10        20        30        40        50        60        70        80        90       100       110       120                    
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                                      I                                                              
structures                        (((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((((( 
Saccharomyces cerevisiae    GAGAGGAAGAUAGGUACCCUAUGAAAAUGUC-AAUGGCUGUUGCGUUUGCUUAAUCGUAUUUUUUUUUUUUUCAGUCCGU-GUUUUUUGUACAUUCUACGUUUGAGUUUUCCAUCAUGCA 
Saccharomyces paradoxus     CAAAGGAAGAUAGGUAACCUAUUAAAAUGUC-AGCGGCUGUUGCGUUUGCUUAGUUG--UUUUU-UUUU----AGUAUUUUUUU-UUUGUACGUUUUCCGUUUGAAUUUUCUAUCAUGCA 
Saccharomyces kudriavzevii  AUGAGG-AGGUCGGUUACCUAUUAAGAUGUC-CAUGGUCGUCACGUUUAGUUACUAGUAUUUUUUCUC--UUUUGUUUCU-GUUUUUUGUGCAUUUUCCAUUUGAGUUUUCUAUUGU-UG 
Saccharomyces cariocanus    UAGAGGAAGAUAGGUAGCCUAUUAAAAUGUC-AGCGGCUGUCGCGUUUGCUUAGUUG--UUUUU-UUUU----AGUAUUUGUCG-UCUGUACAUUUUCCGUUUGAAUUUUCUAUCAUGCA 
Saccharomyces bayanus       GAGAGGAAGGU-AGUAACCUAAUAAUACGUC-AGCGACUGGUAUGUUUGCCUGCCCUUUUUUUA---------UUUUG-CUUGUCAAUGUAUUUUUUCCAUUUGAGUUUUCUGUUG-AUA 
Saccharomyces pastorianus   GAGAGGAAGGU-GGUAACCUAAUAACACGUC-AGCGACUGGUAUGUUUGCUUGCCCUUUUUUAA----------UUUG-CUUCUCAAUGUAUUUUUUCCAUUUGAGUUUUCUGUUG-AUA 
Saccharomyces mikatae       AUGAGGAAGAUGCGUCGCCUAUUAAAAUGUCUGGCGGCUGUUACAUUUGCUUUCUAGCACUUUUCUAU--UCUCGUUUCC-UUUUUUUGUACCUUCCCCUUUUGAAUUUUCCAUCGUAUA 
                                                                                                                                                   ( 

                                    130       140       150       160       170       180       190       200       210       220       230       240           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                IIa                                             IIb                                I 
structures                  ((((((((     (((((((((((((((((((((((((((((((((((((((((((((           (((((((((((((((((((((((((((((((         ))))))))))) 
Saccharomyces cerevisiae    GGCCUCAGAAAUUUGGUAGGCACUCGAUGGUGAAGAGAUAGUGUCGGAUUUCGGAUUGAUCUUUCA-GUUGAUAGCCUGC-UGCUC--U----UUUCUUU------UCCAAAGAAUUUCG 
Saccharomyces paradoxus     AGCCUCAGAGAUUUGGUAGAUGCUUAAUGAUGUAAAGGUUGCGUUGAAUUUUGGAUUGUUCUCUCAAGUUAGCAGGCAG-GUGCAC--U----UUUCUCUUU----UACGAAGGACUUCG 
Saccharomyces kudriavzevii  AGCCUCAGAUAUUUGGUAGACGCUUAAUGGUGGAAUGAUUGGACCGGAUUUAGGGUUGUGUUCUCAGAUUGGCGGGCAGUUACACUGGUUGUUGUUUUUU------AACGAAGGGCUAUG 
Saccharomyces cariocanus    AGCCUCAGAGAUUUGGUAGAUGCUUAAUGAUGUAGAGGUUGCGAUGAAUUUUGGAUUGUUCUCUCAAGUUAGCAGGCAG-GU-CAC--U----UUUCUCUUU----UACGAAGGACUUCG 
Saccharomyces bayanus       AGCCUCAGAGUUUUGGUAGGCGCCUAGUGGUGGAAUGGUUGGGCUGGAAUCGGAAUUGAGAUGUGAUGUUAACGGGCCAUCGUGCAU---------CUUUUUUAAAUUUUGAGCAAUUUG 
Saccharomyces pastorianus   AGCCUCAGAGUUUUGGUAGGCGCCUAGUGGUGGAACGGUUGAGCCGGAAUCGCGAUUGAGAUGUGAUG-----GGGCCAUUGUGCAU---------CUUUUUUAUAUUUUGGGCAAUGCG 
