Testset with pseudoknots in dot-bracket notation. Note that we do not report the secondary structure for a pseudoknotted sequence, only the published pseudoknots. DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model J. Sperschneider and A. Datta. 2009 ----------------- >5SColi UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU ((((((((((.........((((....)))).((((((((((.....(((....)))...(((((.......))))).))))))))))..(((.(((....))))))..)))))))))). >5SDmobilis ACGGUGCCCGACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAUCGGGCACC ..(((((((((((((((....((((((((..(((..((((.............))))..)))...)))))))).(((((((....((((((.((....))))))))....))))))))))))).))))))))) >DA0260 GGGCGAAUAGUGUCAGCGGGAGCACACCAGACUUGCAAUCUGGUAGGGAGGGUUCGAGUCCCUCUUUGUCCACCA ((((((.........((....))..((((((.......))))))..((((((.......)))))))))))).... >DC0010 GUCGGGGUAGCUCAAAAGGUAGAGUGCAGGCCAACAUAGCCAGCAGAUCUCGGUUCAAACCCGAGCCCUGACC (((((((..((((........))))((.(((.......))).))....(((((.......)))))))))))). >DY4441 CCGACUUUAGCUCAGUUGGUAGAGCGGAGGACUGUAGAUCCUUAGGUCGCUGGUUCGAAUCCGGCAAGUCGGA (((((((..((((........)))).(((((.......))))).....(((((.......)))))))))))). >Dros-mel AUUUGACUACGAAACCGGUUUUCGAUUUGGUUUGACUGUUUUUCAUACAAGUGAGAUCAUUUUGAAAGCUGAUUUUGUCAA ..(((((...((((.((((((((((..((((((.(((((.......)).))).))))))..)))))))))).))))))))) >ath-MIR156a CAAGAGAAACGCAAAGAAACUGACAGAAGAGAGUGAGCACACAAAGGCAAUUUGCAUAUCAUUGCACUUGCUUCUCUUGCGUGCUCACUGCUCUUUCUGUCAGAUUCCGGUGCUGAUCUCUUU .((((((...(((..(((.(((((((((((((((((((((.(((((((((..((((......)))).))))))...))).))))))))).))).))))))))).)))...)))...)))))). >Human-mi CCAGAGGUUGUAACGUUGUCUAUAUAUACCCUGUAGAACCGAAUUUGUGUGGUAUCCGUAUAGUCACAGAUUCGAUUCUAGGGGAAUAUAUGGUCGAUGCAAAAACUUCA ...((((((....(((((.((((((((.((((.(((((.((((((((((..(((....)))...)))))))))).))))))))).)))))))).)))))....)))))). >HDV UGGCCGGCAUGGUCCCAGCCUCCUCGCUGGCGCCGGCUGGGCAACAUUCCGAGGGGACCGUCCCCUCGGUAAUGGCGAAUGGGACCC .(((((((..[[[[[[[(((.[[.....))))))))))]]....(((((((((((((...))))))))).)))).....]]]]]]]. >HDVanti GGGUCGGCAUGGCAUCUCCACCUCCUCGCGGUCCGACCUGGGCAUCCGAAGGAGGACGCACGUCCACUCGGAUGGCUAAGGGAGAGCCACU (((((((........[[[[(((.......))))))))))...(((((((....((((....))))..)))))))......]]]]....... >CrPV GCAAAAAUGUGAUCUUGCUUGUAAAUACAAUUUUGAGAGGUUAAUAAAUUACAAGUAGUGCUAUUUUUGUAUUUAGGUUAGCUAUUUAGCUUUACGUUCCAGGAUGCCUAGUGGCAGCCCCACAAUAUCCAGGAAGCCCUCUCUGCGGUUUUUCAGAUUAGGUAGUCGAAAAACCUAAGAAAUUUACCUG .((((((((......(((((((((..........[[[[[[........)))))))))....))))))))....((((..((((....)))).....[[[[.[[[[[))))((((.....))))..]]]]].]]]]..]]]]]]...