P1                    P10   P1'     P2                      P2'  P2.1               P2.1a    P2.1b   P2.1b' P2.1a'                   P2.1'     P3       P4       P5               P5'     P4' P6                 P6'      P7         P3' P8                               P8'        P7'   P9.0                                                                             P9.0' P10'
Pma.m.COB,1         uuuuuugggu--UUGUC----------AA-AUAGCCCAAAAUGA--------(860)--------GUUAUAGUCACAC--GAGUCGAAAACCUUAUGUAACUUAUAAAAGAAAAUAAGG-CUAAAGUGUAAU(30)UUCUUGGCAAUAUCAGUGAAAACGGUUAAAA----AUUUUAAUGUCUA------GACCGUCGGUUAUUUAU-----AUGAUCGCUACAGACUGGGUCACUGGUGGGUAGC--------UGAAAU--------GUUACUU--AAUGUACAGUCGGAACUU------(63)----------------------------------------------------------AAGU----UUG--uauguuuuac
                    ..<<<<<<<<--<....----------[[-[[^>>>>>>>>...--------~~~~~--------......<<<<.<<--..........<<<<<<....<<......>>...>>>>>>-.......>>...~~~~....>>>>...<<<<<<<<..<<<<<<....----.............------>>>>>><<<<<<<....----->>>>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<------~~~~---------------------------------------------------------->>>>---->>.--]]].]]....
Ncr.m.COB,1-1       cuucuugggu--UAUCAACAUAAUCCCAAAAUGGUUUGA--UAU--------(917)--------GCUAUAGUCCUAU--GAGUAUAAAUCUUUUUGUAAUUUUUAUAGAAAAAAAAAGAUUAAAGUGGUAU(30)UAUUUGGCGAUGUUAGUGAAAACGGUUAAAAUCCCUCUACUUAUGCUGGGAUAAGACCGUUGGUUAUAUAA-----AUAAUCGCUGCAGACUGGGUCACUAAUGGGUGGC--------UGAAAU--------GCUGCUU--AAUGUACAGUCGGAACUU------(72)----------------------------------------------------------AAGUAAGUACA--uauguuuuac
                    ....<<<<<<--<<<............[[.^^^>>>>>>--...--------~~~~~--------......<<<<<<<--.......<<<<<<<<<....<<......>>...>>>>>>>>>...>>>>...~~~~.....>>>...<<<<<<<<..<<<<<<...<<<<<............>>>>>..>>>>>><<<<<<<....----->>>>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<.<<<<------~~~~---------------------------------------------------------->>>>.....>.--]]].]]....
Ncr.m.COB,1-2       cuuccugggu--UAUC-----------AACAUAGCCCA---AAA--------(987)--------ACCAUAGUCCCAU--GAGUAUAAAUCUUUUUGCAAUUUUUAUAGAAAAAAAAAGAUUAAAGUGGUAC(32)UAUUUGGCGAUGUUAGUGAAAACGGUUAAAAUCCCUCUACUUAUGCUGGGACAAGACCGUCGGUUAUAUAA-----AUAAUCGCUACAGACUGGGUCACUAAUGGGUGGC--------UGAAAU--------GCUGCUU--AAUGUACAGUCGGAACUU------(72)----------------------------------------------------------AAGUAAGUACG--uauguuuuac
                    .....<<<<<--<<<.-----------[[[^^^>>>>>---...--------~~~~~--------......<<<<<<<--.......<<<<<<<<<....<<......>>...>>>>>>>>>...>>>>...~~~~.....>>>...<<<<<<<<..<<<<<<....<<<<............>>>>...>>>>>><<<<<<<....----->>>>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<.<<<<------~~~~---------------------------------------------------------->>>>.....>.--]]]]]]....
