10        20        30        40        50        60        70        80        90       100       110       120                    
                                ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                      I                  II           II          TEMPLATE                              III         III      V           
structure                       (((((((((((((        (((((((((     )))))))))      CAACCCCA                      <<<<  ((((((>>>>   ))))))  (((((      )) 
Paramecium tetraurelia          gacaaucauuauguucauuc-uucuucuccaa-uaggaaaggaagucauacaaccccagaaaccauuacaaacacccu--gaguauugcuacauucaguguagcguuaauccucu--ugg 
Paramecium primaurelia          gacaaucauuauguucauuc-uuccucuccaa-uaggaaaggaagucauacaaccccagaaaccauuaaacacacccu--gaguauugcuacauucauuguagcguuaauccucu--ugg 
Paramecium multimicronucleatum  gacaaucuuuaugcucauuc-uuccu-ucuga-uagga-ggggagucauacaaccccagaaaccauuuccacaacccugaguauu--guugcauacugugcaau---guaaauauuc-uu 
Paramecium caudatum             gacaauugcugu-auucauucuccuuucucga-uaggaauuggagucauacaaccccagaaaccau-ccuuauaccuu--gagua-ugcugaauuccg-uuagcguagcu-c--uug-gc 
Paramecium primaurelia(pseudo)  gacaauuauuauguucauuc-uuc-uuuucaaauaggaaaggaaaucauacaaccccagaaaccaucacaaacacua---gaguauuguuacauauaguguaacguuaauucucuuaguu 

                                        130       140       150       160       170       180       190       200       210       220         
                                ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|..
                                 V             I                 IV                                    IV                              
structure                       )))))    )))))))))))))  (((((((((((((((((((((((                  ))))))))))))))))))))))))))            
Paramecium tetraurelia          cuauu-cu-cguaacgauugucaaauuuagagu-gcuuau-cguc-aaaaaucagcaaa---uca-ugacgag-ucauaagugcucuaaauaguuauuuu-u 
Paramecium primaurelia          cuauu-cu-cguaacgauugucaaauuuagagu-gcuuau-cguc-aaaaaccagcaaa---uca-ugacgag-ucauaagugcucuaaauaguuauuuu-u 
Paramecium multimicronucleatum  gguacucu-cauuuagauugucaaauuuagag-ca-uguuccaucauuu---caauauua-uuc-augauggaaugauaa-ugcucuaaau-guuauuuu-u 
Paramecium caudatum             uauuc--ucauagu-gauug-cauauuuggaguuacuuauucguc-aauu--caauuaaaauuca-ugacgaaccuaaaaguacucugaaugguuauuuuuu 
Paramecium primaurelia(pseudo)  auucccgu--aa--cgauugucaaauuuagaau-gcuuau-cguc-aaaaaucagcaaa---uca-uaacgaacu-aaaaguacucuaaauaguuauuuuuu