)))))))))))).......(((((((..]]]]].))))))) ((((((((((((...[[[[[))))))))))))................]]]]]........ ((((((((((((...[[[[[))))))))))))................]]]]]........ Energy of known structure: -28.72 Initial sens: 0.708, Initial ppv: 1.000, Initial F-measure: 0.829, Initial Energy: -29.65 New CC sens: 0.708, New CC ppv: 1.000, New CC F-measure: 0.829, New CC Energy: -29.65 ((((((((((((...[[[[[)))))))))))).......(((((((..]]]]].))))))) New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -28.72 ((((((((((((........)))))))))))).......(((((((........))))))) New CC sens: 0.792, New CC ppv: 1.000, New CC F-measure: 0.884, New CC Energy: -28.50 New CC F-measure-avg: 0.904, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 2 > HCV_Ires CCUCCCGGGAGAACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAG (((((((((......(((......)))((.[[[[[[.))))))))))).]]]]]]. (((((((((.(.(((((((....)))).......))).))))))))))........ (((((((((.(.(((((((....)))).......))).))))))))))........ Energy of known structure: -19.98 Initial sens: 0.600, Initial ppv: 0.706, Initial F-measure: 0.649, Initial Energy: -24.29 New CC sens: 0.600, New CC ppv: 0.706, New CC F-measure: 0.649, New CC Energy: -24.29 (((((((((.......(((...)))(..((....))..))))))))))........ New CC sens: 0.450, New CC ppv: 0.600, New CC F-measure: 0.514, New CC Energy: -21.80 ........((((.((.((((...(((..((....))..))))))))).)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -20.35 (((((((((......((((....))))............)))))))))........ New CC sens: 0.600, New CC ppv: 0.923, New CC F-measure: 0.727, New CC Energy: -20.27 (((((((((......((((....))))..[[[[[[[...))))))))).]]]]]]] New CC sens: 0.900, New CC ppv: 0.900, New CC F-measure: 0.900, New CC Energy: -20.25 (((((((((.(.(((.(((...))).........))).))))))))))........ New CC sens: 0.450, New CC ppv: 0.562, New CC F-measure: 0.500, New CC Energy: -19.75 ........((((....((((...(((..((....))..)))))))...)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -19.59 New CC F-measure-avg: 0.470, New CC F-measure-best: 0.900, New CC best-subopt: 4, New CC num-subopt: 6 > HDV-It_g UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCCA .(((((((..[[[[[[[(((.[[.....))))))))))]]....(((((((((((((...))))))))).)))).....]]]]]]].. ((.(((((.((((.(((((......))))).))))))))).)).((((((((((((.....)))))))).)))).............. ((.(((((.((((.(((((......))))).))))))))).)).((((((((((((.....)))))))).)))).............. Energy of known structure: -47.24 Initial sens: 0.375, Initial ppv: 0.429, Initial F-measure: 0.400, Initial Energy: -46.15 New CC sens: 0.375, New CC ppv: 0.429, New CC F-measure: 0.400, New CC Energy: -46.15 ..........(((((((((((....((((....)))).))))..((((((((((((.....)))))))).)))).....))))))).. New CC sens: 0.594, New CC ppv: 0.704, New CC F-measure: 0.644, New CC Energy: -44.45 ((((((((..[[[[[[[(((........))))))))))).((..((((((((((((.....)))))))).))))))...]]]]]]].. New CC sens: 0.906, New CC ppv: 0.906, New CC F-measure: 0.906, New CC Energy: -44.15 ((((((((..[[[[[[[(((........))))))))))).....((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.906, New CC ppv: 0.967, New CC F-measure: 0.935, New CC Energy: -43.65 ((.(((((.((((.(((((......))))).))))))))).)).....(((((((((...)))))))))................... New CC sens: 0.281, New CC ppv: 0.360, New CC F-measure: 0.316, New CC Energy: -42.55 ..((((((..[[[[[[[[[[[....)))))).......]]]]..((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.594, New CC ppv: 0.655, New CC F-measure: 0.623, New CC Energy: -42.37 ((((((((......(((((......))))).)))))))).((..((((((((((((.....)))))))).))))))............ New CC sens: 0.594, New CC ppv: 0.704, New CC F-measure: 0.644, New CC Energy: -41.24 ((((((((......(((((......))))).)))))))).....((((((((((((.....)))))))).)))).............. New CC sens: 0.594, New CC ppv: 0.760, New CC F-measure: 0.667, New CC Energy: -40.74 ..........(((((((((((....((((....)))).))))......(((((((((...)))))))))..........))))))).. New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -40.35 ..((((((......(((((......))))).))))))((((...((((((((((((.....)))))))).))))..........)))) New CC sens: 0.562, New CC ppv: 0.667, New CC F-measure: 0.610, New CC Energy: -40.31 ...(((((..(((.(((((......))))).))).)))))....((((((((((((.....)))))))).)))).............. New CC sens: 0.375, New CC ppv: 0.480, New CC F-measure: 0.421, New CC Energy: -39.95 ((((((((..[[[[[[[(((........)))))))))))(....)...(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.812, New CC ppv: 0.929, New CC F-measure: 0.867, New CC Energy: -39.75 ...(((((..(((.(((((......))))).))).)))))((..((((((((((((.....)))))))).))))))............ New CC sens: 0.375, New CC ppv: 0.444, New CC F-measure: 0.407, New CC Energy: -39.15 ...(((((..[[[[[[[(((........)))....)))))....((((((((((((.....)))))))).)))).....]]]]]]].. New CC sens: 0.688, New CC ppv: 0.815, New CC F-measure: 0.746, New CC Energy: -39.03 ..........(((((((......((((((..(((.....)))......(((((((((...)))))))))...)))))).))))))).. New CC sens: 0.500, New CC ppv: 0.640, New CC F-measure: 0.561, New CC Energy: -38.94 ((((((((..[[[[[[[......[[[[[...))))))))(....)...(((((((((...)))))))))....]]]]].]]]]]]].. New CC sens: 0.719, New CC ppv: 0.767, New CC F-measure: 0.742, New CC Energy: -38.89 ..........(((((((((((..[[[[[(((....)))))))......(((((((((...)))))))))....]]]]].))))))).. New CC sens: 0.500, New CC ppv: 0.571, New CC F-measure: 0.533, New CC Energy: -38.74 ..........(((((((((......))...(((((....(....)...(((((((((...)))))))))...)))))..))))))).. New CC sens: 0.500, New CC ppv: 0.667, New CC F-measure: 0.571, New CC Energy: -38.50 ..........(((((((......((((((..(((.....)))..)...(((((((((...)))))))))....))))).))))))).. New CC sens: 0.500, New CC ppv: 0.640, New CC F-measure: 0.561, New CC Energy: -38.44 ..((((((..[[[[[[[[[[[....)))))).......]]]]......(((((((((...)))))))))..........]]]]]]].. New CC sens: 0.500, New CC ppv: 0.615, New CC F-measure: 0.552, New CC Energy: -38.27 New CC F-measure-avg: 0.614, New CC F-measure-best: 0.935, New CC best-subopt: 3, New CC num-subopt: 19 > HIV-1-RT-1-1 ucaagAAUUCCGUUUUCAGUCGGGAAAAACUGAACAa .......[[[[[..((((((]]]]]...))))))... .......(((((..[[[[[[)))))...]]]]]]... .......(((((..[[[[[[)))))...]]]]]]... Energy of known structure: -5.31 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -5.31 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -5.31 .......(((((........)))))............ New CC sens: 0.455, New CC ppv: 1.000, New CC F-measure: 0.625, New CC Energy: -5.00 (((....(((((........))))).....))).... New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -4.97 ..............((((((........))))))... New CC sens: 0.545, New CC ppv: 1.000, New CC F-measure: 0.706, New CC Energy: -4.40 ....(((.......)))..((((......)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.80 .......((((...[[[[[[..))))..]]]]]]... New CC sens: 0.545, New CC ppv: 0.600, New CC F-measure: 0.571, New CC Energy: -3.53 .......(((..(((((......)))))...)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.85 (((....((((...........))))....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.78 .......((((...........))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.19 .......(((.(((((.........))))).)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.90 ............(((((......)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.60 ....((([[[[[..)))...]]]]]............ New CC sens: 0.455, New CC ppv: 0.625, New CC F-measure: 0.526, New CC Energy: -1.49 .......(((..(((((.....)))))....)))... 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: -1.30 New CC F-measure-avg: 0.282, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 13 > HIV-1-RT-1-3a gAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCaucu .......(((((..[[[[..)))))....]]]].... .......(((((..[[[[..)))))....]]]].... .......(((((..[[[[..)))))....]]]].... Energy of known structure: -9.79 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -9.79 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -9.79 .......((((...[[[[....))))...]]]].... New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -8.20 .....((((..[[.[[[[...))))....]]]].]]. New CC sens: 0.444, New CC ppv: 0.400, New CC F-measure: 0.421, New CC Energy: -7.61 .....(((...[[.[[[[...))).....]]]].]]. New CC sens: 0.444, New CC ppv: 0.444, New CC F-measure: 0.444, New CC Energy: -7.57 ...........((.((((...........)))).)). New CC sens: 0.444, New CC ppv: 0.667, New CC F-measure: 0.533, New CC Energy: -6.64 .....((((.....[[[[...))))....]]]].... New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -6.12 .....(((......[[[[...))).....]]]].... New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -6.08 ..............