((((((...(((.[[[[[)))..)))))).........]]]]]. >BCV GAGAAUGAACCUUAUGUCGGCACCUGGUGGUAAGCCCUCGCAGGAAAGUCGGGAUAAGGCACUCUCUAUCAGAAUGGAUGUCUUGCUGCUAUAAUAGAUAGAGAAGGUUAUAGCAGACUAUAGAUUAAUUAGUUGAAAGUUUUGUGUGGUAAUGUAUAGUGUUGGAGAAAGUGAAAGACUUGCGGAAGUAAUUGCCGACAAGUGCCCAAGGGAAGAGCCAGCAUGUUAAGUUACCACCCAGUAAUUAGUAAAUGAAUGAAGUUAAUUAUGGCCAAUUGGAAGAAUCACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ..............................................................((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]]..................................................................................................................................................................................................................................... >MHV AGAGAAUGAAUCCUAUGUCGGCGCUCGGUGGUAACCCCUCGCGAGAAAGUCGGGAUAGGACACUCUCUAUCAGAAUGGAUGUCUUGCUGUCAUAACAGAUAGAGAAGGUUGUGGCAGACCCUGUAUCAAUUAGUUGAAAGAGAUUGCAAAAUAGAGAAUGUGUGAGAGAAGUUAGCAAGGUCCUACGUCUAACCAUAAGAACGGCGAUAGGCGCCCCCUGGGAAGAGCUCACAUCAGGGUACUAUUCCUGCAAUGCACUAGUAAAUGAAUGAAGUUGAUCAUGGCCAAUUGGAAGAAUCACAAAAAAAAAAAAAA ...............................................................((((((((...............[[[[[[[[[[.))))))))..]]]]]]]]]]...................................................................................................................................................................................................... >NeRNV AGCCUCUCACAGCUUCCUCGUGAGGGUGGCGCACACCACAGUGCGUAGUGUUUCGGCUUCCACUUAAAUCGAAAGCCAACCCCUCCAGUUUUCUGGUUGUUCCUUGGAUUGCUACGUUCACCAGAUUUGUGUAAUCUGGCCGUUAGGAACUUAAAAUUGCGCGGAGUUCGAAUCUCCCCCUGUCCCGGGUAGGGAACC (((..[[[[[.))).....]]]]](((.[[[[[[)))...]]]]]]((((....[[[[[[))))......].]]]]].....................((((((.....[[[((((....(((((((.....))))))).))))))))))........]]]................(((..[[[[)))..]]]]... >TMV UGCAACUUGAGGUAGUCAAGAUGCAUAAUAAAUAACGGAUUGUGUCCGUAAUCACACGUGGUGCGUACGAUAACGCAUAGUGUUUUUCCCUCCACUUAAAUCGAAGGGUUGUGUCUUGGAUCGCGCGGGUCAAAUGUAUAUGGUUCAUAUACAUCCGCAGGCACGUAAUAAAGCGAGGGGUUCGAAUCCCCCCGUUACCCCCGGUAGGGGCCCA ((((.(((((.....))))).)))).........(((((.[[[[)))))...]]]](((.[[[[[[)))...]]]]]]((((.....[[[[[))))......].]]]].(((((((....[[[[((((.....((((((((.....))))))))))))))))))).......]]]]((((.......))))(((...[[[[)))..]]]].... >Ecoli-tmRNA GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAGUGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGUUCAACUCCCGCCAGCUCCACCA (((((((.............((((((((.......((..((((((((((((((.[[[[[[..))))).....]]]]]].............................((((((((((.........)))).))))))(((((((((((..(((...[[[[[)))..))))