Sce.m.COB,2         acauugaggu--AAUAUAAAUAU---------CGCCUCAA-AUA--------(780)--------UUAUUCCUAGUAU-AAAAUAUAAAUUAG---GUAAUUAUUUAUAAAAA(16)UUAAUUAUUAUAUUAU---UAUAAUGCGAUAUUAUUGAAAACAUGUCAAAAUUAUAUUAUUAA---GUAACAAGACAGUGGGUUAUAUAA-UUAUAUGAUCCCAACAGAAUACACCAAUAAUAGGUAUUAUUAU-AAAAAAAAA--AUAAUAAUAUUU--AAUGUUUAUUCGAAGAAAAU---(367)----------------------------------------------------------AUUUUC--UUG--gcacuaguua
                    ...<<<<<<<--...........---------[>>>>>>>-...--------~~~~~--------.........<<<<-........<<<<<<---....<<......>>...~~~~>>>>>>..........---....>>>>...<<<<<<<...<<.<<<<....<<<<........--->>>>...>>>>>><<<<<<<<<..-..>>>>>>>>>...[.[[[[[...>>>>>>><<<<<<<<<<<<-.........-->>>>>>>>>>>>--......]]]]]]<<<<<<<<---~~~~~---------------------------------------------------------->>>>>>-->>.--].........
Sdo.m.COB,1         uuuuuuaggu--UAAAUAAAC-----AACAAUAGCCUAAAAUUAUAUAAUUAUAAUAAUAAUUAUAUGGUAGUCUAUAAUAAUAUAUAUAUAAUAAAUAACUGUUAUUAGAAAUAUUAUAUAAAA-----------AUAUAGGCAAUAUUAGUGAAAACGAUCAAAGAU---CAAUACA------AUUGAGAUCGUCGGUUAAAUAA-CG----AGUCGCGACAGACUGGUUCACUGAUAGAUAUC--------UGUAAU--------GAUAUUU--AAUGCACAGUCGAAUAAUGUAUUUAAAUGAAAUUUUGAAUAUUAUUUUUAAUAAAUAU(1003)GUAUUUAUUAAAAAUAAUAUUCAAAAAUAAUUG--uauuguugug
                    ..<<<<<<<<--<<.......-----[[[[[^^>>>>>>>><<<<<<<<<<<<....>>>>>>>>>>>>..<<<<<<<........<<<<<<<<<.....<<......>>...>>>>>>>>>...-----------.>>>>>>>...<<<<<<<<..<<<<<<...<<<---.......------>>>..>>>>>><<<<<......-..---->>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<.................<<<<<<<<<<<<<<<<<<<<<<<<<<~~~~~~>>>>>>>>>>>>>>>>>>>>>>>>>>...>>>.--]]]]]]]...
Sdo.m.COB,3         acauugaggu--AAUAUAUAUAU---------CGCCUUAA------------(849)-----------------------------------------------------------------------------------AUGCAAUAUUAUUGAAAACAUGUCAAAAUUAUAUUAUUAA---GUAACAAGACAGUGGGUUAUAUAAUUUAUAUGAUCCCAACAGAAUACACCAAUAAUAGAUAUUAUUAUA-AAAAUAA--UAUAAUAAUAUUU--AAUGUUUAUUCGAAGAAAAU---(426)----------------------------------------------------------AUUUUC--UUG--gcacuaguua
                    ...<<<<<<<--...........---------[>>>>>>>------------~~~~~-----------------------------------------------------------------------------------.......<<<<<<<...<<.<<<<....<<<<........--->>>>...>>>>>><<<<<<<<<.....>>>>>>>>>...[.[[[[[...>>>>>>><<<<<<<<<<<<<-.......-->>>>>>>>>>>>>--......]]]]]]<<<<<<<<---~~~~~---------------------------------------------------------->>>>>>-->>.--].........
Sdo.m.COX1,2        cauuuauuuu--A----(245)-----GAGAAUGAGAUAA-UAA-------(1164)--------AUUUUAGUUUUUAUAUAUUAUAAUUAUAUAUAUA--CUUAAUUUAUAUAUAUAA----(89)----AAUAUAUAAAGGCGACACUGAUAG-UACGGUUAAUAAUCUU---CUU----AGGAUCAAGACCGUCGGUUAAUUAA-----GUGAUCGCUACAGACUGCUUUAUCGGUGGCUUUUAUAAUAUGUAUAUAUAUAUUAUAAAGGUU--AAUGUACAGUCGGAACUC-----(120)----------------------------------------------------------GAGU----UUG--gauucuuugg
                    ...<<<<<<<--<----~~~~~-----[[[[[^>>>>>>>-...-------~~~~~~--------......<<<<<<<<<<<<<....<<<<<<<<<<<--.......>>>>>>>>>>>----~~~~---->>>>>>>>>>>>>...<<<<<<<<-.<<<<<<....<<<<<---...---->>>>>...>>>>>><<<<<<.....-----.>>>>>>...[.[[[[[..>>>>>>>><<<<<<<<<<<<<<<<....>>>>>>>>>>>>>>>>--......]]]]]]<<<<<<-----~~~~~---------------------------------------------------------->>>>---->>.--.]]]]]]...