((((...........)))).... New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -5.89 (((....))).((.((((...........)))).)). New CC sens: 0.444, New CC ppv: 0.444, New CC F-measure: 0.444, New CC Energy: -5.34 .......(((([[.[[[[....))))...]]]].]]. New CC sens: 0.444, New CC ppv: 0.400, New CC F-measure: 0.421, New CC Energy: -5.05 (((....)))....((((...........)))).... New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -4.69 .......(((((........)))))............ New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -4.40 ....................(((.....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.30 (((....)))..........(((.....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.10 New CC F-measure-avg: 0.467, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 13 > HIV-1-RT-1-6 gAAGAAGAUUACCCAAGCGCAGGGGAGAAGCGCaucu ...........[[[..((((.]]].....)))).... ...........(((..[[[[.))).....]]]].... ...........(((..[[[[.))).....]]]].... Energy of known structure: -15.07 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -15.07 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -15.07 .....((((..(((..[[[[.))).....]]]])))) New CC sens: 1.000, New CC ppv: 0.636, New CC F-measure: 0.778, New CC Energy: -14.17 ..(((......(((..[[[[.))).....]]]].))) New CC sens: 1.000, New CC ppv: 0.700, New CC F-measure: 0.824, New CC Energy: -13.77 ...........(((..[[[[..)))....]]]].... New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -11.23 .....((((..(((..[[[[..)))....]]]])))) New CC sens: 0.571, New CC ppv: 0.364, New CC F-measure: 0.444, New CC Energy: -10.33 ..(((......(((..[[[[..)))....]]]].))) New CC sens: 0.571, New CC ppv: 0.400, New CC F-measure: 0.471, New CC Energy: -9.93 ...........(((..[[[[.))).(((.]]]].))) New CC sens: 1.000, New CC ppv: 0.700, New CC F-measure: 0.824, New CC Energy: -7.55 ...........(((..[[[[..)))(((.]]]].))) New CC sens: 0.571, New CC ppv: 0.400, New CC F-measure: 0.471, New CC Energy: -6.25 ................((((.........)))).... New CC sens: 0.571, New CC ppv: 1.000, New CC F-measure: 0.727, New CC Energy: -6.20 .....((((.......((((.........)))))))) New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -4.64 ...........(((.......)))............. New CC sens: 0.429, New CC ppv: 1.000, New CC F-measure: 0.600, New CC Energy: -4.00 ...........(((........)))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.00 ...........(((.......))).(((......))) New CC sens: 0.429, New CC ppv: 0.500, New CC F-measure: 0.462, New CC Energy: -2.90 .....((((..(((.......))).........)))) New CC sens: 0.429, New CC ppv: 0.429, New CC F-measure: 0.429, New CC Energy: -2.40 ..(((...........((((.........)))).))) New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -2.21 New CC F-measure-avg: 0.580, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 14 > HIV-1-RT-1-7 agGAAUCGACCCAAGCCAAAGGGGAUAAUGCGGCauc .........[[[..(((...]]]........)))... .........(((..[[[...)))........]]]... .........(((..[[[...)))........]]]... Energy of known structure: -7.33 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -7.33 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -7.33 .........(((..[[[....))).......]]]... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -7.25 .((.......))..(((...(.(.....).))))... New CC sens: 0.500, New CC ppv: 0.429, New CC F-measure: 0.462, New CC Energy: -4.75 .........(((........))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -4.30 .((.......))..(((..............)))... New CC sens: 0.500, New CC ppv: 0.600, New CC F-measure: 0.545, New CC Energy: -4.03 ....(((..(((..[[[...)))))).....]]]... New CC sens: 1.000, New CC ppv: 0.667, New CC F-measure: 0.800, New CC Energy: -3.77 ....(((..(((........))))))........... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -3.70 .........(((..[[[...)))(((.....]]]))) New CC sens: 1.000, New CC ppv: 0.667, New CC F-measure: 0.800, New CC Energy: -3.44 .........(((.........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.20 ....(((.......[[[......))).....]]]... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -2.99 .........(((........)))....(((...))). New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -1.70 .....(((.(((........))).......))).... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -1.39 .........(((........)))(((........))) New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -1.20 .....(((.(((.........)))......))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.14 ....(((..(((........)))))).(((...))). New CC sens: 0.500, New CC ppv: 0.333, New CC F-measure: 0.400, New CC Energy: -0.80 New CC F-measure-avg: 0.512, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 14 > HIV-1-RT-1-8 ucaagGAUUAACCGACGCCAACGGGAGAAUGGCAGGGau ...........[[[..((((.]]].....))))...... ...........(((..[[[[.))).....]]]]...... ...........(((..[[[[.))).....]]]]...... Energy of known structure: -13.27 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.27 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.27 ...........((...((((.(....)..))))..)).. New CC sens: 0.571, New CC ppv: 0.571, New CC F-measure: 0.571, New CC Energy: -6.36 ....((.....))...((((.........))))...... New CC sens: 0.571, New CC ppv: 0.667, New CC F-measure: 0.615, New CC Energy: -5.20 ...........(((.......)))............... New CC sens: 0.429, New CC ppv: 1.000, New CC F-measure: 0.600, New CC Energy: -2.70 New CC F-measure-avg: 0.697, 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: -6.54 Initial sens: 0.400, Initial ppv: 0.444, Initial F-measure: 0.421, Initial Energy: -6.95 New CC sens: 0.400, New CC ppv: 0.444, New CC F-measure: 0.421, New CC Energy: -6.95 ..............((((((.......)))))).... New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -6.70 ....(((((..((((....)))))))))......... New CC sens: 0.300, New CC ppv: 0.333, New CC F-measure: 0.316, New CC Energy: -6.20 .((((((((..((((....)))))))))......))) New CC sens: 0.300, New CC ppv: 0.250, New CC F-measure: 0.273, New CC Energy: -5.30 .........((((.[[[[[[..)))).]]]]]].... New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -5.10 ..........(((((....)))))............. New CC sens: 0.400, New CC ppv: 0.800, New CC F-measure: 0.533, New CC Energy: -5.00 ....(((((..(((...)))...)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.90 ......(((..(((..((....))....))).))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.80 .........(((...(((((.......)))))))).. New CC sens: 0.500, New CC ppv: 0.625, New CC F-measure: 0.556, New CC Energy: -4.80 ....((((.[[[[)))).....]]]]........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.56 ....((((.....))))((.(((....))).)).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.40 .(((((((.[[[[)))).....]]]]........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.36 ...........(((..((....))....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.30 .(((.......(((..((....))....)))...))) 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: -4.00 ..............((((((..[[[[.))))))]]]] New CC sens: 0.600, New CC ppv: 0.600, New CC F-measure: 0.600, New CC Energy: -3.91 .(((..........((((((.......)))))).))) New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -3.65 .(((......(((((....)))))..........))) New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -3.55 .(((((((.....))))((.(((....))).)).))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.50 New CC F-measure-avg: 0.270, New CC F-measure-best: 0.750, New CC best-subopt: 1, New CC num-subopt: 18 > HIV-1-RT-2-10 agUAAAUGAGUCCGUAGGAGGCGGGAUAUCUCCaAcu ..........[[[[..(((((]]]]...))))).... .............((.(((((.......))))).)). .............((.(((((.......))))).)). Energy of known structure: -11.66 Initial sens: 0.556, Initial ppv: 0.714, Initial F-measure: 0.625, Initial Energy: -5.95 New CC sens: 0.556, New CC ppv: 0.714, New CC F-measure: 0.625, New CC Energy: -5.95 .......((((((((.....)))))....)))..... New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -5.90 ................(((((.......))))).... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -5.40 .........(((([[.[[[[[..)))).]]]]].]]. New CC sens: 0.556, New CC ppv: 0.455, New CC F-measure: 0.500, New CC Energy: -5.27 (((....((((((((.....)))))....)))..))) New CC sens: 0.444, New CC ppv: 0.364, New CC F-measure: 0.400, New CC Energy: -5.25 ..........(((((.....)))))............ New CC sens: 0.444, New CC ppv: 0.800, New CC F-measure: 0.571, New CC Energy: -5.20 .........((((...[[[[[..)))).]]]]].... New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -4.71 (((.......(((((.....))))).........))) New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -4.25 ..........(((...)))...(((.....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.20 ...........((......)).(((.....