....)))))))..........]]]]]...((((...((((..[[[[[[))))...))))..........]]]]]]..((((((((((.(((.[[[.[[[))).)))))))))).........]]].]]]...)))))...))))..))......))))))))...(((((.......)))))))))))).... >LP-tmRNA GUGGGUUGCAAAACCGGAAGUGCAUGCCGAGAAGGAGAUCUCUCGUAAAUAAGACUCAAUUAAAUAUAAAUGCAAACGAUGAAAACUUUGCUGGUGGGGAAGCUAUCGCUGCCUAAUAAGCACUUUAGUUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGUAUCCCGUUCGACCGAGCCCGCUUAUCGGUAUCGAAUCAACGGUCAUAAGAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUAUGGCGCGAAACUCAGGGAAUCGCUGUGUAUCAUCCUGCCCGUCGGAGGAGCCACAGUUAAAUUCAAAAGACAAGGCUAUGCAUGUAGAGCUAAAGGCAGAGGACUUGCGGACGCGG ...........................(((((..[[[.[[))))).......]]]]]......................................................................(((.(((....((((.[[[[[[[..........)))).....))).)))............]]]]]]]........(((((((((........................[[[[[[[))))))).))...]]].]]]]...((((((..((.(((.[[[.[[[))).))..))))))...........]]]..]]]........................................ >HIV1-1.3a GAAUAUCUUCCGAAGCCGAACGGGAAAACCGGCAUCU .......(((((..[[[[..)))))....]]]].... >LRSVbeta AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAUUUUAAUUUUUAAAUUAGGAUUUGCUUAAUACAGAGACUGCGACGCCUAUAAACGGGUUCGUAGGGUUGUGUAUUAGGAAUUGGUGAUUAUUUCCGCUUACUCCUGUGCGGAUGCAACAAUGUUUUGACAUUGAUCACUGAGUUUCAGACUGACUAACAGUCUGGGAUCCCCCAAGGGAGACCA .....................................................................................................................((((((((....(((((...[[[[[..))))).....((((((....)))))))))))))).((((((((((.....))))))))))........]]]]].... >TYMV CCUAAGUUCUCGAUCUUUAAAAUCGUUAGCUCGCCAGUUAGCGAGUCUGUCCCCACACGACAGAUAAUCGGGUGCAACUCCCGCCCCUUUUCCGAGGGUCAUCGGAACCA ...(((....[[[[)))....]]]]....(((((......)))))((((((.......))))))....((((.......))))(((....[[[[[)))...]]]]].... >BWYV AAGGAAUUCUAAGGGAAACGGAGUGCGCGGCACCGUCCGCGGAACAAACGGAGAAGGCAGCUCCAAAUG .........................[[[[[..(((.]]]]].......)))................... >JEV CCCUUUUCAGCUGGGCCUUCUGGUGAUGUUUCUGGCCACCCAGGAGGUCCUUCGCAAGAGGUGGACGGCCAGAUUGACCAUUCCUGCGGUUUUGGGGGCCCUACUUGUGCUGAUGCUUGGGGGCAUCACUUACACUGA ............(((((((((((.......[[[[[[[..)))))))))))................]]]]]]]................................................................. >MVEV UCCUUUUCAGUUAGGCCUUCUGGUGAUGUUUCUGGCCACCCAGGAGGUCUUGAGGAAGAGGUGGACGGCCAGACUUACUCUGCCAGCAGCGGUUGGGGCUCUGCUAGUCCUCCUCCUUGGGGGCAUUACCUACACUGA ............(((((((((((.......[[[[[[[..)))))))))))................]]]]]]]................................................................. >VMV GGGAAACAACAGGAGGGGGCCACGUGUGGUGCCGUCCGCGCCCCCUAUGUUGUAACAGAAGCACCACCCAAAAUAGAAA .............