P1                  P10'   P1'          P3             P4        P5      P5a                                                          P5a'        P5'        P4' P6      P6a                     P6a'       P6'     P7       P3'   P8                                P8'         P7' P9.0 P9             P9'        P9.1                              P9.1'        P9.0'  P10'
Sce.m.COX1,5b       auuccacgau--AUUAAUUUAA------UAAGUGUCGUG-CUUAAAAUUCACU(162)CUAACGGGGAAACUCUUAUAAUUAUUAU-------------------------UUAU------------------------------AUAAUAAAUAAGACAAUCCCGUGAUAACUUUAAUAUAUA----UAUAU-----UAUAUAUUAAAGUAUUGUAGAGACUAAACGUGAAUGAUUUUAAUAUU-----AUUUA-----AAUAUUAAAAUUAAGAGAUAGUCCAAUCUUAUAU-GUAA-AUAUAAG------------------(1194)---------------------------UUUUUAUG--acuuacuacg
                    ....<<<<<<--<<<.......------[[^^^>>>>>>-......<<<<<<.~~~~~...<<<<<<....<<<<<<..<<<<<<<-------------------------....------------------------------>>>>>>>>>>>>>...>>>>>><<<<.<<<<<<<<<<<<----.....----->>>>>>>>>>>>>>>>...[.[[[[[...>>>>>><<<<<<<<<<<<-----.....----->>>>>>>>>>>>......]]]]]].<<<<<<<<<-....->>>>>>>------------------~~~~~~---------------------------.....>>.--]]]]].....
Sdo.m.COX1,4        --uccacgau--AUUAAUUUUAAUUUAAUAAGUGUCGUG-CUUAAAAUUCACU(164)CUAACGGGGAAACUCUUAUAAUUAUUAU-------------------------UUAU------------------------------AUAAUAAAUAAGACAAUCCCGUGAUAACUUUAAUAUAUA----UAUAU-----UAUAUAUUAAAGUAUUGUAGAGACUAAACGUGAAUGAUUUUAAUAUU-----AUUUA-----AAUAUUAAAAUUAAGAGAUAGUCCAAUCUUAUAU-GUAA-AUAUAAG------------------(1331)-----------------------------UUGUAG--acuuacuaug
                    --..<<<<<<--<<<.............[[^^^>>>>>>-......<<<<<<.~~~~~...<<<<<<....<<<<<<..<<<<<<<-------------------------....------------------------------>>>>>>>>>>>>>...>>>>>><<<<.<<<<<<<<<<<<----.....----->>>>>>>>>>>>>>>>...[.[[[[[...>>>>>><<<<<<<<<<<<-----.....----->>>>>>>>>>>>......]]]]]].<<<<<<<<<-....->>>>>>>------------------~~~~~~-----------------------------...>>.--]]]]].....
Kla.m.COX1,4        auuccaugau--A-(1189)------UAAAGGUGUCAUGUAGGUAAAUUCACC-(96)CUAACGAAGAAAUCUUAUAUAAAUAAAUU------------------------UAAUGU--------------AAUUUAUAUACCUACAAUUAUAUAAGACAAUUUCGUGGUAACCAUUAUUAUAU-----UUU-----AUAUAAUAAUGGGAACUGUAGAGACUAUACGUGAAUAAUAAUAUAUAA------(87)-----UUAUAUAUUAUUAAGACAUAGUCCAAUCCUUUAU-GUAA-AUAAAGAAUAUAAACCCCGGACGGCAUCGUCCGACCGUAUGGUCGGACGAGCCGUCCGGGG--AAG--cuuauuaug-
                    ....<<<<<<--<-~~~~~~------[[[.[[>>>>>>>.......<<<<<<.-~~~~...<<<<<<...<<<<<<<<<<<<<<<<<------------------------......-------------->>>>>>>..........>>>>>>>>>>...>>>>>><<<..<<<<<<<<<<<<-----...----->>>>>>>>>>>>..>>>...[.[[[[[...>>>>>><<<<<<<<<<<<------~~~~----->>>>>>>>>>>>......]]]]]]....<<<<<<-....->>>>>>........<<<<<<<<<<<.<<<<<<<<<<....>>>>>>>>>>>>>>>>>>>>>--...--.]].]]]..-
Spo.m.COX1,4        uuuccaugau--AUU-(44)------AAUAGGUAUCAUG-AAUAAAUGCCACC-(44)CUAACGGUGAAAUCUUAUGCUUUCCAUAAAGUUUUUAAUUAAAACAACAACACCCAAAA----------------GGUGUUUGUACUUUAGAAACUAAGACAAUACCGUGGAAACCAAAAACCCC-----AAAA-----GGUGUUUAGUAGGAUCCGUAGAGACUAAACGUGGCAAUCGAUA-----------(68)----------UAUCGAUAAGUUAUAGUCCGAUCCAUCGU-GUGA-ACGAUGU------UGUAUGAAAUUAAUUAAUU-UUA------------AAUUAAAUUAAAUUACAG--accuauuucg
                    ....<<<<<<--<<<-~~~~------[[[[^^^>>>>>>-......<<<<<<.-~~~~...<<<<<<...<<<<<...<<<<..<<<<<<...........<<<<...<<<<.....---------------->>>>.>>>>>>>>>>>>>>.>>>>>...>>>>>><<<..<<..<<<<.<<-----....----->>.>>>>....>>.>>>...[.[[[[[...>>>>>><<<<<<<-----------~~~~---------->>>>>>>......]]]]]]....<<<<<<-....->>>>>>.------<<<<.....<<<<<<<<<<-...------------>>>>>.>>>>>..>>>>.--]]]]]]]...