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.20 (((.......(((...)))...(((.....))).))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.60 (((........((......)).(((.....))).))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.60 (((......(((...[[[.)))......]]]...))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.57 .........(((...[[[.)))......]]]...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.47 ........(((((......)).(((.....))).))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.20 .........(((.......))).(((....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.10 (((......(((....[[[)))......]]]...))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.07 ........(((.....(((((.......))))).))) New CC sens: 0.556, New CC ppv: 0.625, New CC F-measure: 0.588, New CC Energy: -3.05 .........(((....[[[)))......]]]...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.97 .........(((.......)))(((.....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.90 New CC F-measure-avg: 0.245, New CC F-measure-best: 0.714, New CC best-subopt: 2, New CC num-subopt: 19 > HIV-1-RT-2-11 gUCAUAUUACCGUUACUCCUCGGGAUAAAGGAGaucu .........[[[...(((((]]].....))))).... .........(((...[[[[[))).....]]]]].... .........(((...[[[[[))).....]]]]].... Energy of known structure: -13.14 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.14 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.14 ...............(((((........))))).... New CC sens: 0.625, New CC ppv: 1.000, New CC F-measure: 0.769, New CC Energy: -6.10 ....((((.(((...[[[[[))))))).]]]]].... New CC sens: 1.000, New CC ppv: 0.667, New CC F-measure: 0.800, New CC Energy: -5.11 (((......(((...[[[[[))))))..]]]]].... New CC sens: 1.000, New CC ppv: 0.727, New CC F-measure: 0.842, New CC Energy: -3.75 ....((((.(((........))))))).......... New CC sens: 0.375, New CC ppv: 0.429, New CC F-measure: 0.400, New CC Energy: -3.60 .........(((........))).............. New CC sens: 0.375, New CC ppv: 1.000, New CC F-measure: 0.545, New CC Energy: -3.40 ...............(((((..[[[[..)))))]]]] New CC sens: 0.625, New CC ppv: 0.556, New CC F-measure: 0.588, New CC Energy: -2.87 New CC F-measure-avg: 0.706, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > HIV-1-RT-2-12 ucaagAAUAAUCCGACUCGCGGGAUAACGAGAAGaGc ..........[[[[.((((]]]]....))))...... ..........((((.[[[[))))....]]]]...... ..........((((.[[[[))))....]]]]...... Energy of known structure: -6.06 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -6.06 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -6.06 ...............((((........))))...... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -4.00 ..........((((.....)))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.50 .........((((........))))............ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.30 .........((((..[[[[..))))..]]]]...... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -2.87 .........((((..[[[...))))........]]]. 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: -1.50 New CC F-measure-avg: 0.405, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > HIV-1-RT-2-1b caagAAUAUAUCCGAACUCGACGGGAUAACGAGAAGaGc ..........[[[[..((((.]]]]....))))...... ..........((((..[[[[.))))....]]]]...... ..........((((..[[[[.))))....]]]]...... Energy of known structure: -9.86 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -9.86 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -9.86 ........(((((..........)))))........... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.79 ................((((.........))))...... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.20 ........(((((...[[[....))))).......]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.19 ........(((((...[[[[...))))).]]]]...... New CC sens: 0.500, New CC ppv: 0.444, New CC F-measure: 0.471, New CC Energy: -3.15 ..........((((.......)))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.00 ................(((..((......))....))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.90 ..........((((..[[[..))))..........]]]. New CC sens: 0.500, New CC ppv: 0.571, New CC F-measure: 0.533, New CC Energy: -2.35 New CC F-measure-avg: 0.417, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 7 > HIV-1-RT-2-2b gacaaucaagUACCUAGGUGAUAAAAGGGAGAACACGUGUGa ............[[[..(((.....]]].....)))...... .....(((....(((..[[[.....))).....]]]...))) .....(((....(((..[[[.....))).....]]]...))) Energy of known structure: -3.83 Initial sens: 1.000, Initial ppv: 0.667, Initial F-measure: 0.800, Initial Energy: -4.43 New CC sens: 1.000, New CC ppv: 0.667, New CC F-measure: 0.800, New CC Energy: -4.43 .....(((....(((..[[[......)))....]]]...))) New CC sens: 0.500, New CC ppv: 0.333, New CC F-measure: 0.400, New CC Energy: -4.30 ............(((..[[[.....))).....]]]...... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -3.83 ............(((..[[[......)))....]]]...... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -3.70 .(((........(((..[[[.....))).....]]].))).. New CC sens: 1.000, New CC ppv: 0.667, New CC F-measure: 0.800, New CC Energy: -3.13 .(((........(((..[[[......)))....]]].))).. New CC sens: 0.500, New CC ppv: 0.333, New CC F-measure: 0.400, New CC Energy: -3.00 .(((((((....[[[...))))...]]].........))).. New CC sens: 0.500, New CC ppv: 0.300, New CC F-measure: 0.375, New CC Energy: -2.43 ....((((....[[[...))))...]]].............. New CC sens: 0.500, New CC ppv: 0.429, New CC F-measure: 0.462, New CC Energy: -2.33 .(((((((....[[[...))))....]]]........))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.23 .(((........(((..........))).........))).. New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -2.22 ....((((....[[[...))))....]]]............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.13 .(((........(((...........)))........))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.59 ............(((..........))).............. New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -1.19 ..........(((....)))...................... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.00 ............(((...........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -0.89 .................(((.............)))...... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -0.31 ....((((..........)))).................... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: 0.11 .(((......(((....))).................))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: 0.14 .....(((..(((....)))...................))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: 0.65 ..........(((....(((.............)))..))). New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: 0.69 New CC F-measure-avg: 0.353, New CC F-measure-best: 1.000, New CC best-subopt: 2, New CC num-subopt: 19 > HIV-1-RT-2-3a gUUAAACAUAAUCCGUGAUCUUUCACACGGGAGaucuaugaaaga ...........[[[[[[.(((((((]]]]]].......))))))) ...........((((((.[[[[[[[)))))).......]]]]]]] ...........((((((.[[[[[[[)))))).......]]]]]]] Energy of known structure: -14.49 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -14.49 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -14.49 .............((((((((..(....)..))))).)))..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.69 ................((((((((....))))))))......... 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: -8.40 ......((((.((((((........)))))).....))))..... New CC sens: 0.462, New CC ppv: 0.600, New CC F-measure: 0.522, New CC Energy: -7.80 ...........(((....[[[[[[[....)))......]]]]]]] New CC sens: 0.538, New CC ppv: 0.700, New CC F-measure: 0.609, New CC Energy: -7.78 ...........((((((........)))))).............. New CC sens: 0.462, New CC ppv: 1.000, New CC F-measure: 0.632, New CC Energy: -7.60 ((((....)))).((((((((..(....)..))))).)))..... 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: -7.49 ......(((..[[[))).(((((((....]]]......))))))) New CC sens: 0.538, New CC ppv: 0.538, New CC F-measure: 0.538, New CC Energy: -6.80 ...........((((((........))))))...(((.....))) New CC sens: 0.462, New CC ppv: 0.667, New CC F-measure: 0.545, New CC Energy: -6.80 ((((....))))....((((((((....))))))))......... 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: -6.20 ......(((.....))).(((((((...(((...))).))))))) New CC sens: 0.538, New CC ppv: 0.538, New CC F-measure: 0.538, New CC Energy: -5.70 New CC F-measure-avg: 0.313, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 13 > HIV-1-RT-2-4a agUAGAUAUCCGAAGCUCAACGGGAUAAUGAGCaucu ........[[[[..(((((.]]]]....))))).... ........((((..[[[[[.))))....]]]]].... ........((((..[[[[[.))))....]]]]].... Energy of known structure: -13.26 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.26 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.26 ...