P1 P10 P1' P2 P2' P2.1 P2.1' P3 P4 P5 P5a P5a' P5' P4' P6 P6' P7 P7.1 P7.1' P7.2 P7.2' P3' P8 P8' P7'P9.0 P9 P9' P9.1 P9.1' P9.2 P9.2' P9.0' P10'
Cac.cS508 agcaucggcu--AAAUAA----------UUGGCC---CCCACAUCGA-GUGA-UCGAGUGG------------------------------------------UGCAAA-CUUGGCUC-AUAACGGUGAAA-CCCUAACGAAGAUGCGGC-------(31)-----------GUUGUCA--GGCGAGGGCAAUACCGUGGG-AAGUAUUGUAC-----------(289)---------GUACAAUACCCUGUAACGACUGAGGA--AUAGUUACU----------UUUU---AGUAACUUAGU----ACGAGAUAGAGAGAUCACUCAGAAAAA-------ACAAGC--------UUUUUUUGAAAUUUCUUUAUAAUACGCCGAG-CCCUCUU--------GAUAUGG--------AAGAGGUG-AUGGUAUAGUCUAUGCUCUUG------GAAA------CAAGGG----------------------------------------------------------------------------------------------------------------AUUAUCAUG--aacucugugc
......<<<<--<<....----------^^>>>>---.<<<<.<<<<-....->>>>>>>>------------------------------------------......-<<<<<<..-...<<<<<<...-<<<<..<<....<<<<<<-------~~~~----------->>>>.>>--..>>>>>>...>>>>>><<<-..<<<<<<<<<-----------~~~~~--------->>>>>>>>>>>>...[.[[[[[....--<<<<<<<<<----------....--->>>>>>>..>>----.....<<<<<<<<<<...<<<<<<<<<-------......-------->>>>>>>>>.>>>>>>>>>>.....>>>>>>-<<<<<<<--------.......-------->>>>>>.>-......]]]]]]<<.<<<<<<------....------>>>>>>----------------------------------------------------------------------------------------------------------------......>>.--]]........
Cpa.cS508 agccccggcu--AAAU----------GGUUGGCCG----CCUAUCUU-GCGA-GAGAUAGG------------------------------------------GCAAUA-UUCAGCUC-AUAACGGUGAAA-CCCAAACGA---UGAGGCGGA----(94)-----UCUGUUAAUCUCA--GGCGUGGGCAAUACCGUGGG-AAGUUGUUU-------------(729)------------GAAAACCCCGUAACGACUGAGGAACAUAGGUUUCUAUGGAAGCUGUAAAGCUUGGGACUUAUAAGUACGAGAUGGAG-----------------------(209)-----------------------CUCCAUAAUACGCUGAA-CUUCUUUCCA-------(35)-------UGGAAAGAAG-AUGGUAUAGUCUAUGUCAAGAU-----GAAGA----AUCUUGA-----AAAAUAAAAAAACUU----(48)--------AGGUUGGAUU-----------------------------------------------------------------------CAUG--aacucugugc
.....<<<<<--<<..----------[[^^>>>>>----<<<<<<<<-....->>>>>>>>------------------------------------------......-<<<<<<..-...<<<<<<...-<<<..<<<.---<<<<<<<<<----~~~~----->>>>>....>>>>--..>>>>>>...>>>>>><<<-..<<<.<<<-------------~~~~~------------>>>>>>>>>...[.[[[[[......<<<<<<<<<.....<<<<<....>>>>>>>>>>>>>>.........<<<<<<-----------------------~~~~~----------------------->>>>>>.....>>>>>>-<<<<<<<<<<-------~~~~------->>>>>>>>>>-......]]]]]]<<.<<<<<<<-----.....---->>>>>>>-----..<<<.....<<<<<----~~~~-------->>>>>..>>>-----------------------------------------------------------------------.>>.--]]]]......