(((((((.....[[[[[[[.......)))))))..............]]]]]]]............ >SARS-CoV UUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCACUAGUACUGAUGUCGUCUACAGGGCUUUUGAUAUUUACAACGAAAAAGUUGCUGGUUUUGCAAAGUUCCUAAAAACUAAUUGCUGUCGCUUCCAGGAGAAGGAUGAGGAAGGCAAUUUAUUAGACUCUUACUUUGUAGUUAAGAGGCAUACUAUGUCUAACUACCAACAUGAAGAGACUAUUUAUAACU .............((((((((((...[[[[[[[))))))))))(((((((((.........))).))))))..]].]]]]]................................................................................................................................................................... >Human-telo GGGUUGCGGAGGGUGGGCCUGGGAGGGGUGGUGGCCAUUUUUUGUCUAACCCUAACUGAGAAGGGCGUAGGCGCCGUGCUUUUGCUCCCCGCGCGCUGUUUUUCUCGCUGACUUUCAGCGGGCGGAAAAGCCUCGGCCUGCCGCCUUCCACCGUUCAUUCUAGAGCAAACAAAAAAUGUCAGCUGCUGGCCCGUUCGCCCCUCCCGGGGA ................................................................((((((((.....(((((.......(((((((((........[[[[[[[[[)))))))))..)))))....))))).))).............................]]].]]]]]]........................... >Tetra-telo AUACCCGCUUAAUUCAUUCAGAUCUGUAAUAGAACUGUCAUUCAACCCCAAAAAUCUAGUGCUGAUAUAACCUUCACCAAUUAGGUUCAAAUAAGUGGUAAUGCGGGACAAAAGACUAUCGACAUUUGAUACACUAUUUAUCAAUGGAUGUCUUAUUUU ...(((((..........(((.(((.....))).)))...............................((((...[[[[.[[[))))....]]].]]]]...)))))....(((((.(((..((((.((((.......))))))))))))))))..... >HPeV1 5'UTR UUUGAAAGGGGUCUCCUAGAGAGCUUGCCUAGGGCCUUAUAACCCGACUUGCUGAGCUUCUAUAGGAAAAAACCCUUUCCCAGCCUUGGGGUGGCUGGUCAAUAAAAACCCCCAUAGUAACCAACACCUAAGACAAUUUGAUCAACCCUAUGCCUGGUCCCCACUAUUCGAAGGCAACUUGCAAUAAGAAGAGUGGAACAAGGAUGCUUAAAGCAUAGUGUAAAUGAUCUUUUCUAACCUGUAUUAUGUACAGGGUGGCAGAUGGCGUGCCAUAAAUCUAUUAGUGGGAUACCACGCUUGUGGACCUUAUGCCCACACAGCCAUCCUCUAGUAAGUUUGUAAAAUGUCUGGUGAGAUGUGGGAACUUAUUGGAAACAACAAUUUGCUUAAUAGCAUCCUAGUGCCAGCGGAACAACAUCUGGUAACAGAUGCCUCUGGGGCCAAAAGCCAAGGUUUGACAGACCCAUUAGGAUUGGUUUCAAAACCUGAAUUGUUGUGGAAGAUAUUCAGUACCUAUCAAUCUGGUAGUGGUGCAAACACUAGUUGUAAGGCCCACGAAGGAUGCCCAGAAGGUACCCGCAGGUAACAAGAGACACUGUGGAUCUGAUCUGGGGCCAACUACCUCUAUCAGGUGAGUUAGUUAAAAAACGUCUAGUGGGCCAAACCCAGGGGGGAUCCCUGGUUUCCUUUUAUUGUUAAUAUUGACAUU ...............................................................................((((((..[[[[[)))))).........]]]]]..................