Pma.m.COX1,6        auccagaggu--UA----------AAAAUAUAGGCCUCU----UAACGUUACU-----AUAUGCUGAGACUGCUUCGUUACUAAGUUUUAAAUACUUCAUCAAUAGUACAACAUUAUAUUUACUUAAUGACAUAGUAAAAAAGUUAAAACAAAGAAGUAAAUCAGCAGGUUAUAUUCUGAUUUCAUCGAAAA-----GUAAAUCGGAUAUAACCUCAGAGACUUUACGUAACGGAAUUGUAGUAAAUUCG(773)UGAAGAUACUACAAUUUAAGAUAAAGUCCUAACAAGGAUAUAAAAGUUCUUGAGUGUUAGAUAUAACAAAUAUAUAUAUAUAUAUAUAUUGUUAUUCUAAUCAAAAUUUAG--uuauauuuua
                    ....<<<<<<--<.----------[[[[[[[[^>>>>>>----...<<<<<<.-----...<<<<<<...<<<<<<.....<<<.<<<<...<<<<...<<<..<<<<............>>>>...>>>...>>>>.>>>>.>>>.......>>>>>>..>>>>>><<<<<<<<.<<<<<<<.<<......----->>>>>>>>>>>>>>>>>...[.[[[[[...>>>>>><<<<<<<<<<<..<<<<~~~~~>>>>..>>>>>>>>>>>......]]]]]]<<.<<<<<<<......>>>>>>>...<<<<<<.<<<<<<<.<<<<<<<....>>>>>>>>>>>>>>>>>>>>.......>>.--]]]]]]]]].
Pan.m.COX1,15       auuccacgau--AC(880)------UAGUAAGUGUCGUG-UUGUCAUGUCACC-(75)CUAACGGUGAAGCCUUAUGUGUUUUCUUAAUGCAGAAAA---------UAGAA---------GGGUCGCUGCGAAGCCAAAAAUGUACCCUCAUGUAAGGUAAUACCGUGGAAACCAAAGCAAAUAAAUUCCACAAUUUAUUGGCGAGUAGGAUCCGUAGAGACUAAACGUGACAAUCAAAAGUUUA-----UUAAGU---UAAACGAUUAGAUAAGUUAUAGUCCGAUCCACUGC-GUGA-GCAGUGU--------UGUAUGUAAAAA-----AAAA-----------UUUUUGAGCAAUCUUCUUG--acuuacuaug
                    ....<<<<<<--<<~~~~~------[[[[[[^^>>>>>>-......<<<<<<.-~~~~...<<<<<<..<<<<<<<<<<<<<<<<......>>>>>>---------.....---------<<<<<<<<....>>>.......>.>>>>.>>>>>>>>>>..>>>>>><<<..<<...<<.<<<<<<<<....>>>>>>>>.>>.....>>.>>>...[.[[[[[...>>>>>><<<....<<<<<-----......--->>>>>.....>>>......]]]]]]<<..<<<<<<-....->>>>>>.--------<<<...<<<<<<-----....----------->>>>>>.>>>......>>.--]]]]]]]]..
Mvi.m.COX1,2        uuuacaugau--A---(705)--------AAGUGUCAUGU-UGUCACAUCACU-(42)CUAACGGUGAAAUCUUGAUAAUACUCU------------------------AUAAGCAAA-------------AGGGUUAUAUACUACAAGUUAUCAAGACAAUACCGUGGAAACCAAAAUAAUGUA----AUA---UAUAUUAUGAGUAGGAUCCGUAGAGACUAUACGUGGUGACCUGAUAUUGA-----UUAAGU-----UCAAUAAGGGGAAGAUAGAGUCCGAUCCUUACC-GCGA-GGUAAGU-----------------------------------------------UAAACAAUUUUG--acuuauuaug
                    ...<<<<<<<--<---~~~~~--------[[[^>>>>>>>-.....<<<<<<.-~~~~...<<<<<<...<<<<<<<<<<<<<<<------------------------.........------------->>>>>............>>>>>>>>>>...>>>>>><<<..<<...<<<<<<<<----...--->>>>>>>>.....>>.>>>...[.[[[[[...>>>>>><<<<..<<<<<<-----......----->>>>>>.>>>>......]]]]]]<<..<<<<<<-....->>>>>>.-----------------------------------------------.........>>.--]]]]......