((((.((((..[[[[[.))))....]]]]])))) New CC sens: 1.000, New CC ppv: 0.692, New CC F-measure: 0.818, New CC Energy: -11.76 ......((((([[.[[[[[...))))).]]]]].]]. New CC sens: 0.556, New CC ppv: 0.417, New CC F-measure: 0.476, New CC Energy: -6.74 ...........((.(((((.........))))).)). New CC sens: 0.556, New CC ppv: 0.714, New CC F-measure: 0.625, New CC Energy: -6.55 ......(((((...[[[[[...))))).]]]]].... New CC sens: 0.556, New CC ppv: 0.500, New CC F-measure: 0.526, New CC Energy: -6.02 ..............(((((.........))))).... New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -5.80 (((...[[[[[...))).....]]]]].......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.64 ...((((.......(((((.........))))))))) New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -4.04 ......(((((...........))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.69 ........((((........))))............. New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -3.30 (((.....[[[[..)))...]]]]............. New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -3.19 New CC F-measure-avg: 0.530, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 10 > HIV-1-RT-2-5a ucaagAUAGUAUCCGUUCUUGAUCAUCGGGACAAAUGaucu ...........[[[[.....((((((]]]]....)))))). ...((((...(((.[[[[[.)))....]]]]].....)))) ...((((...(((.[[[[[.)))....]]]]].....)))) Energy of known structure: -9.78 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -10.02 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.02 ...........((((.....[[[[[[))))....]]]]]]. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -9.78 (((.......(((.[[[[[.)))....]]]]]...)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.22 ((((((.....[[[[.))))))....]]]]........... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -8.66 ..........(((.[[[[[.)))....]]]]]......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -8.22 ...........(((......[[[[[[..)))...]]]]]]. New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -6.93 ..............(((((.[[[[[[.)))))..]]]]]]. New CC sens: 0.600, New CC ppv: 0.545, New CC F-measure: 0.571, New CC Energy: -6.05 ((((((.....[[[..))))))..((((]]]....)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.62 ....................((((((........)))))). New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -4.90 ....(((.......[[[[[..)))...]]]]]......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.69 (((.(((.......[[[[[..)))...]]]]]...)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.69 ....(((....[[[[......)))..]]]]........... New CC sens: 0.400, New CC ppv: 0.571, New CC F-measure: 0.471, New CC Energy: -4.51 (((.(((....[[[[......)))..]]]].....)))... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -4.51 ((((((..........))))))((((........))))... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -4.29 ....(((...))).(((((.[[[[[[.)))))..]]]]]]. New CC sens: 0.600, New CC ppv: 0.429, New CC F-measure: 0.500, New CC Energy: -4.25 ((((((..........)))))).....(((........))) 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: -4.19 ....(((...[[[.[[[[[..)))...]]]]]....]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.83 ...((((.......(((((........))))).....)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.71 ..............(((((........)))))......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.40 New CC F-measure-avg: 0.256, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 19 > HIV-1-RT-2-6b agUGAAACUUAACCGUUAUCAUAGAUCGGGACAAaucuauga ............[[[...((((((((]]].....)))))))) ............(((...[[[[[[[[))).....]]]]]]]] ............(((...[[[[[[[[))).....]]]]]]]] Energy of known structure: -13.57 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -13.57 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -13.57 (((...)))...(((...[[[[[[[[))).....]]]]]]]] New CC sens: 1.000, New CC ppv: 0.786, New CC F-measure: 0.880, New CC Energy: -11.27 ..................((((((((........)))))))) New CC sens: 0.727, New CC ppv: 1.000, New CC F-measure: 0.842, New CC Energy: -6.90 .....(((......))).((((((((........)))))))) New CC sens: 0.727, New CC ppv: 0.727, New CC F-measure: 0.727, New CC Energy: -6.20 (((...))).........((((((((........)))))))) New CC sens: 0.727, New CC ppv: 0.727, New CC F-measure: 0.727, New CC Energy: -4.60 ..............(((.[[[[[[[[...)))..]]]]]]]] New CC sens: 0.727, New CC ppv: 0.727, New CC F-measure: 0.727, New CC Energy: -3.98 .((((..........))))(((((((........))))))). New CC sens: 0.636, New CC ppv: 0.636, New CC F-measure: 0.636, New CC Energy: -3.09 New CC F-measure-avg: 0.791, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 6 > HIV-1-RT-2-7a agAUAUGAUCCGUAAGAGGACGGGAUAAACCUCAac ........[[[[...((((.]]]].....))))... ........(((((..[[[[))))).....]]]]... ........(((((..[[[[))))).....]]]]... Energy of known structure: -11.70 Initial sens: 1.000, Initial ppv: 0.889, Initial F-measure: 0.941, Initial Energy: -11.99 New CC sens: 1.000, New CC ppv: 0.889, New CC F-measure: 0.941, New CC Energy: -11.99 .......((((....[[[[...))))...]]]]... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -6.75 ........(((((......)))))............ New CC sens: 0.500, New CC ppv: 0.800, New CC F-measure: 0.615, New CC Energy: -5.20 ........(((......))).((......))..... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.30 ...............((((..........))))... New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -4.29 ........(((......))).(((......)))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.20 .....((((((((......))))).......))).. New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -4.14 ........(((......))).(((.....))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.30 ...((((...)))).((((..........))))... New CC sens: 0.500, New CC ppv: 0.500, New CC F-measure: 0.500, New CC Energy: -3.09 .....((((((......))).((......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.80 .(((...))).....((((..........))))... New CC sens: 0.500, New CC ppv: 0.571, New CC F-measure: 0.533, New CC Energy: -2.59 .......((((...........)))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -2.39 New CC F-measure-avg: 0.355, New CC F-measure-best: 0.941, New CC best-subopt: 0, New CC num-subopt: 11 > HIV-1-RT-2-9 ucaagGUUUCCGAAAGAAAUCGGGAAAACUGucu .......(((((..[[[...)))))......]]] .((...(((((((......)))))))...))... .((...(((((((......)))))))...))... Energy of known structure: -1.86 Initial sens: 0.625, Initial ppv: 0.556, Initial F-measure: 0.588, Initial Energy: -7.30 New CC sens: 0.625, New CC ppv: 0.556, New CC F-measure: 0.588, New CC Energy: -7.30 ......(((((((......)))))))........ New CC sens: 0.625, New CC ppv: 0.714, New CC F-measure: 0.667, New CC Energy: -7.20 ....(((((((((......))))..))))).... New CC sens: 0.375, New CC ppv: 0.333, New CC F-measure: 0.353, New CC Energy: -6.30 ...((((((((((......))))))).....))) New CC sens: 0.625, New CC ppv: 0.500, New CC F-measure: 0.556, New CC Energy: -5.10 ....((((((.....))))))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.40 ....(((((.(....)))))).(((......))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.70 New CC F-measure-avg: 0.361, New CC F-measure-best: 0.667, New CC best-subopt: 1, New CC num-subopt: 5 > Hs_SRP_pkn GCCGGGCGCGGUGGCGCGUGCCUGUAGUCCCAGCUACUCGGGAGGCU (((.((((((.[[[[.)))))).....((((.]]]]...))))))). (((.((((((......)))))).....((((........))))))). (((.((((((......)))))).....((((........))))))). Energy of known structure: -11.55 Initial sens: 0.765, Initial ppv: 1.000, Initial F-measure: 0.867, Initial Energy: -19.80 New CC sens: 0.765, New CC ppv: 1.000, New CC F-measure: 0.867, New CC Energy: -19.80 ..((((((((......))))))))...((((........)))).... New CC sens: 0.588, New CC ppv: 0.833, New CC F-measure: 0.690, New CC Energy: -18.60 (((..((((....))))...((((((((....)))))..))).))). New CC sens: 0.176, New CC ppv: 0.200, New CC F-measure: 0.188, New CC Energy: -18.00 (((..(((((....))))).((((((((....)))))..))).))). New CC sens: 0.176, New CC ppv: 0.188, New CC F-measure: 0.182, New CC Energy: -18.00 ((((((((((......)))))))(((((....)))))......))). New CC sens: 0.529, New CC ppv: 0.600, New CC F-measure: 0.562, New CC Energy: -18.00 (((..((((....))))...((((((((....))))..)))).))). New CC sens: 0.176, New CC ppv: 0.200, New CC F-measure: 0.188, New CC Energy: -17.20 (((..(((((....))))).((((((((....))))..)))).))). New CC sens: 0.176, New CC ppv: 0.188, New CC F-measure: 0.182, New CC Energy: -17.20 (((..(((((....)))))........((((........))))))). New CC sens: 0.412, New CC ppv: 0.583, New CC F-measure: 0.483, New CC Energy: -16.70 ....((((((......)))))).((..((((........)))).)). New CC sens: 0.588, New CC ppv: 0.833, New CC F-measure: 0.690, New CC Energy: -16.50 (((..