Saccharomyces mikatae       AGCCUCAGAAAUUUGGUAGACACUUAAUGAUGAAUAGGUUGGGUUAGAUUU-GAUUUGAGAUCUUGAGUCACCAGGCAGU-CCCA----------AUUUUUUU---UACGAAAUAUUAGG 
                            ((((((((     ((((((((                                                                                                    
                              CS1     template boundary                                                                                              

                                    250       260       270       280       290       300       310       320       330       340       350       360           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                            Ib                             IIb 1                       IIc                                                       IIc 
structures                  ))))))))))))))))              ((((((        ((((((((((((((((((((((((((((((((((((                        )))))))))))))))) 
Saccharomyces cerevisiae    AGUAUGCU-GGUGUCAGU-GUAGAUG-CUUGUGU-GUGCGCA-AUU-UGUGGUUUUUUAUUGUGUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUUAGAAA-A 
Saccharomyces paradoxus     AGUGCACU-GGGGUCAGCAU-AGAUA-CUUGUGU-GUACGUAUAUU-UGUGGUUU-UUGUUAUUUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAAAGA 
Saccharomyces kudriavzevii  AGUGCGCU-GGUGUCAGUGU-AGAUA-CAUAUG-UAUGCG--UACA-UGUGGUUU-UUGUUGUUCUUCUACUUAUAGAUCGCU-----------------AAAAUCUGAGUUU-GA-GAA 
Saccharomyces cariocanus    AGUGCACU-GGGGUCAGCAU-AGAUA-CUUGUGU-GUACGUAUAUU-UGUGGUUU-UUGUUAUUUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAAAGG 
Saccharomyces bayanus       AGUACGCUAG-UGCCACUAU-GCAUGUUUCAUG-UAUACAUGUAUG-CGCGGUUU-CUGUUCUUGUCGUACUUAUAGAUCGCUACGUUAUUUCAAUUUUGAAAAUCUGAGUCC-UGG-GA 
Saccharomyces pastorianus   AGCACGCUAG-UGCCA-------------------------GUAUG-CGCGGUUU-CUGUUC-----GUACUUAUAGAUCGCUACGUUAUUUCAUUUUUGAAAAUCUGAG-CC-CGGGGA 
Saccharomyces mikatae       AGUGUGCU-GAUGUCAGCAU-AGAUG--AUGUAUUAUACAUGUUUUGUGUGGUU---UGCUAUAUUUCUACUUAUAGAUGGCU-----------------AAAAUCUGAGUUU-GAGA-G 
                                                                                       ((((((((((((((((((((                        ))))))))))))))))) 
                                                                                           Ku80 site                                      Ku80 site  

                                    370       380       390       400       410       420       430       440       450       460       470       480           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                  IId          IId                  IId 1              IId 1           |IIb1||---------------------- 
structures                  )))))))))))))))))  ((((((((((    ))))))))))     ((((((((((((((((((    )))))))))))))))      ))))))))))))))))))))))))))))) 
