>pairs
.....AAAAA.............BBB...BBB.........bbb....bbb....................................CCCC......DDDDDDDDcccc..........dddddddd..........aaaaa............EEEEE..........EEE.....EEE.EEEEE.............EEEE........................eeee............eeeee.eee.eee...eeeee...........
>Paramecium primaurelia
UGACAAUUA----UAUGUUCAUU-UUC-UUUU-CAAAU-AGGAAA-GGAA-UC-AUAC--AACCCCAGAAACC-AU-CACA-AACAC--G--G---UA-UGUUAC-U---------AGUGUAACG-UAAU---UCUC-UAGUUAU--UCCCG---AA-G----------AUUGUCAAAUUUAGA-UGC-U-U---AUC-GU-AAAAAUCAGCAAAUCA---------U-ACGAACUAAAAGU-A-UCUAAAU-AGUUAUU-UU--GUAUAU-UUU
>Paramecium tetraurelia 
UGACA-UCA----UAUGUUCAUUCUUC-UUCU-CCAAU--AGGAAAGGAAGUC-AUAC--AACCCCAGAAACC-AU-UACA-AACA-----UGAG-UA-UGCUAC-----------AGUGUAGCG-UAAU---CCUC-UGG-UAU--UCUCG--UAA-G----------AUUGUCAAAUUUAGAGUGC-U-U---AUC-GUCAAAAAUCAGCAAAUCA---------UGACGAGUCAUAAGU-GCUCUAAAU-AGUUAUU-UUA--UAUUU-UUU
>Paramecium multimicronucleatum 
UGACAAUC-----UAUGCUCAUUCUUCCUUCU-GAUAG--GAGGG---GAGUC-AUAC--AACCCCAGAAACC-AUUUCCA-C--AA----UGAG-U--UGUUGC-----------UGUGCAAUG--AAU---AUUC--GGU-----ACUCUCAUU-AG----------A-UGUCAAAUUUAGAGC-A-UGUUCCA---UCAUUUCAAUAUUAUUCAUGAUGG---AAUGAUAAU--------GCUCUAAAU-G-UAUUUU-AA-UAUAUUAUUU
>Paramecium caudatum
UGACAAU-GCU--GUA-UUCAUUCUCCUUUCU-CGAUA---GGAAUUGGAGUC-AUAC--AACCCCAGAAACC-A--UCCU-UAUA----UUGA--GUAUGCUGAA---C--------GUUAGCGUAGCU---CUUGGC-AU-----UCUCA---AGUG----------AUUGCAU-AUUUGGAGU-U-ACUU--AUUCGUCAAUUCAAUUAAAAUUCA--------UGACGAACCUAAAAGUACUCUGAAU-GGU---UAUU--UUUAUA-AUU
>Colpidium colpoda
GUAUCCCCGC---AAC-UCCAUUCAG--UUC--GAAAU----GAA---CUGUC-AUUC--AACCCCAAAAAUCUAG-UAAAAAAUAUUGCC-G---A-ACUUUC-GGCAU------UAA-GAAAGU-AA--------GCGGG-----AU------AGAUA---------CUCCGA--C-UGUGAUA-C-ACU---AUU---------------------------------------------UAUCACA-GGGAG---AUCU---UUUUUAUUU
>Colpidium campylum 
AUAUCCCCGC---AAA-UUCAUUCUG--UUU--GCAUU----AAA---CAGUC-AUUC--AACCCCAAAAAUCUAG-ACCA-AAUAU---CUU---C-CUUCUU-G---A------AAC-AAGAAG-GAC-------GCGGG-----AUA----AAGAUA---------CUCCGA--CG-UUGAUA-C-AAU---AUU---------------------------------------------UAUCA--CGGGAG---GUCUU-ACUUUU-UUG
>Glaucoma chattoni