((((....))))..........((((........))))))). New CC sens: 0.412, New CC ppv: 0.636, New CC F-measure: 0.500, New CC Energy: -16.50 (((..(((((....)))))....(((((....)))))......))). New CC sens: 0.176, New CC ppv: 0.231, New CC F-measure: 0.200, New CC Energy: -16.20 (((..((((....))))......(((((....)))))......))). New CC sens: 0.176, New CC ppv: 0.250, New CC F-measure: 0.207, New CC Energy: -16.00 New CC F-measure-avg: 0.411, New CC F-measure-best: 0.867, New CC best-subopt: 0, New CC num-subopt: 11 > MMTVgag-pro GGGGCAGUCCCCUAGCCCCGCUCAAAAGGGGGAU [[[[[.(((((((.]]]]]........))))))) (((((.[[[[[[[.)))))........]]]]]]] (((((.[[[[[[[.)))))........]]]]]]] Energy of known structure: -25.74 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -25.74 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -25.74 (((((..[[[[[[.))))).......]]]]]].. New CC sens: 0.417, New CC ppv: 0.455, New CC F-measure: 0.435, New CC Energy: -23.03 (((((....[[[[.))))).........]]]].. New CC sens: 0.417, New CC ppv: 0.556, New CC F-measure: 0.476, New CC Energy: -18.39 .((((.[[[[[[[......))))....]]]]]]] New CC sens: 0.583, New CC ppv: 0.636, New CC F-measure: 0.609, New CC Energy: -15.56 .(((..[[[[[[[...)))........]]]]]]] New CC sens: 0.583, New CC ppv: 0.700, New CC F-measure: 0.636, New CC Energy: -15.46 (((((.....[[[.)))))..........]]].. New CC sens: 0.417, New CC ppv: 0.625, New CC F-measure: 0.500, New CC Energy: -14.36 (((...[[[[[[[..))).........]]]]]]] New CC sens: 0.583, New CC ppv: 0.700, New CC F-measure: 0.636, New CC Energy: -14.13 (((((..[[[[...)))))........]]]]... New CC sens: 0.417, New CC ppv: 0.556, New CC F-measure: 0.476, New CC Energy: -14.05 ((((....))))...((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.00 ((((...))))....((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.90 ((((....))))...((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.40 ((((.....))))..((((........))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.00 ((((...))))....((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.30 .((((..........[[[[))))....]]]]... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.10 .((((..........[[[[)))).....]]]].. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.90 (((((.........))))).(((....))).... New CC sens: 0.417, New CC ppv: 0.625, 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: -10.50 ((((.....))))..((((.........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.40 New CC F-measure-avg: 0.293, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 17 > Ni_VS GGGCGUCGUCGCCCCGAGUCGUAGCAGUUGACUACUGUUAUG ((((...[[[)))).....(((((((((.]]].))))))))) (((((....))))).....(((((((((.....))))))))) (((((....))))).....(((((((((.....))))))))) Energy of known structure: -13.21 Initial sens: 0.812, Initial ppv: 0.929, Initial F-measure: 0.867, Initial Energy: -18.00 New CC sens: 0.812, New CC ppv: 0.929, New CC F-measure: 0.867, New CC Energy: -18.00 New CC F-measure-avg: 0.867, New CC F-measure-best: 0.867, New CC best-subopt: 0, New CC num-subopt: 0 > PEMV UUCCGGUCGACUCCGGAGAAACAAAGUC ((((((..[[[[))))))......]]]] ((((((..[[[[))))))......]]]] ((((((..[[[[))))))......]]]] Energy of known structure: -10.10 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -10.10 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -10.10 ((((((......)))))).......... New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -8.40 New CC F-measure-avg: 0.875, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 1 > PLRV-S GCGGCACCGUCCGCCAAAACAAACGG [[[[..((((]]]]........)))) ((((..[[[[))))........]]]] ((((..[[[[))))........]]]] Energy of known structure: -11.15 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -11.15 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -11.15 ..(((.[[[[..))).......]]]] New CC sens: 0.500, New CC ppv: 0.571, New CC F-measure: 0.533, New CC Energy: -8.08 ((((......))))............ New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -5.00 ..(((.......)))........... 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: -1.99 ......((((............)))) New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -1.89 New CC F-measure-avg: 0.478, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 5 > PRRSV-16244B GCCGCCAGCGGCUUGACCCGCUGUGGUCGCGGCGGCUUGGUUGUUACUGAGACAGCGG ((((((.((((((....[[[[[[[))))))))))))...............]]]]]]] ((((((.((((((....[[[[[[[))))))))))))(..((....))..).]]]]]]] ((((((.((((((....[[[[[[[))))))))))))(..((....))..).]]]]]]] Energy of known structure: -31.97 Initial sens: 1.000, Initial ppv: 0.864, Initial F-measure: 0.927, Initial Energy: -30.22 New CC sens: 1.000, New CC ppv: 0.864, New CC F-measure: 0.927, New CC Energy: -30.22 ((((((.((((((...........))))))))))))...((((((.....)))))).. New CC sens: 0.632, New CC ppv: 0.667, New CC F-measure: 0.649, New CC Energy: -26.99 ((((....)))).....((((((((((.(((((......))))).)))...))))))) New CC sens: 0.368, New CC ppv: 0.368, New CC F-measure: 0.368, New CC Energy: -24.20 (((((((((((......)))))).....)))))......((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -24.10 .((((((((((......))))))..(((.(((..((......))..))).))).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.85 ((((....))))..((.(((((((....))))))).)).((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.65 ((((....)))).....(((((((....)))))))....((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.60 (((((.(((((......))))))))))(((.....((..((....))..))...))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.04 (((((((((((......)))))).....)))))..((((((....))))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -22.70 (((((..(((((.......)))))....)))))......((((((.....)))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.85 ((((....)))).....(((((((....)))))))((((((....))))))....... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -21.60 New CC F-measure-avg: 0.177, New CC F-measure-best: 0.927, New CC best-subopt: 0, New CC num-subopt: 10 > PRRSV-LV GCCGCCAGCGGCUUGACCCGCUGUGGCCGCGGCGGCCUAGUUGUGACUGAAACGGCGG ((((((.((((((....[[[[[[[))))))))))))...............]]]]]]] ((((((.((((((....[[[[[[[)))))))))))).((((....))))..]]]]]]] ((((((.((((((....[[[[[[[)))))))))))).((((....))))..]]]]]]] Energy of known structure: -33.57 Initial sens: 1.000, Initial ppv: 0.826, Initial F-measure: 0.905, Initial Energy: -34.07 New CC sens: 1.000, New CC ppv: 0.826, New CC F-measure: 0.905, New CC Energy: -34.07 ((((((.((((((...........))))))))))))...(((((.......))))).. New CC sens: 0.632, New CC ppv: 0.706, New CC F-measure: 0.667, New CC Energy: -27.99 ((((....)))).....(((((((((.((((((......)))))).))...))))))) New CC sens: 0.368, New CC ppv: 0.368, New CC F-measure: 0.368, New CC Energy: -24.60 ((((....)))).....((((((((((((...)))))((((....))))..))))))) New CC sens: 0.368, New CC ppv: 0.350, New CC F-measure: 0.359, New CC Energy: -24.40 ((((....)))).....(((((((...((((((......))))))......))))))) New CC sens: 0.368, New CC ppv: 0.412, New CC F-measure: 0.389, New CC Energy: -23.62 .(((((.((((((....(((((((....)))))))...)))))).........))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.49 .(((((.((((......))))...(((((...)))))................))))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.30 (((((((((((......)))))).....))))).(((((((....))))....))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.30 (((((.(((((......))))))))))..((.((...((((....))))...)).)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.25 ((((...((((((....(((((((....)))))))...))))))........)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.19 ((((.((((((......)))))).(((((...)))))((((....))))...)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -23.10 ((((....)))).....((((((((((((...)))))..............))))))) New CC sens: 0.368, New CC ppv: 0.438, New CC F-measure: 0.400, New CC Energy: -22.89 (((((((((((......)))))).....)))))......(((((.......))))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -22.80 (((((((((((......)))))).)..((((((......)))))).......)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -22.40 New CC F-measure-avg: 0.221, New CC F-measure-best: 0.905, New CC best-subopt: 0, New CC num-subopt: 13 > SARS-CoV UGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCU (((((((((((...[[[[[[[)))))))))))((((((((.........))).)))))...]].]]]]] (((((((((((...[[[[[..)))))))))))((((((((((....)).))).)))))......]]]]] (((((((((((...[[[[[..)))))))))))((((((((((....)).))).)))))......]]]]] Energy of known structure: -30.58 Initial sens: 0.923, Initial ppv: 0.923, Initial F-measure: 0.923, Initial Energy: -27.78 New CC sens: 0.923, New CC ppv: 0.923, New CC F-measure: 0.923, New CC Energy: -27.78 .((((((((((.((.....))))))))))))