Saccharomyces cerevisiae    UGCA--AACCGUAAAUUCUUAAACACUGCUAUUGC-AUUUAGUUGCUAAAGCAGUGUUU--UUGAACUUAUUCCUGUUAUUCCUU--CUU-C-GUACCGAUCCUCUUCUC-GACCUAACC 
Saccharomyces paradoxus     UGGC--CACCAUAAAUUCUUAAAA-GUGGUAUCGC-AUUUAGCCCCC----------------------------------------CUU-C-GUACCAAUUCUGUUUUC-GUCUCAAGC 
Saccharomyces kudriavzevii  AUGCGGGACCAUCCAUGUCCGAAUAUAACUGACGC-AUUUUGUAGCUAGAACACGUUUU-UCCUA-CAA-UUA------UCCCGCUCCUCUUAG-AAAAAUUCUGCUUUC-ACUCCAA-C 
Saccharomyces cariocanus    UGGC--CACUAUAAAUUCUUAAAAAGUGGCACCGC-AUUUAGCCCCC----------------------------------------CUU-C-GUACCGAUUCUGUUUUC-GUCUCAAGC 
Saccharomyces bayanus       GUGCGGAGCCAUGCAUACAUGUACUUUAUUGUUGCAUAGUAUU-GCUAGAGUACACUUU-CUCCAUGA--UUG---UCUGU-CUU--CUU-UA-CACCAGUUCUGUUUUCUGUCUUAACC 
Saccharomyces pastorianus   GUGCGGAUCCAUACAUACAUGUAAUUUGUUGUUGC--AGUAUU-GCUAGAGUACAUUUUUCUCCGCGA--UUG---UCUGU-CUU--CUU-UA-CACCAGUUCUGUUUUCCGUCUCAACC 
Saccharomyces mikatae       CAGCA-UGCCACAGAUGCUUGGAUUUUACUAUUGG-AUUUUGCUGCCGGAAUAGGGCUU-UCGGGACAC-UUA------UUCCUUUGCUUA-AG-ACCAACUCUGUUUUC-GCCUUUGCC 
                            )))))))                                                                                                                  

                                    490       500       510       520       530       540       550       560       570       580       590       600           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                            ----------------IIa---------------------|     template                III       III                              IVa     
structures                  )))))))))))))))))))))))))))))))))))))))))  |||||||||||||||           ((((((    ))))))  ((((((((((((((((((((((((((((((((( 
Saccharomyces cerevisiae    UUUUAAUUACCAUG-----G-G---------AAGCCUACCAUCACCACACCCACACACAAAUGUUACAGCUAAUUGUUUAUUAGCAAAGUUUGCACGAGUUCGC-UGU-UUAUU-UUUUU 
Saccharomyces paradoxus     UCUUCAUUACUACA-----GCG--------CAAGUCUACCAUUACCACACCCACACACAGAUACCACGGCUAAU-GUUUAUUAGUUAAGUUUCCAUGAGCUCAC-UCU-UUAUUCUUUUC 
Saccharomyces kudriavzevii  UCUUCAUCA--UUU-----U-AUAAGAAUUU--GUCUACCAUUACCACACCCACACACAAACAUUACGGCUAGUAGUUUAUUAGUCAAAUUUCCAU-G-GCCACACAUUUUGUC-UUUUU 
Saccharomyces cariocanus    UCUUCAUUACUACA-----GCG--------CAAGUCUACCAUUACCACACCCACACACAGAUAUUACGGCUAAU-GUUUAUUAGUCAAGUUUCCAUGAGCUCAC-UCU-UUAUUCUUUUU 
Saccharomyces bayanus       UCUUCACUA--UCAUGGAAA-G--------U--UUCUACCAUUACCACACCCACACACGAACAUUAAGGCUAAUCGUU-AUUAGUUCAAUCUCCAUA-----GC-CACAC-----UCUUU 
Saccharomyces pastorianus   UCUUCAUUA--UUAUGGAAA-G--------C--AUCUACCAUUACCACACCCACACACGAACGUUAAGGCUAAUCGUU-AUUAGUUGAAUCUCCAUA-----GC-CAAGC-----UCUUU 
Saccharomyces mikatae       CCUUCAUCA--UUA-----U-ACAAAA---U--GUCUACCAUUACCACACCCACACAUUGAUAUUAUGACUAAUUGUUUAUUAGCUAAGUUCCCAU-G-GCCAC-UUU-UUACU-UUUUU 
                                                             ))))))))                                                                                
