10        20        30        40        50        60        70        80        90       100       110       120                    
                      ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                             I                              TEMPLATE                          III                    III           I           
structure             ((((((((((((                         CAAAACCCCAA            <<<<      (((((((( >>>>          ))))))))   ))))))))))))   ( 
Euplotes aediculatus  aguuucucgauaauugaucuguagaauc--ugucaagcaaaaccccaaaaccuuacacugagagcauuuagccugauuacucuu--uaaaucaaaucaggcaa-uagagagaaacucg-a 
Euplotes eurystomus   aguuucucgauaauugaucuguagaauc--ugucaagcaaaaccccaaaaccuuacacugagagcauuuagcuugauuacucuu--uaaauuaaaucaggcaa-uagagagaaacucg-a 
Euplotes crassus      -guucuccauugacuaauccgucaaauc--ugucaaacaaaaccccaaaaccgaucaauaggugcguuuagcuugauuacaccucuuaaaugaaaucuugcaa-uucuggagagcuug-a 
Oxytricha nova        agcuggug-ga-agugcgucagucauagcacugucaacaaaaccccaaaaccguaaacucagagcaauucgccugguuccucuu-uaaagcaaaaccaggagguu-ccgcc-agcuacca 
Oxytricha trifallax   agucggcg-ga-aaucagucagucauagcgcugucaacaaaaccccaaaaccguaaaauuagagcaauucgccugguuccucuu-uaaagcaaaaccaggaggcu-ccgccga-cu--ca 
Stylonychia mytilis   aguucggcgga-aauccgucagcuauaacgcugucaagaaaaccccaaaaccguaaauugagagcaauucgccugguuccucuu-uaaaguuaaaccaggaagcu-ccgccgaacu---a 
Stylonychia lemnae    aguucggcgga-aauccgucagcuauaacgcugucaagaaaaccccaaaaccguaaaaugagagcaauucgccugguuccucuu-uaaagucaaaccaggaggcu-ccgccggacu---a 

                              130       140       150       160       170       180       190       200       
                      ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|..
                                         IV                                     IV                       
structure             ((((          ((((((((((((            (((((    )))))   ))))))))))))))))))          
Euplotes aediculatus  gaggugaaaaccccacagcauucugaaaugua---uuuggga-guaa-ucucauauuaguuugcugu-ccucucau-cuuuu 
Euplotes eurystomus   gaggugaaaaccccacagcauucugaaaugua---uuuggga-guaa-ucucauauugguuugcugu-ccucucau-cuuuu 
Euplotes crassus      gaggugaaacccccacaguuaggucaaacauag--uuugagauuuguaucucauaugcucuagcugu-ccucucau-c--uu 
Oxytricha nova        gaggacgaagu----gggcuaagugaaaugaaa-auuugagaguuu-cucuc-caucacuuagccccgccucucauucuuuu 
Oxytricha trifallax   gagggcacugu----gggcugagcaaaaugaaa-auuugagaguuu-cucuc-cauugcuuagcccuaccucu-au-cuuuu 
Stylonychia mytilis   gaggucgauaa----gggcugaguaaaauacugcauuugagagcuu-cucuc-cauugcaaaguccucccucuc-uucuuuu 
Stylonychia lemnae    gaggucgaaaa----ggacugaguaaaauacugcauuugagaguuu-cucuc-cauugcaaaguccucccucuc-uucuuuu