Ama.m.ND5,1-1       augggaaggu--GAUUCA-----------CUUUGCCUU---AUA--------(814)--------UUCAUAGUAGAUAAUAC(41)UAAAUCCUUAGUAAUCGGAAUGGAAAAUAAGGAUUAU----------GUAUUAUUUGCGACAUCAUUGAAAACGGUCAAGGAUA--UUUGCC-UAUUUUUUCAAGACCGUCGGUCACA--UUUU---UGAUCGCUAUCGACUGGUGCAAUGAUGGGUGCC--------UGAAAU--------GGUGCUU--AAUGUACAGUCAGAACC------(240)---------------------------------------------------------------GGUUUG--auaggaguau
                    .....<<<<<--<<....-----------[[>^>>>>>---...--------~~~~~--------......<<<<<<<<<<<~~~~..<<<<<<<<....<<......>>...>>>>>>>>..---------->>>>>>>>>>>...<<<<<<<...<<<<<<<<<<<<<--......->>>>>>>....>>>>>><<<<<<..--....--->>>>>>...[.[[[[[...>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<------~~~~~--------------------------------------------------------------->>>>>.--].]]......
Ama.m.ND5,1-2       augggaaggu--GAUUCA-----------CUUUGCCUU---AUA--------(814)--------UUCAUAGUAGAUAAUAC(41)UAAAUCCUUAGUAAUCGGAAUGGAAAAUAAGGAUUAU----------GUAUUAUUUGCGACAUCAUUGAAAACGGUCAAGGAUA--UUUGCC-UAUUUUUUCAAGACCGUCGGUCACA--UUUU---UGAUCGCUAUCGACUGGUGCAAUGAUGGGUGCC--------UGAAAU--------GGUGCUU--AAUGUACAGUCAGAACC------(240)---------------------------------------------------------------GGUUUG--auaggaguau
                    .....<<<<<--<<....-----------[[>^>>>>>---...--------~~~~~--------......<<<<<<<<<<<~~~~..<<<<<<<<....<<......>>...>>>>>>>>..---------->>>>>>>>>>>...<<<<<<<...<<<<<<<<<<<<<--......->>>>>>>....>>>>>><<<<<<..--....--->>>>>>...[.[[[[[...>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<------~~~~~--------------------------------------------------------------->>>>>.--].]]......
Ama.m.COB,2         accuuggggu--CAAAUUAUUACAGA-----UGGCCC----AAU--------(785)--------AACAUAGUUCAAUUAUCUUUACU--------GCAAUCUUAAAAGAAAAAGUAAAC---(21)---AGAUAAUUUUGAGCGACACUAGUGAAAACGGUUAACGAUAUUGUUCUUG---GAUAUUAAAACCGUCGGUU----UAUAC----AAUCGCUACCGACUGGUUCUCUAGUGGGUACC--------UGAAAU--------GGUGCUU--AAUGUACAGUCGAAGCAUAGGC-(116)----------------------------------------------------------GUUUAUGCUUG--caaaugagu-
                    ......<<<<--<<............-----^^>>>>----...--------~~~~~--------......<<<<<<<<<<<<<<<<<--------....<<<....>>>...>>>>>..---~~~~--->>>>>>..>>>>>>...<<<<<.<<..<<<<<<...<<<<<<.......--->>>>>>..>>>>>><<<<<----.....---->>>>>...[.[[[[[..>>.>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<<<<<-~~~~~---------------------------------------------------------->>>>>>>>>>.--]].......-
Ama.m.COB,3         -uuuuggggu--GAUUUUA-----------GUUGCCCUA--UAU--------(696)--------AUUAUAGUUCACCGUAA-----AUAUAGU--GUAAUUUGUAUAAAAAAAACUAU(43)UUACGGUG--(29)CUCUUGCUACAUUAGUGAAAACGGUUAACGAGAU-UUCUUCU----AUUUCUAGACCGUCGGAG---GUAUACAA--CUUCGCUACAGACUGGGACACUAAUGGGUGGC--------UGUAAU--------GCUGCUU--AAUGUACAGUCGGUAUUUC----(142)-------------------------------------------------------------GAAAUAUG--gcaacuguaa
                    -...<<<<<<--<<<....-----------^^^>>>>>>--...--------~~~~~--------......<<.<<<<<<<<-----..<<<<<--....<<......>>....>>>>>~~~~>>>>>>>>--~~~~.....>>...<<<<<<<<..<<<<<<...<<<<<-.......---->>>>>..>>>>>><<<<<---........-->>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<<----~~~~~------------------------------------------------------------->>>>>>>.--..]]].....