                                                         template boundary                                                                           

                                    610       620       630       640       650       660       670       680       690       700       710       720           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                      IVb                IVb                        IIc                                       IVc    
structures                  ((((((((((           ((((((((((((((     ))))))))))))))   (((((((((((((((((((((((((((((((((((     ))))))))))))))))))))))) 
Saccharomyces cerevisiae    CUCGUUUUCUUAUACCUAGUAUUUUUUCUGACACUGUUUAAGGUGACAGAAAAAA-AGGAGUUUA-AGUUAGAUUUGCAAA-CAGACGGUGCUA--AGCGCUGUCACU-UU-AUGUCUAU 
Saccharomyces paradoxus     CUCGUUUUCUUAUACCUAGUAUGUUUUCUGGCGCUUUUUGAAGUGACAGAAAAAA--GGAGUUUA-AAUUAGAUUUGCAAA-CGGACGGUACUA--AAUACCGUCACU-UUUACGUCUAA 
Saccharomyces kudriavzevii  CUCGUUUUCUUAU------UGUGUUUUCUGUCACUGUG-AAAGUGACGGAGAAAA-AGGAGUUUGGAAUCAGAUUUGCAAAACGGGCUGUAUCAAUAAUACUGUCAUUCCUAAUGUCUGA 
Saccharomyces cariocanus    CUCGUUUUCUUAUACCUAGUAUUUUUUCUGACGCUUUUUGAAGUGACAGAACAAA--GGAGUUUA-AAUUAGAUUUGCAAA-CGGACGGAACUA--AAUACUGUCACU-UUUAUGUCUAA 
Saccharomyces bayanus       UUUUCUUCC----------AAUAUUUUCCGUCGCUUUC-CAAGUGACAGAAAAAAAAGGAGUUUG-AAUUAGGCUUGCAAAAGGGACAAUAUAUAUGAUACUGUCACUCCUAAUGUCUAA 
Saccharomyces pastorianus   UUUUUUUC-----------AAUGUUUUCCGUCGCUUUC-CAAGUGACAGAAAAAA-AGGAGUUUG-AAUUAGGCUUGCAAAAGGGGCAAUAUCAAUGAUACUGUCACCCUUAAUGUCUGA 
Saccharomyces mikatae       CUCAUUUUCUUAUUUUUAUUAUAUUUUCUGUCACUUCU-GAAGUGACGGAAAAGA--GGAGUUUG-AAUUAGAUUUGCAAAACGGGCGGUAUCAAGAAUACUGUCACUCUAUAUGUCUAA 
                                                                                     (((((((((((((((((                                        )))))) 
                                                                                            CS2                                                      

                                    730       740       750       760       770       780       790       800       810       820       830       840           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                      IVa                         V                              V              IV   
structures                  )))))))))))))))        (((((((((((((((((((((((((((((((((((((((     ((((((((<<<<<<<                 ))))))))  ((((((((((( 
Saccharomyces cerevisiae    CUUAUCGUUAACUCUGGAAAAAGAAAAA-GGAAAAAGAACG-UCAGGGAACA-UGAGUAUAU---AUAGAAAUGGUUUAUUCUAG--------UUUUUUCCGUUUUUUCAGUAGAUUUUU 
Saccharomyces paradoxus     CUUAUCGUUAACUCUGCAAAAAGAAAACAAGAAAAAGAAAA-UCAGUGAAUA-GGAGUAUAU---AUAGAAAUGGUUUAUUCUA--------UUUUUUUUUGUUUUU-CAGUAGAUUUUC 
Saccharomyces kudriavzevii  UUCAUCGUCAACUCUGUAAAAAGAGAACAAGAAAGGDAAAA-UUGAUGGGCA-AAAGUAUAU---AUAGAAAUGGUUUAUUCCCG--------UUUUUUCCAUUUCU-CAGUAGAUUUUU 