Cse.cS508 agcaucggcu--AAAUA--------AAAUUGGCC---CUUUAAAGAA-GGAA-UUCUUUA------------------------------------------UAGCAAA-CUCGGCU--AUAACGGUCAA-ACCC--------------------UAACUUUUAGU--------------------GGGUAAUACCGUGGG-AAGUUUUU---GAACUUUUGAACAU(595)---------GAAAACCCCGUAACGACUA---AA-GU----------------UAUCU------------GC--------GAUAAACAAUUGGAAUAAAAAGAUU----AUUUUUAGA-----AAUCUGCGAUUCUUUGUUUAUAAUACGCCGAG-CUCUAAU---------UUAUUU--------AUUAGAUG-AUGGUAUAGUCUAUGCUCUAG------GUAA------CUAGAG---------------------------------------------------------------------------------------------------------------AACUUACAUG--aacuucgugc
......<<<<--<<...--------[[.^^>>>>---...<<<<<<<-....->>>>>>>------------------------------------------.......-<<<<<<.--...<<<<<...-<<<<--------------------...........-------------------->>>>...>>>>><<<-..<<<<<<---..............~~~~~--------->>>>>>>>>...[.[[[[[---..-<<----------------.....------------>>--------.<<<<<<<<..<<<<<....<<<<<----.........----->>>>>...>>>>>>>>>>>>>.....>>>>>>-<<<<<<<---------......-------->>>>>>.>-......]]]]]]<<.<<<<<<------....------>>>>>>---------------------------------------------------------------------------------------------------------------.......>>.--]].]].....
Cmo.cS531 cagccgcggu--CUGGCG(20)--------GCCGC----CAUAGCGA-GUGA-UCGUUAUG----------------------------------------UAAAAAAA-CCCUGCUC-AUAACGGUGAA-GCCUUAGUAAUU-UAUCU---------UUUUA-----------GGGUA--UUUUACGGUAAUACCGUGGG-AAGUUUAUCAACA---------(51)-------UGUUGAUAUAACCCCGUAACGACUU------UUCUU--------------GAAA---------GAGAA-------AGAGGUG----------------------CUUUAUUAG----------------------CGCCUAACACGCAGG--CACUUAC----------(89)---------GUAAGUUG-AAGGUAUAGUCUGAGCCUCUG------GAAA------CAGGGG-----------------------------------------------------------------------------------------------------------------AAUAAUCG--aauacauagg
.....<<<<<--......~~~~-------->>>>>----<<<<<<<<-....->>>>>>>>----------------------------------------........-.<<<<<..-...<<<<<<..-.<<...<<<<..-<<<<<---------.....----------->>>>>--..>>>>>>...>>>>>><<<-..<<<<<<<<<<<---------~~~~------->>>>>>>>.>>>>>>...[.[[[[[------<<<<<--------------....--------->>>>>-------..<<<<<----------------------.........---------------------->>>>>.....>>>>>--<<<<<<<----------~~~~--------->>>>>>.>-......]]]]]]<<.<<<<<<------....------>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--..........
Ceu.mS531 cagccgcggu--AGGCUGU--UCUGUAAAUGCCGC---UAUAAUAAA-(67)-UUUAUUAUA-----------------------------------------UAAAAA--CCAGCUC-AUAUCGGUGAAGUUUGUAAUAUG--UCAGGUAUUG----CUUUU------UAGUACCUGA-AUUUUAUGAUAAUACCGAGGG-AAGUUA----------------UAAG---------------UAACCCCGUAACGACUG-----ACCC----------------GAAA------------GG-----AGAGAGUUAUUAU--------------------(112)--------------------GUAAUAGCUAACACGCUGG--CGUCAU----------(204)---------GUGACAUG-AAAGUAUAGUCUAAUCCUUUUA-----GUAA----UAAAAAGG------UCCCCC------------UUAC------------GGGGG-CUUACCAUGCUCAAGC------GAA------GCUUGGUGGUAAG-----------------------UAAAAAUG--aagacagaua
.....<<<<<--<......--[[[[[...^>>>>>---<<<<<<<<<-~~~~->>>>>>>>>-----------------------------------------......--<<<<<..-...<<<<<<....<<<<<<....--<<<<<<<<<<----.....------>>>>>>>>>>-...>>>>>>...>>>>>><<<-..<<<<----------------....--------------->>>>>>>...[.[[[[[-----..<<----------------....------------>>-----....<<<<<<<<<--------------------~~~~~-------------------->>>>>>>>>.....>>>>>--.<<<<<----------~~~~~--------->>>>>...-......]]]]]]<<.<<<<<<<-----....---->>>>>.>>------.<<<<<------------....------------>>>>>-<<<<<<<<...<<<<<------...------>>>>>>>>>>>>>-----------------------.....>>.--]..]]]]]..