AGAUACCUCCUGUGGA-UCCAUUCAG--GAUU-AAUGA---AAUC---CUGUC-AUUC--AACCCCAAAAAUCUUG-UCAA-AUUAUUGCC-U---CG-CUUUUGGGCAC------AAACAAAAG-CACG-----CAGGAGG-----UU------AGACA---------UUCGA---CAUAAGAUA-C-ACU---AUU---------------------------------------------UAUCUUAUG-GAA--GGUCU-----GUU-UUU
>Tetrahymena silvana 
UUAUACCCGC---AAA-UUCACUCAA--AUCU-GUAAU---AGGU---UUGUC-AUUC--AACCCCAAAAAUCUAG-UGCA-AAUAUUACUUU---CGCCA-UUAGGUA-------UAAUAA-UGGUAA--------GCGGG-----AC-----AAGAC-----------UCGA---CAUUUGAUA-C-ACU---AUU---------------------------------------------UAUCA-AUG-GA----GUCUU----UUU-UCU
>Tetrahymena vorax  
UUAUACCCGC---ACA-UUCACUCAA--AUCU-GUAAU---AGAC---UUGUC-AUUC--AACCCCAAAAAUCUAG-UGCA-AAUAUUACCUU---CGCCA-U-AGGUA-------CAAU-A-UGGUUCU------CGCGGG-----ACAA---AAGACU---------AUCGA---CAUUUGAUA-C-AUU---AUU---------------------------------------------UAUCA-AUG-GAU---GUCUU-AUUUUU-CUU
>Tetrahymena borealis 
UUAUACCCGC---AAA-UUCAUUCAG--GUCU-GUAAU---AGAU---CUGUC-AUUC--AACCCCAAAAAUCUAG-UGCA-AAUAUUACCUU---CACCA-U-AGGUA-------UAAU-A-UGGUAUC-------GCGGG-----ACAA---AAGACU---------AUCGA---CAUUUGGUA-C-ACU---AUU---------------------------------------------UAUCA-AUG-GAU---GUCUU----AUU-UUU
>Tetrahymena thermophila
UUAUACCCGC---UUAAUUCAUUCAG--AUCU-GUAAU---AGAA---CUGUC-AUUC--AACCCCAAAAAUCUAG-UGCU-GAUAUAACCUU---CACCA-UUAGGUUC------AAAUAA-UGGUAAU-------GCGGG-----ACAA---AAGACU---------AUCGA---CAUUUGAUA-C-ACU---AUU---------------------------------------------UAUCA-AUG-GAU---GUCUU-AUUUUU-UUU
>Tetrahymena capricornis 
UUAUACCCGC---AUU-UUCAUUCAG--AUCU-UUAAU---GGAG---CUGUC-AUUC--AACCCCAAAAAUCUAG-UGCA-ACUACUGCCUU---AAC-ACUUAGGCA-------AAAUAAGU-GUAAA-------GCGGG-----AC-----AAGG-----------AUCGA---CAUUUGAU-CA-AAU---AUU----------------------------------------------AUCA-AUG-GAU----UCUU-AUUUUU-UAU
>Tetrahymena australis
UUAUACCCGC----AU-AUCAUUCAG--A-CC-UUUAU---GG-A---CUGUC-AUUC--AACCCCAAAAAUCUAG-UGCA-AAUAU-GUCUU---AA-UACUUAGGC-AAAAG--AAAUAAGUA-UAAA-------GCGGG-----AC-----AAGGC----------AUCGA---CAUUUGAU-CA-AAU---AUU----------------------------------------------AUCA-AUG-GAU---GUCUU----AUU-UUU
>Tetrahymena paravorax 
UUAAUCCCGC---UAU-UGCAUUC---------UUUCG--A---------GUC-AUUC--AACCCCAAAAUUCUAG-UACACACUAA-GCU------UGCCUUUGGGC--------UAUCAGGGGCA----------GCGGGAGA--AUU----UAGAAU---------UUCGA---CAUG-GGUA-C-ACU---AUU---------------------------------------------UAUC-CAUG-GAG--AUUCUA----AUU-UUU