Saccharomyces cariocanus    CUUAUCGUUAACUCUGCAAAAAGAAAAUAAGAAAAAGAAAA-UCAGUGGAUA-GGAGUAUAU---AUAGAAAUGAUUUAUUCUAG-------UUUUUUUUCGUUUUU-CAGUAGAUUUUC 
Saccharomyces bayanus       UUUAUCGUCAACUCUGUAA--AGGAAGCAAGAAAGAGAAAGGUUGCUGGAAAUAAAAUUUGUACAAACAAGACGGUUUAUUCUAG---------UUAUUCCAUUUUU-CAGUAGAUUUUU 
Saccharomyces pastorianus   UUUAUCGUCAACUCUGUAA--AGGAAACAAGAGAGAGAAAGGUUGGUGGAGAUUAAAUCUGUAGAAAGAGGAAGGUUUAUUCUAG---------UUAUUCCAUUUUU-CAGUAGAUUUUU 
Saccharomyces mikatae       UUUAUCGUCAACUCUGCAAAAAGAAAAUAGGAAGAAGAAAA-UAGGCGGAUA-AGAGUAUAU---AGAGAAAUGAUUUAUUCUAUUUUUUUUUUCUUUUUCGUUUUU-CAGUAGAUUUUU 
                            )))))))))))))))                                                    ((((((((                        ))))))))  ((((((((((( 
                               CS2                                                                CS3                             CS3        CS4     

                                    850       860       870       880       890       900       910       920       930       940       950       960           
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                       VI                                                                         I  
structures                  (((((      >>>>>>>              ))))))))))))))))))))))))  )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))) 
Saccharomyces cerevisiae    GCCUUUAAA-AGAAUAAAUCCCACU----ACAAAAAGGUAAAAUAAAAAAUCUAUUCACUGAACUUAC-UGAU-GAAAUUUCCAAAUGUGCCCCGUACAUCGAACGAUGUGAC----AGA 
Saccharomyces paradoxus     GCCUUUAAA-AGAAUAAAUUCCAUU----AAAAAAAGG-AAAAAGAAAAAUCUAUUCACUGAACUUGC-UGAUAGAA-UUUGCAAAUGUGUCAAGUGCAUC-AAGGAGAAGAU----AGA 
Saccharomyces kudriavzevii  CCCUUUUGCGAGAAUAAAUUGACACUUGAACAAAAAGCUUCGAAGAAAAAUCUAUUCACUGAACUUAUAU-AUAGAAAAAU-CAAAUGUGCUAAGUAUAUUUAAAAUGGAAACAAAUAGG 
Saccharomyces cariocanus    GCCUUCAAA-GGAAUAAAUUCCAUU----AAGAAAAGGUAAAAAGAAAAAUCUAUUCACUGAACUUAC-UGAUAGGA-UUUGCAAAUGUGUCAAGUGCAUC-AAGGAGAAGAU----AGA 
Saccharomyces bayanus       GCCUUUUACUAGAGUCAAUUUAACCA-GUA-UAAAAGGUUCAAGGAAAAAUCUAUUCACUGAACUUAU-CA--CGAAACCU-CAAAUGUGUCAGACGCAUUAAAAAGAUAAAU------- 
Saccharomyces pastorianus   GCCUUUUACUAGAAUUAAUUUAACCA-AUA-UAAAAGGUUCAAGGAAAAAUCUAUUCACUGAACUUAU-UA--GAAAACCU-CAAAUGUGUUGGAUGCAUUGAAAAGAUUAAC------- 
Saccharomyces mikatae       GCCUUUCGAGAGAAUAAAUUCCACU-----AAAAAGGGU-UAAAGAAAAAUCUAUUCACUGAACUUAU-UGAUGAAAACUU-UAAAUGCGUCAAGUACAUCAAAAGAGGAAAC----AGA 
                                                                          ))))))))))  ))))))))                                                       
                                                                              CS4       CS1                                                          

                                    970       980       990       1000      1010      1020      1030      1040      1050      1060      1070      1080          
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                                                                       |-------------------------------------------V 