(((((((((((....)).))).)))))).......... New CC sens: 0.692, New CC ppv: 0.783, New CC F-measure: 0.735, New CC Energy: -24.00 .((((((((((.(([[[[[))))))))))))(((((((((((....)).))).)))))).....]]]]] New CC sens: 0.885, New CC ppv: 0.821, New CC F-measure: 0.852, New CC Energy: -23.78 (((((((((((.((.....)))))))))))))((((((((((....)).))).)))))........... New CC sens: 0.731, New CC ppv: 0.826, New CC F-measure: 0.776, New CC Energy: -22.10 (((((((((((.(([[[[[)))))))))))))((((((((((....)).))).)))))......]]]]] New CC sens: 0.923, New CC ppv: 0.857, New CC F-measure: 0.889, New CC Energy: -21.83 (((((((((((((.....)).)))))))))))((((((((((....)).))).)))))........... New CC sens: 0.731, New CC ppv: 0.826, New CC F-measure: 0.776, New CC Energy: -21.20 (((((((((((..........)))))))))))((((((((((....)).))).)))))........... New CC sens: 0.731, New CC ppv: 0.905, New CC F-measure: 0.809, New CC Energy: -20.99 .((((((((((.((.[[[.))))))))))))((((((..]]]...........)))))).......... New CC sens: 0.577, New CC ppv: 0.714, New CC F-measure: 0.638, New CC Energy: -19.83 New CC F-measure-avg: 0.800, New CC F-measure-best: 0.923, New CC best-subopt: 0, New CC num-subopt: 7 > SNV GGGUUCUCCCGCCCUCCGUGAACCCAGGCUAAAAGUUAAGGUAGGGGGGC [[[[[[.[..(((((((].]]]]]]..................))))))) ((((((....[[[[[[[..))))))..................]]]]]]] ((((((....[[[[[[[..))))))..................]]]]]]] Energy of known structure: -22.21 Initial sens: 0.929, Initial ppv: 1.000, Initial F-measure: 0.963, Initial Energy: -19.03 New CC sens: 0.929, New CC ppv: 1.000, New CC F-measure: 0.963, New CC Energy: -19.03 (((....)))(((((((....(((..(((.....)))..))).))))))) New CC sens: 0.500, New CC ppv: 0.438, New CC F-measure: 0.467, New CC Energy: -18.10 (((....)))(((((((.((..((..(((.....)))..))))))))))) New CC sens: 0.500, New CC ppv: 0.412, New CC F-measure: 0.452, New CC Energy: -15.85 (((....)))(((((((....(((...............))).))))))) New CC sens: 0.500, New CC ppv: 0.538, New CC F-measure: 0.519, New CC Energy: -15.00 New CC F-measure-avg: 0.600, New CC F-measure-best: 0.963, New CC best-subopt: 0, New CC num-subopt: 3 > TMV-L GGGAUUCGAAUUCCCCCGGAACCCCCGGUUGGGGCCCA ...............[[[...((((]]]..)))).... (((........((((((((.....))))..))))))). (((........((((((((.....))))..))))))). Energy of known structure: -12.37 Initial sens: 0.429, Initial ppv: 0.273, Initial F-measure: 0.333, Initial Energy: -13.29 New CC sens: 0.429, New CC ppv: 0.273, New CC F-measure: 0.333, New CC Energy: -13.29 ((((.......))))..((..(((......)))..)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.95 (((.........(((((((.....)))...))))))). New CC sens: 0.286, New CC ppv: 0.200, New CC F-measure: 0.235, New CC Energy: -11.77 (((.((((........))))..((((....))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -11.70 (((.((((........)))).((((.....))))))). New CC sens: 0.571, New CC ppv: 0.364, New CC F-measure: 0.444, New CC Energy: -11.30 ((((.......))))......((((.....)))).... New CC sens: 0.571, New CC ppv: 0.500, New CC F-measure: 0.533, New CC Energy: -11.00 ((((.......)))).......((((....)))).... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.90 (((((....)))))...((..(((......)))..)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.65 ...........((((((((.....))))..)))).... New CC sens: 0.429, New CC ppv: 0.375, New CC F-measure: 0.400, New CC Energy: -10.30 (((..........))).((..(((......)))..)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.24 (((.......((((...)))).((((....))))))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.00 ((((.......))))((((.....)))).......... New CC sens: 0.429, New CC ppv: 0.375, New CC F-measure: 0.400, New CC Energy: -9.70 (((..........[[[[[[..)))....]]]]]].... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.66 (((.((((........)))).(((......))).))). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.50 (((...........)))((..(((......)))..)). New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -9.34 New CC F-measure-avg: 0.156, New CC F-measure-best: 0.533, New CC best-subopt: 5, New CC num-subopt: 14 > BChV GCGGCGCCGACCGCCAAACAACCGGC [[[[.((((.]]]]........)))) ((((.[[[[.))))........]]]] ((((.[[[[.))))........]]]] 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: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.00 ((((......))))............ New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -5.60 .....((((.............)))) New CC sens: 0.500, New CC ppv: 1.000, New CC F-measure: 0.667, New CC Energy: -3.91 .((....))...(((........))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -3.70 New CC F-measure-avg: 0.467, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > CABYV GGCGGCGGCGACCGCCGAAACAACCGC (((((..[[[.)))))........]]] (((((..[[[.)))))........]]] (((((..[[[.)))))........]]] Energy of known structure: -12.82 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -12.82 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -12.82 ..((((((...)))))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.40 .((((((((....))))......)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -10.20 (((((......)))))........... New CC sens: 0.625, New CC ppv: 1.000, New CC F-measure: 0.769, New CC Energy: -9.80 .....((((....)))).......... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.80 New CC F-measure-avg: 0.354, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > GaLV GGGUUCGGACCCCCUCCCCGAACCUAGGGUAACACUGACUGUGGAGGGG ((((((((..[[[[[[[)))))))).................]]]]]]] ((((((((..[[[[[[[)))))))).................]]]]]]] ((((((((..[[[[[[[)))))))).................]]]]]]] Energy of known structure: -26.72 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -26.72 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -26.72 ((((((((..[[[[[[.)))))))).......(((.....)))]]]]]] New CC sens: 0.933, New CC ppv: 0.824, New CC F-measure: 0.875, New CC Energy: -24.40 (((((((([[[[{{{{.)))))))).]]]]..(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.421, New CC F-measure: 0.471, New CC Energy: -18.11 (((((((([[[[.{{{{)))))))).]]]]..(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.421, New CC F-measure: 0.471, New CC Energy: -18.11 ((((((((....[[[[.)))))))).......(((.....)))..]]]] New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -17.81 ((((((((.[[[[....)))))))).......(((.....)))..]]]] New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -17.62 ((((((((.....[[[[)))))))).......(((.....)))..]]]] New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -17.28 ((((((((..[[[{{{{)))))))).]]]...(((.....)))..}}}} New CC sens: 0.533, New CC ppv: 0.444, New CC F-measure: 0.485, New CC Energy: -16.58 ((((((((...[[[[..)))))))).......(((.....)))..]]]] New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -16.46 (((.......[[[[[[)))..(((...)))..(((.....)))]]]]]] New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -15.77 ..........(((((((((.......)))...(((.....))))))))) New CC sens: 0.400, New CC ppv: 0.500, New CC F-measure: 0.444, New CC Energy: -14.60 ((((....))))...((((..(((...)))..(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -14.60 ((((((((.........)))))))).......(((.....)))...... New CC sens: 0.533, New CC ppv: 0.727, New CC F-measure: 0.615, New CC Energy: -14.40 ((((....))))...((((....(((.(((.......))).))).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.70 (((........))).((((..(((...)))..(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -13.20 ((((((((...[[[[..))))))))]]]]...(((.....)))...... New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -13.20 .........((((...(((.......)))...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.90 (((((((([[[[.....)))))))).]]]]..(((.....)))...... New CC sens: 0.533, New CC ppv: 0.533, New CC F-measure: 0.533, New CC Energy: -12.68 (((.......)))..((((..(((...)))..(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.60 (((........))).((((....(((.(((.......))).))).)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -12.30 New CC F-measure-avg: 0.398, 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: -11.89 Initial sens: 0.444, Initial ppv: 0.364, Initial F-measure: 0.400, Initial Energy: -13.69 New CC sens: 0.444, New CC ppv: 0.364, New CC F-measure: 0.400, New CC Energy: -13.69 .......(((((..[[[[..)))))....]]]].... New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -11.89 (((...........[[[[.))).......]]]].... New CC sens: 0.444, New CC ppv: 0.571, New CC F-measure: 0.500, New CC Energy: -9.79 ......((((....((((...........)))))))) New CC sens: 0.444, New CC ppv: 0.500, New CC F-measure: 0.471, New CC Energy: -9.19 .......(((((.[[[[...)))))........]]]] New CC sens: 0.556, New CC ppv: 0.556, New CC F-measure: 0.556, New CC Energy: -8.05 .............((((...(((.....)))..)))) New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.60 ..............