>Euplotes aediculatus 
AGUUUCUC-----UAA-UUGA-UC-G--U----AGAAU----------C-GUC-AAGCAAAACCCCAAAACCUUA--CACU-GAGAG---UUU---AGCCUGAUUA---UUUAAA-UCAAAUCAGGCAAU------A--GAGAA---ACUCG--AGAGGUGAAAACCCCACA-----GCAU-CUGAAA-UGU---AUUUGGGAGU--------------------AAUCUCAUA---------UUAG-UUGC-UGU---CCUCU--CAUCU-UUU
>Euplotes eurystomus
AGUUUCUC-----UAA-UUGA-UC-G--U----AGAAU----------C-GUC-AAGCAAAACCCCAAAACCUUA--CACU-GAGAG---UUU---AGCUUGAUUA---UUUAAA-UUAAAUCAGGCAAU------A--GAGAA---ACUCG--AGAGGUGAAAACCCCACA-----GCAU-CUGAAA-UGU---AUUUGGGAGU--------------------AAUCUCAUA---------UUGG-UUGC-UGU---CCUCU--CAUCU-UUU
>Moneuplotes crassus 
GGAUAUAGGG---UAG-UUC-UCCA----UGA-CUAAUCCGUCAA-AU-UGUC-AAACAAAACCCCAAAACCG-AU-CAAU-AGGUG--G-UUAGCU-GAUU-CA-C--UU-----AAAUG-AAUC-UGC-----AAUUCUG---GAGAGCUUGAGAGGUGAAACCCCCACA-----GUUAGG-CA-AACAUA--GUUUGAGAUU------------------UGUAUCUCAUA---------UG-UCUAGC-UGU---CCUCUCAUCUUU-UUG
>Oxytricha nova
AGCUGGUGGA----AG-UGCG-UCAG-----U-CAUAG--CA------CUGUCAACAA--AACCCCAAAACCGUA--AACU-CAGAG----UU---C-CCUGGUU----UUUAAAGCAAAACCAGG-GGU-------UCCGCCAGCUACC----AGAGGACGAAG----UGG-----GCUAAGUGAAA-UGAAA-AUUUGAGAGU-------------------UUCUCUCCA----------UCACUUAGCCCCG---CCUCU-CAUUCU-UUU
>Oxytricha trifallax
AGUCGGCGGA----AA-UCAG-UCAG-----U-CAUAG--CG------CUGUCAACAA--AACCCCAAAACCGUA--AAAU-UAGAG----UU---C-CCUGGUU----UUUAAAGCAAAACCAGG-GGC-------UCCGCCG---ACUCA--GAGG-C---------A--GUGG-GCUGAGCAAAA-UGAAA-AUUUGAGAGU-------------------UUCUCUCCA----------UUGCUUAGC---U----CCUC--UAUCU-UUU
>Stylonychia mytilis
GUUCGGCGGA----AA-UCCG-UCAG----C--UAUAA----G-----CUGUCAAGAA--AACCCCAAAACCGUA--AAUU-GAGAG----UU---C-CCUGGUU----UUUAAAGUUAAACCAGG-AGC-------UCCGCCGA--ACU----AGAGGUCGAUA----AGG-----GCUG-GUAAAAUACUGC-AUUUGAGAGC-------------------UUCUCUCCA----------UUGC-AAGU-CCU--CCCUCU--CUUCU-UUU
>Stylonychia lemnae 
GUUCGGCGGA----AA-UCCG-UCAG----C--UAUAA----G-----CUGUCAAGAA--AACCCCAAAACCGUA--AAAU-GAGAG----UU---C-CCUGGUU----UUUAAAGUCAAACCAGG-GGC-------UCCGCCGG--ACU----AGAGGUCGAAA----AGG-----ACUG-GUAAAAUACUGC-AUUUGAGAGU-------------------UUCUCUCCA----------UUGC-AAGU-CCU--CCCUCU--CUUCU-UUU