structures                  )))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))  ((((((((((((((((((((((((((((((((((((((((((((( 
Saccharomyces cerevisiae    G--AAAAAUACG---AGUAGGUAAAUAAGCCAAAAGGCAAGGGUGU-CCU-------------------UUCUUAAGCAUCGGUUAGG--U-UUGCG-GGCGAUCAGUAACUG-----AA 
Saccharomyces paradoxus     GG-AAAAACUCG---AUAAGGCAAACAAGCCAAAAGGCAAGGAUGC-CCU-------------------UUCUCAAGCAUUG-UUAGG--AUUA-UG-GGCUACCAGUAAGCG-----AA 
Saccharomyces kudriavzevii  GGGAAAGAGAUA---GGUAGAUAAACAGCCCAAGGGACAAGGACAC-CCU-------------------UCCUCAGGCACUGAAUAUA--UUGG-AGA-GUGGACAGUAACAG-----AG 
Saccharomyces cariocanus    GG-AAAAAC-CU---AUUAGGCAAACAAGCCAAAAGACAAGGAUAC-CCU-------------------UUCUCAAGCAUUG-UUAG---UUUA-UG-GGCUACUAGUAAGCG-----AA 
Saccharomyces bayanus       ---CAAAAAAAC---GGUAUGCAAGCGAGUCAAAAGACUGGUACUC-CCUUCGUUUCCUGUCCCAUUUUGCCUCAAGCAUUGAAU--AAGUUUG-CGA-GCGAAUAAUAACCG----GGG 
Saccharomyces pastorianus   ---CAAAAAAAAAAAGGCACGCAAGCAGGUCAAAAGACUAGGACUC-CCUUCGUUUCCUUUCCCAUUUUGCCUCAAGCAUCGAAU--AAGUUUG-CGA-GCAAAACAUAACCG----GGC 
Saccharomyces mikatae       GGGAAAGAACCA---GGUUGGCAAACAAGCAAAAAGGCAAGGACGAACCU-------------------UCCUCAAGCACUGAAU-GU--UUUG-CGA-GUGAAUGGUAAGCGCGAGAAA 

                                    1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200          
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                            IIa----------------------------||----------VIIb----------|                VIIb                  VIIc     VIIc            
structures                  ((((((((((((((((((((((((((((((((((((((((((((((((((((((((((      )))))))))))))))))))))))))))    (((((    ))))))           
Saccharomyces cerevisiae    CAAUGACACAAGAUC--AAGAACGUAAUUUGAGAUUUUUCAA-GAUGG-UUUUUUUAGGUAU--CUAUUAAAA-CUACU--UUGAUGA-UCAAUACGGUAUUUUUGU-CGCAUU------ 
Saccharomyces paradoxus     AAAUGAUACAGGACAGAAAAAACAUAAUUCGAGAUUUUUCAG-GAUGGAUUUUUUUAGGUAU--CUAUCAAAA-CUAUU--CUGAUGA-UCAAUACAGUAUUUUUGU-CGCAUUACUAUU 
Saccharomyces kudriavzevii  AAAUGAUACAAGAUG-GAAAGCCAUAAAUUGAGAUUU-UCUUGAAUGGGUUCAUUUAGAUAUUUCUC-UUUAGCCAUUUU--UGAUAA-UCAAUACAGUAUUCUUGUUCCCAUCCUUGUC 
Saccharomyces cariocanus    GAAUGAUACAGGAUGAAAAAAACAUAUUAUGAGAUUUUUCAG-GAUGGAUUCUUUUAGGUAU--CUAUCGAAA-CCAUU--CUGAUGA-UCAAUACAGUAUUUUUGU-CGCAUUCUUAUU 
Saccharomyces bayanus       AAAUGAUACAA-GAG-AAAAUCCAUAAUUUGGGAUCU-UCUUGGAUGGAUUCAUUUAUGUAUUUAU--UUG--CUCAUUU-UUGAGGA-UCAAUACAAUAUUCUUGU-CCUAUCCUUGCU 
Saccharomyces pastorianus   AAAUGUUACAA-GAG-AAAAUACAUGAUUUGGGAUCU-UCUUGGAUGGAUUUGUUUACAUAUUUCU--UUA--CUCAUUUUUUGAGGA-UCAAUACAAUAUUCUUGU-CCCAUCCUUGCU 
Saccharomyces mikatae       UGAUGAUACAAGUUG-AAAAGACAUAAUUUGAGAUUUUUCAA-AAUAGAUUAUUUUAGACAU-CCUACUUUAAUCAUUU--UUGAUGAAUCAAUACGGUAUUUUUGU-CGCUUCCUUAUU 
                                                     ((((((((((((((((                                         ))))))))) (((((((((((((                