Cpa.cS793 aggauuagau--AAUCCG(38)------GUGU-----CCCUCAUUAUUGUGAAGUAAUGAG--------------------------------------------UGCA-UCUAGCU--AUAUCGGUGAA-CGUGACUGA----GUC-----------UAAAA-------------GAC----AGUCACCAACCCCGAGGG-AAGUAUC---------------(48)--------------GGUACCCCGUAGAGACUA-------------------------------------------(951)----------------------------------------------------------------------ACGCUGGA-AAACUGAGG--------(67)---------CUCAGUUU-AAGAUAUAGUCCAAU--AACCA-AUAAAAUCAAAAUGGUU------------------------------------------------------------------------------------------------------------------------UUUG--acccuaguag
........<<--<.....~~~~------[^>>-----..<<<<<<<<<....>>>>>>>>>--------------------------------------------....-<<<<<<.--...<<<<.<..-.<<<<<<..----<<<-----------.....------------->>>---->>>>>>...>.>>>><<<-..<<<<<---------------~~~~-------------->>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>-<<<<<<<<.--------~~~~--------->>>>>>>>-......]]]]]]<<.--<<<<<-............>>>>>------------------------------------------------------------------------------------------------------------------------.>>.--]]........
Cse.cS793 aggauuagau--AAAUUC(30)-----GGUGUC----CUGCUAUAUU-ACGA-AAUAUAG-------------------------------------------UUUGUA-UCUAGCU--AUAUCGGUGAA-GCCACUU-------------------UUUCAC--------------------AGGAGGUAACCCCGAGGG-AAGUUU----------------UAAAU--------------AAACCCCGUAGAGACUA-------------------------------------------(717)----------------------------------------------------------------------ACGCUGGA-UUUCUGAGAU-------(74)-------AUUUCAGAAA-AUGAUAUAGUCCAUUUCAGAUUUUAAAUUCUCGUUUUUAAUCU-----------------------------------------------------------------------------------------------------------------UUAUAAUG--acccuaguag
.......<<<--<.....~~~~-----[[^>>>----...<<<<<<<-....->>>>>>>-------------------------------------------......-<<<<<<.--...<<<<<...-<<<.<<<-------------------......-------------------->>>.>>>..>.>>>><<<-..<<<<----------------.....-------------->>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>-<<<<<<<<<<-------~~~~------->>>>>>>>>>-......]]]]]]<<...<<<<<..<<<......>>>..>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--]]].......
Ihi.mS793 aggauuagau--GGAUCCGC---ACCAGGUGUC----CCCUUUGAUCGGCGA-GGUCAUAG------------------------------------------UGUGCA-UCCAGCU--AUUCCGGGGAAACCUU----------------------------------------------------AGCAAUCCCGGGGG-AAG-------------------UGCA------------------CCCCGUAGAGACUACGAACAGAAGAGGAGAUAGAGAAAAGCUCUUUGCUUUGUCGUUUCCAAUUCUUCG------------------------------------------------------------ACAACGCCGGA-UCUCUGG---------UUGGUAU--------CCAGAGA-AUGAGAUAGUCCAUG--AAGAC----ACGUAC------GUCUU----------------------------------------------------------------------------------------------------------------------CAG--acccugguag
.......<<<--<.......---[[[[[[^>>>----..<<.<<<<<.....->>>>>.>>------------------------------------------......-<<<.<<.--...<<<<<<.......----------------------------------------------------.....>>>>>><<<-..<-------------------....------------------>>>>...[.[[[[[<<<..<<<<..<<<<<<.<<.<<<.<<.....>>>>>.>>>>>>>>..>>>>>>>------------------------------------------------------------.....>>.>>>-<<<<<<<---------.......-------->>>>>>>-......]]]]]].<<--<<<<<----......------>>>>>---------------------------------------------------------------------------------------------------------------------->>.--]]].]]]]..