Pwi.m.COX1,2        cacuuauucu--A----(229)---AAAAAACUGGAAUAA-AGG--------(116)--------ACUCUAGUCCUGAUU-CAUAUAAUCUAAU-AAUAACUCUUAGAAGAAAAUUAGAUAAAAUCAGUCA-(40)UGUUUGGCUACACUAGUGAAAACGGUCAAAA-----CUCCUCA-----AAGCAAGACCGUCGGUUAU---CUAA--GUAAUCGCUACAGACUGGGUCAUUAGUGGGUGCC--------UGAAAU--------GGUGCUU--AAUGUACAGUGGAUCCUUC----(452)-------------------------------------------------------------GAGGGAUG--gguuuuuugg
                    ...<<<<<<<--<----~~~~~---[[[[[[[^>>>>>>>-...--------~~~~~--------......<<<<<<<<<-......<<<<<<<-.....<<......>>...>>>>>>>..>>>>>>...-~~~~.....>>>...<<<<<<<<..<<<<<<....-----.......-----......>>>>>><<<<<<<---....-->>>>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<<----~~~~~------------------------------------------------------------->>>>>>>.--]]]]]]]]..
Pan.m.COB,2         uuuccugggu--UAU-----------GAAUAUAGCCCA---AAA--------(972)--------AUUAUAGUUCCAU-GAGUAACAAUCUUUUU-GUAAUCUUUAUAGAAAAAAAAAGAUUAAAGUGGUA-(34)UAUUUGGCAAUGUUAGUGAAAACGAUCAAAGAAGU--UUAA------ACUUCAAGAUCGUCGGUUAU---AUAA--AUGAUCGCGACAGACUGGGUCACUAAUGGGUGGC--------UGAAAU--------GCUGCUU--AAUGCACAGGCGAAACUU------(83)--------------------------------------------------------------AAGUUUG--uauguucugc
                    .....<<<<<--<<<-----------[[[[^^^>>>>>---...--------~~~~~--------......<<<<<<<-.......<<<<<<<<<-....<<......>>...>>>>>>>>>...>>>>..-~~~~.....>>>...<<<<<<<<..<<<<<<...<<<<<--....------>>>>>..>>>>>><<<<<<<---....-->>>>>>>...[.[.[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]].]]<<<<<<------~~~~-------------------------------------------------------------->>>>>>.--]]]]]]]...
Pan.m.COX1,8        caucuuuucu--U----(943)----AAUAUUAGGAAAA--AAA--------(102)--------GAUUUAGUUAGUAUUAAGUAAUUAUUGCUU-GCAACU-(64)-AGGAAAAGUUAAUA-----------UUAAUACUAGCCACAUUGGUGUUUACGGUCAAGGAAU--UUUUUUC----GUUCAAAGACCGUUGGUUAU---UUAA--GUGACCACUACAGACUAGUUCACCGAUGGGUAGC--------UGAAAU--------GCUGCUU--AAUGUAUAGUCGAUUUCUUC----(87)------------------------------------------------------------GAAGAAAUG--gauucuucgg
                    ....<<<<<<--<----~~~~~----[[.[.[>>>>>>>--...--------~~~~~--------......<<<<<<<<<<<.....<<<<<<<<-....<<-~~~~->>...>>>.>>>>>----------->>>>>>>>>>>...<<<<<<<...<<<<<<...<<<<--.......---->>>>...>>>>>><<<<<<<---....-->>>>>>>...[.[[[[[...>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<<<----~~~~------------------------------------------------------------>>>>>>>>.--.].].]]...