                                                     |-CS5a||--CS5b-|                                         |--CS5b-| |----CS6----|                

                                    1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320          
                            ....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|....|
                                                       VIId         VIId                                      VIIa                                   
structures                                           ((((((((      ))))))) ))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))))) 
Saccharomyces cerevisiae    --------------------AUUUUCCAAGCGGAAGGAACCGUGUGUUCAUUUUAUGAAUCUU-GGUGUUGUAU---------UCA----------CAGCUACU----UCUCC-UAAU-G 
Saccharomyces paradoxus     ACGGUA-GU-GCAGACAUUAGUU-UCCAAGCGGAAGAAACUGUGUGUUCAUUUUAUGGAUUUU-CGUGUUGUA-CGAUUUUUUUCAGUUGCGUUAGCAC-UAC-G---UGCCCACAAUA- 
Saccharomyces kudriavzevii  AGAUUAAGGAAGGAACAUUAAUU--CCAAACAGGAAAAACUGUGUGUUCACUUCGUGGGUUUG-CGUGUUGUA-CAUUUC-CUUCAUCCGUGUUGGCGGUUACU-U----UCCUCAAU-A 
Saccharomyces cariocanus    ACGGUACGU-GCARACAUUAGUU-UCCAAGCGGAAGAAACUGUGUGUUCAUUUUAUGGAUUUU-CGUGUUGUA-CGAUUUUUGUCAGUUGCCUCAACAACUAC-G---UGCCCACAAUA- 
Saccharomyces bayanus       AAAGUAAAGAACGGGCAUUAAUU-UCUGAACGGAAAGAAUUGUGUGUUCACUUUAUGG--UUUUCGCAUUGUA-CAUUUUUC--AACUUGCAUGAGCAGU-CGGU--UU--CCUCAAU-A 
Saccharomyces pastorianus   AAAGUAAAGAACGGGCAUUAAUU-UCCGAACAGAAAGAAUUGUGUGUUCACUUUAUGG--UUUUCGCAUUGUA-C-UUUUCCU--ACUUGCAUUAGCAGU-UGUU--UG--GCUCACU-A 
Saccharomyces mikatae       ACAGUAA-U-GCAGACAUUAACU-UCUGAGCGGAAGGAACCGUGUGUUCAGUUUAUGGAUUUU-CGUGUAAAG-CGUUUUUU--CGGUUGCGAUAGCAGUUACU-UACUUUCCUCGAU-G 
                                                            )))))))))))))  )))))))                                                                   
                                                            |----CS6----|  |-CS5a|                                                                   

                                    1330      1340      1350      1360  
                            ....|....|....|....|....|....|....|....|.
                                                   Sm site            
structures                  )))))))))))))))       |||||||||           
Saccharomyces cerevisiae    --CCU--UCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU 
Saccharomyces paradoxus     --CUU--CCGAUGCAUUUAGAUAAUUUUUGGAAA--CAUUU 
Saccharomyces kudriavzevii  UACC--UUCAGUGCAUACA---AAUUUUUGGAA---CAAUU 
Saccharomyces cariocanus    --CUU--CCGAUGCAUUCAGAUAAUUUUUGGAAA--CAUUU 
Saccharomyces bayanus       CUU--UUUCGGUGCUUACGAAUAAUUUUUGGAACUUCAAUU 
Saccharomyces pastorianus   CUUU-UUUCGAUGCUCACGAAUAAUUUUUGGAACCUCAUUU 
Saccharomyces mikatae       --CC--UUUGAUGCAUUCAGAUAAUUUUUGGAA---CAUUU 
                                                  |||||||||           
                                                      CS7