Tle.mS793 aggauuagau--AGAUCC(24)CCAAAGGUGUC----CCCUCCGAUC-GCAA-GGUCAGAG------------------------------------------UGUGC-AUCCAGCU--AU-UCGGG--AAC-UUGAUGCG---GA---------UGUACCAUUCU-----------UC-AACAUCAGACAAUCC-GAGGG-AAGUGCUUU------------GAGCUCAU-----AUCAAGAGCACCCCGUAGAGACUA-------------------------------------------(514)----------------------------------------------------------------------ACGCUGGAUCUCUGAGAU--------(78)--------AUUUCAGAGAAUGAUAUAGUCCAUUUUUGAAGAUG--(90)---CAUCUUCAA---------------------------------------------------------------------------------------------------------------------UAUG--acccugguag
.......<<<--<.....~~~~[[[..[[^>>>----..<<<.<<<<-....->>>>.>>>------------------------------------------.....-<<<<<<<.--..-<<<<<--...-<<<<<<..---<<---------...........----------->>-..>>>>>>....>>>->><<<-..<<<<<<<------------........-----....>>>>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>><<<<<<<<<--------~~~~-------->>>>>>>>>.......]]]]]]<<..<<<<<<<<<--~~~~--->>>>>>>>>---------------------------------------------------------------------------------------------------------------------.>>.--]]].]]]...
Pco.mS793 aggauuagau--AGAUCC(24)UCAAAGGUGUC----CCCUCUGAUC-GCGA-GGUCAGAG------------------------------------------UGUGC-AUCCAGCU--AUUUCGGGGAAACUUUGAUGU----GAAUG----------UAC------------CAUUU-AACAUCAGACAAUCCCGAGGGGAAGUGCUUUUA----------AUCUCGG------ACUAAGAGCACCCCGUAGAAACUA-------------------------------------------(527)----------------------------------------------------------------------ACGCUGGAUCUCUGAA----------(82)----------UUCAGAGAAUGAUAUAGUCCAUUUUUGAAGAUA--(97)---UAUCUUCAA---------------------------------------------------------------------------------------------------------------------UAUG--acccugguag
.......<<<--<.....~~~~[[[..[[^>>>----..<<<.<<<<-....->>>>.>>>------------------------------------------.....-<<<<<<<.--...<<<<<<....<<<<<<<<----<<<<<----------...------------>>>>>-.>>>>>>>>...>>>>>><<<...<<<<<<<<<----------.......------..>>>>>>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>><<<<<<<----------~~~~---------->>>>>>>.......]]]]]]<<..<<<<<<<<<--~~~~--->>>>>>>>>---------------------------------------------------------------------------------------------------------------------.>>.--]]].]]]...