((((...........)))).... New CC sens: 0.444, New CC ppv: 1.000, New CC F-measure: 0.615, New CC Energy: -6.59 .......(((((........)))))............ New CC sens: 0.556, New CC ppv: 1.000, New CC F-measure: 0.714, New CC Energy: -5.80 New CC F-measure-avg: 0.532, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 7 > PLRV-W GCGGCACCGCCCGCCAAAACAAACGG ((((..[[[.)))).........]]] ((((..[[[.)))).........]]] ((((..[[[.)))).........]]] Energy of known structure: -8.96 Initial sens: 1.000, Initial ppv: 1.000, Initial F-measure: 1.000, Initial Energy: -8.96 New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -8.96 ((((......))))............ New CC sens: 0.571, New CC ppv: 1.000, New CC F-measure: 0.727, New CC Energy: -5.20 ..(((.......)))........... 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: -3.39 ..(((...)))............... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -1.90 New CC F-measure-avg: 0.345, New CC F-measure-best: 1.000, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=PDB_00716; TYPE=Other Ribozyme; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=1SJF; ORGANISM=HOMO SAPIENS AUGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACACCAUUGCACUCCGGUGGUGAAUGGGAC ..(((((((...[[[[[[(((.{{.....))))))))))}}....((((..........)))).....]]]]]] .((.(((((.((((.(((((......))))).))))))))).)).((((((((.....))))))))........ .((.(((((.((((.(((((......))))).))))))))).)).((((((((.....))))))))........ Energy of known structure: -27.19 Initial sens: 0.000, Initial ppv: 0.000, Initial F-measure: 0.000, Initial Energy: -35.05 New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -35.05 .((((((((...[[[[[[(((........))))))))))).....((((((((.....))))))))..]]]]]] New CC sens: 0.727, New CC ppv: 0.640, New CC F-measure: 0.681, New CC Energy: -30.99 .((.(((((.((((.(((((.[[[[.))))).))))))))).)).((((((((.....))))))))...]]]]. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -30.27 .((.(((((.((((.(((((......))))).))))))))).)).((((..........))))........... New CC sens: 0.182, New CC ppv: 0.200, New CC F-measure: 0.190, New CC Energy: -29.74 .((((((((......(((((......))))).)))))))).....((((((((.....))))))))........ New CC sens: 0.318, New CC ppv: 0.333, New CC F-measure: 0.326, New CC Energy: -29.64 ............((((((((((....((((....)))).))))..((((((((.....))))))))..)))))) New CC sens: 0.273, New CC ppv: 0.273, New CC F-measure: 0.273, New CC Energy: -28.95 ....(((((..(((.(((((......))))).))).)))))....((((((((.....))))))))........ New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -28.55 New CC F-measure-avg: 0.210, New CC F-measure-best: 0.681, New CC best-subopt: 1, New CC num-subopt: 6 > SSTRAND_ID=PDB_00944; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2B57; ORGANISM=SYNTHETIC GACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGAUUAUGUC ((((((.....(((((..[..[[)))))..........((((((]]...].))))))..)))))) ((((((.....(((((.......)))))..........((((((.......))))))..)))))) ((((((.....(((((.......)))))..........((((((.......))))))..)))))) Energy of known structure: -9.47 Initial sens: 0.850, Initial ppv: 1.000, Initial F-measure: 0.919, Initial Energy: -19.30 New CC sens: 0.850, New CC ppv: 1.000, New CC F-measure: 0.919, New CC Energy: -19.30 ((((((.....(((.......((.((....)).))...[[[[[[.)))...]]]]]]..)))))) New CC sens: 0.600, New CC ppv: 0.632, New CC F-measure: 0.615, New CC Energy: -18.83 ...........(((((..[[[[[)))))..........((((((]]]]]..))))))........ New CC sens: 0.650, New CC ppv: 0.812, New CC F-measure: 0.722, New CC Energy: -16.32 ((((((.....(((((..[[[[[)))))..........((((((]]]]]..))))))..)))))) New CC sens: 0.950, New CC ppv: 0.864, New CC F-measure: 0.905, New CC Energy: -16.02 ((((((.......(((((......((....)).)))))((((((.......))))))..)))))) New CC sens: 0.600, New CC ppv: 0.632, New CC F-measure: 0.615, New CC Energy: -15.44 New CC F-measure-avg: 0.755, New CC F-measure-best: 0.919, New CC best-subopt: 0, New CC num-subopt: 4 > SSTRAND_ID=PDB_01009; TYPE=Other RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2DU3; ORGANISM=ARCHAEOGLOBUS FULGIDUS GCCAGGGUGGCAGAGGGGCUUUGCGGCGGACUGCAGAUCCGCUUUACCCCGGUUCGAAUCCGGGCCCUGGC ((((((([.(((.].......)))..((((.......))))......(((((.......)))))))))))) (((((((....((((.((.(((((((....))))))).)).))))..(((((.......)))))))))))) (((((((....((((.((.(((((((....))))))).)).))))..(((((.......)))))))))))) Energy of known structure: -13.66 Initial sens: 0.600, Initial ppv: 0.480, Initial F-measure: 0.533, Initial Energy: -36.15 New CC sens: 0.600, New CC ppv: 0.480, New CC F-measure: 0.533, New CC Energy: -36.15 ((((((((((.((((.((.(((((((....))))))).)).)))).))((((.......)))))))))))) New CC sens: 0.550, New CC ppv: 0.407, New CC F-measure: 0.468, New CC Energy: -36.10 ((((((((...((((.((.(((((((....))))))).)).))))...((((.......)))))))))))) New CC sens: 0.550, New CC ppv: 0.440, New CC F-measure: 0.489, New CC Energy: -34.95 (((((((..((((...........[[[[[[))))...]]]]]]....(((((.......)))))))))))) New CC sens: 0.800, New CC ppv: 0.727, New CC F-measure: 0.762, New CC Energy: -34.47 ((((((((.((((...........[[[[[[))))...]]]]]].....((((.......)))))))))))) New CC sens: 0.750, New CC ppv: 0.682, New CC F-measure: 0.714, New CC Energy: -32.57 (((((((..((((((...))))))((((((.......))))))....(((((.......)))))))))))) New CC sens: 0.950, New CC ppv: 0.792, New CC F-measure: 0.864, New CC Energy: -32.30 ((((((((.((((((...))))))((((((.......)))))).....((((.......)))))))))))) New CC sens: 0.900, New CC ppv: 0.750, New CC F-measure: 0.818, New CC Energy: -31.10 ((((((((.((((((...))))))..((((.....((.(((........))).))...)))).)))))))) New CC sens: 0.500, New CC ppv: 0.435, New CC F-measure: 0.465, New CC Energy: -30.04 ((((((((......((((......((((((.......))))))...))))((.......))..)))))))) New CC sens: 0.650, New CC ppv: 0.650, New CC F-measure: 0.650, New CC Energy: -29.92 New CC F-measure-avg: 0.640, New CC F-measure-best: 0.864, New CC best-subopt: 5, New CC num-subopt: 8 > SSTRAND_ID=PDB_01021; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2EET; ORGANISM=SYNTHETIC GGACAUGUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACCAUGUCCa .((((((...(.(((((..[..[[))))).)........((((((]]...].))))))..)))))).. (((((((.....(((((.......)))))..........((((((.......))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). Energy of known structure: -9.70 Initial sens: 0.810, Initial ppv: 0.944, Initial F-measure: 0.872, Initial Energy: -25.60 New CC sens: 0.810, New CC ppv: 0.944, New CC F-measure: 0.872, New CC Energy: -25.60 (((((((.....(((.......((.((....)).))...[[[[[[.)))...]]]]]]..))))))). New CC sens: 0.571, New CC ppv: 0.600, New CC F-measure: 0.585, New CC Energy: -25.13 (((((((.....(((((..[[[[[)))))..........((((((]]]]]..))))))..))))))). New CC sens: 0.905, New CC ppv: 0.826, New CC F-measure: 0.864, New CC Energy: -22.32 (((((((.......(((((......((....)).)))))((((((.......))))))..))))))). New CC sens: 0.571, New CC ppv: 0.600, New CC F-measure: 0.585, New CC Energy: -21.74 (((((((.....(((((..[[[[[)))))................]]]]]..........))))))). New CC sens: 0.619, New CC ppv: 0.765, New CC F-measure: 0.684, New CC Energy: -21.18 ...............(((((((((.((....))......((((((.......)))))).))))))))) New CC sens: 0.286, New CC ppv: 0.353, New CC F-measure: 0.316, New CC Energy: -20.80 New CC F-measure-avg: 0.651, New CC F-measure-best: 0.872, New CC best-subopt: 0, New CC num-subopt: 5 > SSTRAND_ID=PDB_01023; TYPE=Synthetic RNA; EXT_SOURCE=RCSB Protein Data Bank; EXT_ID=2EEV; ORGANISM=SYNTHETIC GGACAUACAAUCGCGUGGAUAUGGCACGCAAGUUUCUGCCGGGCACCGUAAAUGUCCGACUAUGUCCa (((((((...(.(((((..[..[[))))).)........((((((]]...].))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). (((((((.....(((((.......)))))..........((((((.......))))))..))))))). Energy of known structure: -12.50 Initial sens: 0.818, Initial ppv: 1.000, Initial F-measure: 0.900, Initial Energy: -24.20 New CC sens: 0.818, New CC ppv: 1.000, New CC F-measure: 0.900, New CC Energy: -24.20 (((((((.....(((.......((.((....)).))...[[[[[[.)))...]]]]]]..))))))). New CC sens: 0.591, New CC ppv: 0.650, New CC F-measure: 0.619, New CC Energy: -23.73 (((((((.....(((............(((......)))[[[[[[.)))...]]]]]]..))))))). New CC sens: 0.591, New CC ppv: 0.684, New CC F-measure: 0.634, New CC Energy: -21.53 (((((((.....(((((..[[[[[)))))..........((((((]]]]]..))))))..))))))). New CC sens: 0.909, New CC ppv: 0.870, New CC F-measure: 0.889, New CC Energy: -20.92 (((((((.....(((((..[[[[[)))))................]]]]]..........))))))). New CC sens: 0.636, New CC ppv: 0.824, New CC F-measure: 0.718, New CC Energy: -19.79 New CC F-measure-avg: 0.752, 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: -22.48 Initial sens: 0.407, Initial ppv: 0.367, Initial F-measure: 0.386, Initial Energy: -43.00 New CC sens: 0.407, New CC ppv: 0.367, New CC F-measure: 0.386, New CC Energy: -43.00 .