10        20        30        40        50        60        70        80        90       100       110       120                    
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                                 I                    II         II         TEMPLATE                            III                 III          I   
structure                      (((((                ((((((     ))))))      CAACCCCAA                         ((((((((            ))))))))     )))))) 
Tetrahymena thermophila     AUACCCGC----UUAAUUCAU-UCAGAUCUGUAAUAGAACUGUCAUUCAACCCCAAAAAUCUAGUGCU-GAUAUAACCUUCACCAAUUAGGUU----CAAAUAAGUGGU-AAU--GCGGG 
Tetrahymena malaccensis     AUACCCGC----UUAAUUCAU-UCAGUUCUGUAAUAGAACUGUCAUUCAACCCCAAAAAUCUAGUGCU-GAUAUAACCUUCACCAAUUAGGUU----CAAAUAAGUGGU-AAU--GCGGG 
Tetrahymena pyriformis      AUACCCGC-----AUAUUCAU-UCAAAUCUGUAAUAGAUUUGUCAUUCAACCCCAAAAAUCUAGUGCA-ACUAAUACCUUCGCCAAUUAGUGU----AUAAUUAAUGGUUCUC--GCGGG 
Tetrahymena vorax           AUACCCGC-----ACAUUCAC-UCAAAUCUGUAAUAGACUUGUCAUUCAACCCCAAAAAUCUAGUGCA-AAUAUUACCUUCGCCAAUUAGGUA----CAAUUAA-UGGUUCUC--GCGGG 
Tetrahymena borealis        AUACCCGC-----AAAUUCAU-UCAGGUCUGUAAUAGAUCUGUCAUUCAACCCCAAAAAUCUAGUGCA-AAUAUUACCUUCACCAAUUAGGUA-----UAAUCAAUGGU-AUC--GCGGG 
Tetrahymena australis       AUACCCGC------AUAUCAU-UCAGACCCUUUAUGGAACUGUCAUUCAACCCCAAAAAUCUAGUGCA-AAUAUUGUCUUAAUUACUUAGGCUAAAAGAAAUAAGUAUU-AAA--GCGGG 
Tetrahymena silvana         AUACCCGC-----AAAUUCAC-UCAAAUCUGUAAUAGGUUUGUCAUUCAACCCCAAAAAUCUAGUGCA-AAUAUUACUUUCGCCAAUUAGGUA-----UAAUAA-UGGU-AA---GCGGG 
Tetrahymena pigmentosa      AUACCCGC--------AUCAU-UCAGAUCUAUUAUGGAGCUGUCAUUCAACCCCAAAAAUCUAAUGCA-ACUACUGCCUUAACUAUUUAGGCA--UUAUAAUAAAUAUA-AAA--GCGGG 
Tetrahymena hyperangularis  AUGCCCGC--------AUCAU-UCAGAUCUAUUAUGGAGCUGUCAUUCAACCCCAAAAAUCUAAUGCA-A-UACUGCCUUAACUAUUUAGGCA--UAAUAAUAAAUAUA-AAA--GCGGG 
Tetrahymena capricornis     AUACCCGC-----AUUUUCAU-UCAGAUCUUUAAUGGAGCUGUCAUUCAACCCCAAAAAUCUAGUGCA-ACUACUGCCUUAACUACUUAGGCA-----AAAUAAGUCGU-AAA--GCGGG 
Tetrahymena hegewishii      AAACCCGC-----AUACUCAU-UCAGAUCUGUAAUGGUUCUGUCAUUCAACCCCAAAAAUCUAGUGCU-ACUACUGCCUUAACUACUUAGGCA-----AAAUAAGUUGG-AAA--GCGGG 
Glaucoma chattoni           A--CCUCCUG-GUAGAUCCAU-UCAGGAUUAAUGAAAUCCUGUCAUUCAACCCCAAAAAUCUUGUCAA-AUUAUUGCCU-CGUCUUUUGGGCA----ACAACAAAAGUC-ACGCAGGAGG 
Tetrahymena paravorax       AAUCCCGCUAUUGCAUUCCAUUUCGA---------------GUCAUUCAACCCCAAAAUUCUAGUACACACUAAAGCUU---GCCUUUGGGCA-----UAUCAGGGGC------AGCGGG 

                                    130       140       150       160       170          
                            ....|....|....|....|....|....|....|....|....|....|....|...
                                           IV                        IV                
structure                   )    ((((((((((  (((((((((        ))))) ))))) ))))))       
Tetrahymena thermophila     -ACAA-AAGACUAUCGACAUUUGAUAC-ACUAUUUAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena malaccensis     -ACAA-AAGACUAUCGACAUUUGAUAC-ACUAUUUAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena pyriformis      -ACAA-AAGACUAUCGACAUUUGAUAC-ACUAUUUAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena vorax           -ACAA-AAGACUAUCGACAUUUGAUAC-AUUAUUUAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena borealis        -ACAA-AAGACUAUCGACAUUUGGUAC-ACUAUUUAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena australis       -ACAA---GGC-AUCGACAUUUGAUACAAAUAUUGAUCA-AUGGA-UGUCUUAUUU-U 
Tetrahymena silvana         -AC---AAGAC--UCGACAUUUGAUAC-ACUAUUUAUCA-AUGGA-UGUCUU-UUU-U 
Tetrahymena pigmentosa      -AC----GGAC-AUCGACAUUGGAUCCUAAUAUUGACCA-AUGGA-UGUCUU-UUUUU 
Tetrahymena hyperangularis  -AC----GGAC-AUCGACAUUGGAUCCUAAUAUUGACCA-AUGGA-UGUCUU-UUUUU 
Tetrahymena capricornis     -AC---AAGGC-AUCGACAUUUGAUACAAAUAUUGAUCA-AUGGA-UAUCUUAUUUUU 
Tetrahymena hegewishii      -AC---AAGGC-AUCGACAUUUGAUACAAAUAUUGAUCA-AUGGA-UGUCUUAUUU-U 
Glaucoma chattoni           -UUCA--GGUG-UUCGACGUAAGAUAC-ACUAUUUAUCUUAUGGAAUGCCAAGUUU-U 
Tetrahymena paravorax       AGAAUUUAGAAUUUCGACAUGUGGUAC-ACUAUUUAUCUCAUGGAGAUUCUAAUUU-U