Pan.m.COX1,12       aaaggagcau--A----(887)----UACAAUUGUGUUUU-AAA--------(128)--------UCCCACCUAGUUAUUAUU-----AUUAGUG-GCAACUUCCCAGAGAAACACGAA------(20)-----AAUAAUAACCGGACAUGGUGAAAACGGUUAACAAU---GCCCUUA-----GUUGAAGACCGUCGGUGA---CUCGGA--UCAUCGCUACAGACUGGUUCACCUACGUAGAGC--------UGAAAC--------GCUUGCG--AAUGUACAGUCGGGACUUAG---(160)------------------------------------------------------------CUAAGUUUG--cauauguaua
                    ...<<<<<<<--<----~~~~~----[[[[[[>>>>>>>>-...--------~~~~~--------......<<.<<<<<<<<<-----....<<<-....<<......>>...>>>...------~~~~----->>>>>>>>>.>>....<<<<<..<<<<<<..<<<<---.......----->>>>..>>>>>><<<<<<---......-->>>>>>...[.[[[[[..>>>>>...<<<<.<<--------......-------->>>>>>.--......]]]]]]<<<<<<<<---~~~~~------------------------------------------------------------>>>>>>>>.--.]].]]]]..
Pan.m.ND5,1         guuuaacagu--UU----(32)--------GAAGCUGU---GUUGG-----UUUUAAU-------CCAACUGUAUAAGAAUA(1901)GGAAUUGAGCAAGAUUAUAAUCAAACAAUUCU--------------AUACUUAUACAAAAGUGGUGAAAACGGUUAAGGAG---GAUAUA------CUUUAAGACCGUCGGCAG---UUAUAAA--UGUCGCUACAGACUGGUUCACCGGGGUUAGGC--------UGAAAU--------GUCUGUCCAAAUGUACAGUCGGAUCCUAG---(152)------------------------------------------------------------CUAGGAUUG--uucaauguua
                    .....<<<<<--<<----~~~~--------[^^>>>>>---<<<<<-----.......------->>>>>....<<<<<<<<~~~~~~<<<<<<<.....<<......>>...>>>>>>>--------------...>>>>>>>>....<<<<<<..<<<<<<..<<<<---......------>>>>..>>>>>><<<<<.---.......-->>>>>...[.[[[[[..>>>>>>....<<<<<--------......-------->>>>>..........]]]]]]<<<<<<<<---~~~~~------------------------------------------------------------>>>>>>>>.--]]].......
Csm.m.COB           accauggggu--UUUCACAAU------------GCCC----AAA--------(686)--------GUUAUAGUCUAACUC-CGUA----CGUAGU-GUAAUGAUAAUACAAAAACUACGCCAUUAGAGUU-(40)-AUAUAGGCAAUGCGAGUGAAAACGGUUAAAAGUUU--CAACAC----AAAUCAAGACCGUCGGUUAG---AUCA--UUGAUCGCUACAGACUAGGUCACUCGUGGGUAUC--------UGAAAU--------GAUGCUU--AAUGUAUAGUCGGAGAGUUC---(133)------------------------------------------------------------GAAUUCUCG--caaaugucuu
                    ......<<<<--.........------------>>>>----...--------~~~~~--------......<<<<<<<<<-....----<<<<<<-....<<......>>...>>>>>>......>>>>>-~~~~-....>>>>...<<<<<<<<..<<<<<<....<<<<--......---->>>>...>>>>>><<<<<<<---....-->>>>>>>...[.[[[[[..>>>>>>>><<<<<<<--------......-------->>>>>>>--......]]]]]]<<<<<<<<---~~~~~------------------------------------------------------------>>>>>>>>.--..........