((.(((((.((((.(((((......))))).))))))))).))......(((((((......)))))))......(((.......))).. New CC sens: 0.222, New CC ppv: 0.231, New CC F-measure: 0.226, New CC Energy: -41.40 ...........(((((((((((....((((....)))).))))..((((((((((((......))))))).).)))).....))))))).. New CC sens: 0.630, New CC ppv: 0.630, New CC F-measure: 0.630, New CC Energy: -41.15 .((.(((((.((((.(((((......))))).))))))))).)).......((((((....)))))).........(((.......))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -41.10 .((((((((..[[[[[[[(((........))))))))))).((..((((((((((((......))))))).).))))))...]]]]]]].. New CC sens: 0.963, New CC ppv: 0.812, New CC F-measure: 0.881, New CC Energy: -40.55 ..(((((((......(((((......))))).)))))))((((..((((((((((((......))))))).).)))).........)))). New CC sens: 0.630, New CC ppv: 0.607, New CC F-measure: 0.618, New CC Energy: -40.49 ..(((((((.((((.(((((......))))).)))))))..((..((((((((((((......))))))).).))))))......)))).. New CC sens: 0.407, New CC ppv: 0.367, New CC F-measure: 0.386, New CC Energy: -40.40 .((((((((..[[[[[[[(((........))))))))))).....((((((((((((......))))))).).)))).....]]]]]]].. New CC sens: 0.963, New CC ppv: 0.867, New CC F-measure: 0.912, New CC Energy: -40.05 ..(((((((.((((.(((((......))))).)))))))......((((((((((((......))))))).).))))........)))).. New CC sens: 0.407, New CC ppv: 0.393, New CC F-measure: 0.400, New CC Energy: -39.90 ...........((((((((((........)))(((((...(....)..(((((((((......))))))).)).)))))...))))))).. New CC sens: 0.593, New CC ppv: 0.640, New CC F-measure: 0.615, New CC Energy: -38.90 ...........((((((((((........)))(((((..(((......)))((((((....)))))).......)))))...))))))).. New CC sens: 0.333, New CC ppv: 0.375, New CC F-measure: 0.353, New CC Energy: -38.20 ..((((........(((((((.((.....))....)))))))...((((((((((((......))))))).).))))........)))).. New CC sens: 0.407, New CC ppv: 0.440, New CC F-measure: 0.423, New CC Energy: -38.00 ...........((((((((((........)))(((((...(....)....(((((((......)))))))....)))))...))))))).. New CC sens: 0.556, New CC ppv: 0.652, New CC F-measure: 0.600, New CC Energy: -37.90 ...(((((...[[[[[[[((((....((((....)))).)))).....(((((((((......))))))).)).)))))...]]]]]]].. New CC sens: 0.481, New CC ppv: 0.448, New CC F-measure: 0.464, New CC Energy: -37.77 ...((((((..(((....))).....))))))(((((..[[[[.....(((((((((......))))))).)).))))).......]]]]. New CC sens: 0.259, New CC ppv: 0.259, New CC F-measure: 0.259, New CC Energy: -37.77 .((.(((((.((((.(((((......))))).))))))))).))....(((....)))..(((((..(((.....))).....)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -37.39 ...((((((..(((....))).....))))))(((((..[[[[.......(((((((......)))))))....))))).......]]]]. New CC sens: 0.222, New CC ppv: 0.240, New CC F-measure: 0.231, New CC Energy: -37.27 ..(((((((......(((((......))))).)))))))((((........((((((....))))))(((.....)))........)))). New CC sens: 0.222, New CC ppv: 0.240, New CC F-measure: 0.231, New CC Energy: -37.14 ..(((((...)))))(((((......))))).(((((..[[[[.....(((((((((......))))))).)).))))).......]]]]. New CC sens: 0.259, New CC ppv: 0.250, New CC F-measure: 0.255, New CC Energy: -37.03 .((((((((......(((((......))))).))))))))(((..((((((((((((......))))))).).)))).........))).. New CC sens: 0.630, New CC ppv: 0.607, New CC F-measure: 0.618, New CC Energy: -36.99 New CC F-measure-avg: 0.424, New CC F-measure-best: 0.912, New CC best-subopt: 7, 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: -28.68 Initial sens: 0.429, Initial ppv: 0.429, Initial F-measure: 0.429, Initial Energy: -42.95 New CC sens: 0.429, New CC ppv: 0.429, New CC F-measure: 0.429, New CC Energy: -42.95 ...........(((((((((((....((((....)))).))))..((((((((((((......)))))))).)))).....))))))).. New CC sens: 0.643, New CC ppv: 0.667, New CC F-measure: 0.655, New CC Energy: -41.05 .((((((((..[[[[[[[(((........))))))))))).((..((((((((((((......)))))))).))))))...]]]]]]].. New CC sens: 0.964, New CC ppv: 0.844, New CC F-measure: 0.900, New CC Energy: -40.70 .((((((((..[[[[[[[(((........))))))))))).....((((((((((((......)))))))).)))).....]]]]]]].. New CC sens: 0.964, New CC ppv: 0.900, New CC F-measure: 0.931, New CC Energy: -40.20 .((.(((((.((((.(((((......))))).))))))))).)).....((((((((......))))))))................... New CC sens: 0.286, New CC ppv: 0.333, New CC F-measure: 0.308, New CC Energy: -39.65 ...((((((..[[[[[[[[[[[....)))))).......]]]]..((((((((((((......)))))))).)))).....]]]]]]].. New CC sens: 0.643, New CC ppv: 0.621, New CC F-measure: 0.632, New CC Energy: -38.97 .((((((((......(((((......))))).)))))))).((..((((((((((((......)))))))).))))))............ New CC sens: 0.643, New CC ppv: 0.667, New CC F-measure: 0.655, New CC Energy: -38.04 .((((((((......(((((......))))).)))))))).....((((((((((((......)))))))).)))).............. New CC sens: 0.643, New CC ppv: 0.720, New CC F-measure: 0.679, New CC Energy: -37.54 ...........(((((((((((....((((....)))).))))......((((((((......))))))))..........))))))).. New CC sens: 0.500, New CC ppv: 0.609, New CC F-measure: 0.549, New CC Energy: -37.25 .((((((((..[[[[[[[(((........)))))))))))(....)...((((((((......))))))))..........]]]]]]].. New CC sens: 0.821, New CC ppv: 0.852, New CC F-measure: 0.836, New CC Energy: -36.60 ....(((((..(((.(((((......))))).))).)))))....((((((((((((......)))))))).)))).............. New CC sens: 0.429, New CC ppv: 0.480, New CC F-measure: 0.453, New CC Energy: -36.55 .((.(((((.((((.(((((......))))).))))))))).))....(((....)))..(((((..(((.......)))..)))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -36.40 ...((((((..[[[[[[[[[[[....))))))(((((..]]]]........(((((.....))))).))))).........]]]]]]].. New CC sens: 0.214, New CC ppv: 0.222, New CC F-measure: 0.218, New CC Energy: -36.32 .((((((((..[[[[[[[......[[[[[...))))))))(....)...((((((((......))))))))....]]]]].]]]]]]].. New CC sens: 0.714, New CC ppv: 0.690, New CC F-measure: 0.702, New CC Energy: -35.99 ...........(((((((......((((((..(((.....)))......((((((((......))))))))...)))))).))))))).. New CC sens: 0.500, New CC ppv: 0.583, New CC F-measure: 0.538, New CC Energy: -35.84 ....(((((..(((.(((((......))))).))).)))))((..((((((((((((......)))))))).))))))............ New CC sens: 0.429, New CC ppv: 0.444, New CC F-measure: 0.436, New CC Energy: -35.75 ...........(((((((((((..[[[[[(((....)))))))......((((((((......))))))))....]]]]].))))))).. New CC sens: 0.500, New CC ppv: 0.519, New CC F-measure: 0.509, New CC Energy: -35.48 ...........(((((((((......))...(((((....(....)...((((((((......))))))))...)))))..))))))).. New CC sens: 0.500, New CC ppv: 0.609, New CC F-measure: 0.549, New CC Energy: -35.40 ...........(((((((......((((((..(((.....)))..)...((((((((......))))))))....))))).))))))).. New CC sens: 0.500, New CC ppv: 0.583, New CC F-measure: 0.538, New CC Energy: -35.34 ....(((((..[[[[[[[(((........)))....)))))....((((((((((((......)))))))).)))).....]]]]]]].. New CC sens: 0.750, New CC ppv: 0.778, New CC F-measure: 0.764, New CC Energy: -35.33 New CC F-measure-avg: 0.564, New CC F-measure-best: 0.931, New CC best-subopt: 3, 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: -16.06 Initial sens: 0.600, Initial ppv: 0.667, Initial F-measure: 0.632, Initial Energy: -17.60 New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -17.60 ((((..[[[[[[.)))).....]]]]]]. New CC sens: 1.000, New CC ppv: 1.000, New CC F-measure: 1.000, New CC Energy: -16.06 ((((.(((((....))...))).)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -7.90 ......((((((..........)))))). New CC sens: 0.600, New CC ppv: 1.000, New CC F-measure: 0.750, New CC Energy: -7.59 ...((([[[[[[.)))......]]]]]]. New CC sens: 0.600, New CC ppv: 0.667, New CC F-measure: 0.632, New CC Energy: -7.22 (((([[[[[[...))))...]]]]]]... New CC sens: 0.400, New CC ppv: 0.400, New CC F-measure: 0.400, New CC Energy: -6.64 ((((((((....)))).......)))).. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.24 ....((((....))))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -6.10 ((((.........))))............ New CC sens: 0.400, New CC ppv: 1.000, New CC F-measure: 0.571, New CC Energy: -5.60 ..(((........)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.10 ....((((((..........))))))... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -5.09 ...(((.......)))............. New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.80 (((.((((....))))....)))...... New CC sens: 0.000, New CC ppv: 0.000, New CC F-measure: 0.000, New CC Energy: -4.75 New CC F-measure-avg: 0.307, New CC F-measure-best: 1.000, New CC best-subopt: 1, New CC num-subopt: 12