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................... >T2 CUGACCAGCUAUGAGGUCAUACAUCGUCAUAGCACCAACUGUUAAUUAAAUUAAAAAGGAAAUAAAAAUGUUUAAACGUAAAUCUACUGCUGAACUCGCUGCACAAAUGGCUAAACUGGCUGGAAAUAAAGGUGGUUUUUCUUCUGAAGAUAAAGGCGAGUGGAAACUGAAACUCGAUAAUGCGGGUAACGGUCAAGCAGUAAUUCGUUUUCUUCCGUCUAAAAAUGAUGAACAAGCACCAUUUGCAAUUCUUGUAAAUCACGGUUUCAAGAAAAACGGUAAAUGGUAUAUCGAAAAUUGCUCAUCUACCCACGGUGAUUACGAUUCUUGUCCAGUAUGUCAGUACAUCAGUAAAAAUGAUUUGUACAACACUGACAAUAAAGAGUACGGUCUUGUUAAACGUAAAACUUCUUACUGGGCUAACAUUCUUGUAGUAAAAGAUCCAGCUGCUCCAGAAAACGAAGGUAAAGUAUUUAAAUACCGUUUCGGUAAGAAAAUCUGGGAUAAAAUCAAUGCAAUGAUUGCAGUUGAUGUUGAAAUGGGUGAAACUCCGGUUGAUGUAACUUGUCCGUGGGAAGGUGCUAACUUUGUACUGAAAGUUAAACAAGUUUCCGGAUUUAGUAACUACGACGAAUCUAAAUUCCUGAAUCAAUCUGCGAUUCCAAACAUUGACGAUGAAUCUUUCCAGAAAGAACUGUUCGAACAAAUGGUUGACCUUUCUGAAAUGACUUCUAAAGAUAAAUUCAAAUCGUUUGAAGAACUGAGCACUAAGUUUAGUCAAGUUAUGGGAACUGCUGCUAUGGGUGGUGCCGCAGCGACUGCUGCUAAGAAAGCUGAUAAAGUGGCUGAUGAUUUGGAUGCAUUCAAUGUUGAUGACUUCAAUACAAAAACUGAAGAUGAUUUUAUGAGCUCAAGCUCUGGCAGUUCAUCUAGUGCUGAUGACACG .(((((.[[[[[[[))))).......]]]]]]]................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. > T4 CCGGAAGUUAGAGAGCAUAUGAGAUUGGCUAAUUAUAUGAACCGUGACGAUUUUAGACCUUGGAAAACAUCACGAGCUAAUAUAGAGUCUUGGAAAUUAUCUCAUAUUGCUUACGAGAAUUAUGUGUUAUUAUUAUCCUCUAAUCUGUACGGUAAAACUCCUGGAUGGCGAAGAGUUAAAGGUAAUAUAAAUAUAACUGAUACAACUGCUAAAUCGAUGGUAAAGUAUUUCAACUCAGGUUGGAUACCUCUCGAAGACCCAGAGUAUUGCGAAUUAUGCCAGCUAUGAGGUAAAGUGUCAUAGCACCAACUGUUAAUUAAAUUAAAUUAAAAAGGAAAUAAAAAUGUUUAAACGUAAAUCUACUGCUGAACUCGCUGCACAAAUGGCUAAACUGAAUGGCAAUAAAGGUUUUUCUUCUGAAGAUAAAGGCGAGUGGAAACUGAAACUCGAUAAUGCGGGUAACGGUCAAGCAGUAAUUCGUUUUCUUCCGUCUAAAAAUGAUGAACAAGCACCAUUCGCAAUUCUUGUAAAUCACGGUUUCAAGAAAAAUGGUAAAUGGUAUAUUGAAACAUGUUCAUCUACCCAUGGUGAUUACGAUUCUUGCCCAGUAUGUCAAUACAUCAGUAAAAAUGAUCUAUACAACACUGACAAUAAAGAGUACAGUCUUGUUAAACGUAAAACUUCUUACUGGGCUAACAUUCUUGUAGUAAAAGACCCAGCUGCUCCAGAAAACGAAGGUAAAGUAUUUAAAUACCGCUUUGGUAAGAAAAUCUGGGAUAAAAUCAAUGCAAUGAUUGCGGUUGAUGUUGAAAUGGGUGAAACUCCAGUUGAUGUAACUUGUCCGUGGGAAGGUGCUAACUUUGUACUGAAAGUUAAACAAGUUUCUGGAUUUAGUAACUACGAUGAAUCUAAAUUCCUGAAUCAAUCUGCGAUUCCAAACAUUGACGAUGAAUCUUUCCAGAAAGAACUGUUCGAACAAAUGGUUGACCUUUCUGAAAUGACUUCUAAAGAUAAAUUCAAAUCGUUUGAAGAACUUAAUACUAAAUUCGGUCAAGUUAUGGGAACUGCUGUGAUGGGCGGUGCUGCUGCAACUGCUGCUAAGAAAGCUGAUAAAGUGGCUGAUGAUUUGGAUGCAUUCAAUGUUGAUGACUUCAAUACAAAAACUGAAGAUGAUUUUAUGAGCUCAAGCUCUGGUAGUUCAUCUAGUGCUGAUGACACGGACCUGGAUGACCUUUUGAAUGACCUUUAAUAGAUUAUAUUACUAAUUAAUUGGGGACCCUAGAGGUCCCCUUUUUUAUUUUAAAAAUUUUUUCACAAAACGGUUUACAAGCAUAAAGCUU ....................................................................................................................................................................................................................................................................................((((.[[[[[[[)))).....]]]]]]]............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................