Spa.mS793 aggauuagau--AGAUCC(24)CCAAAGGUGUC----CUCUCCGAUU-GCGA-GGUCAGAG------------------------------------------UGUGU-AUUCAGCU--AU-UCGGGGAAACUUUGAUGCA---GA-----------UGUACCAU------------UC-AAUAUCAGACAAUCCCGAGGG-AAGUGCUUU------GAU--GAUAUUCU------AUCAAGAGCACCCCGUAGAGACUA-------------------------------------------(759)----------------------------------------------------------------------ACGCUGG-UUUCUGAGAUGAA-----(75)-----UUUAUUUCAGAAAAUGAUAUAGUCCAUUUUUGGAGAUA--(91)---CAUCUUCAA---------------------------------------------------------------------------------------------------------------------UAUG--accccgguag
.......<<<--<.....~~~~[[[..[[^>>>----..<<<.<<<<-....->>>>.>>>------------------------------------------.....-<.<<<<<.--..-<<<<<<....<<<<<<<..---<<-----------........------------>>-..>>>>>>>...>>>>>><<<-..<<<<<<<------...--........------....>>>>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>-><<<<<<<<<<<<-----~~~~----->>>>>>>>>>>>.......]]]]]]<<..<<<<<<<<<--~~~~--->>>>>>>>>---------------------------------------------------------------------------------------------------------------------.>>.--]]].]]]...
Csp.mS793 AGGAUUAGAU--AGAUCC(23)CCAAAGGUGUC----CCCUCUAAUC-GUAA-GAUUAGAG------------------------------------------UGUGCA-UCCAGCU--AUAUCGGGAAAACAUUCAUUUA----------------CAUUACU----------------UGGAUGGAUCAAUCCCAAGGG-AAGUCCU---GUGUUGAUUUGAUAAAUAAAAGUUAGCAAGAGGAUCCCUUAGAGACUA-------------------------------------------(710)----------------------------------------------------------------------ACGCUGGA--UCUCUGAG--------(63)--------CUCAGAGA--AUGAUAUAGUCCAUUUUUGA-----UUGAAAU------UCAAA----------------------------------------------------------------------------------------------------------------------AUG--ACCCUGGUAG
.......<<<--<.....~~~~[[[..[[^>>>----..<<<.<<<<-....->>>>.>>>------------------------------------------......-<<<<<<.--.....<<<<....<<<<<<<<<----------------.......---------------->>>>>>>>>...>>>>..<<<-..<<<<<---..............................>>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>--<<<<<<<<--------~~~~-------->>>>>>>>--......]]]]]]<<.<<<<<-----.......------>>>>>---------------------------------------------------------------------------------------------------------------------->>.--]]].]]]...
Cha_vu.mS793 aggauuagau--AGAUCC(23)CCAAAGGUGUC----CCCUCUAAUC-GUAA-GAUUAGAG------------------------------------------UGUGCA-UCCAGCU--AUAUCGGGAAAACAUUCAUUUA----------------CAUUACU----------------UGGAUGGAUCAAUCCCAAGGG-AAGUCCU---GUGUUGAUUUGAUAAAUAAAAGUUAGCAAGAGGAUCCCUUAGAGACUA-------------------------------------------(711)----------------------------------------------------------------------ACGCUGGA--UCUCUGAG--------(63)--------CUCAGAGA--AUGAUAUAGUCCAUUUUUGA-----UUGAAAU------UCAAA----------------------------------------------------------------------------------------------------------------------AUG--acccugguag
.......<<<--<.....~~~~[[[..[[^>>>----..<<<.<<<<-....->>>>.>>>------------------------------------------......-<<<<<<.--.....<<<<....<<<<<<<<<----------------.......---------------->>>>>>>>>...>>>>..<<<-..<<<<<---..............................>>>>>>>>...[.[[[[[-------------------------------------------~~~~~----------------------------------------------------------------------..>>>>>>--<<<<<<<<--------~~~~-------->>>>>>>>--......]]]]]]<<.<<<<<-----.......------>>>>>---------------------------------------------------------------------------------------------------------------------->>.--]]].]]]...
Aae.mL580 cauaaauggu--GAA---------UUGCUUGCC-----CAUAGAAUU-GAGA-AAUUCUA--AUUAAAACUGACUCGUAGAUCUAAAAGGUCGGUAUUA------UUUA-UAUAAGU--CUAACGGUGAA-UCCUAA-------GGAUU----------UUA------------AAUCU------AUGGAAAUACCGUGGG-AAGCU-----------------(82)----------------AGCCCUGUAACGACUG-----AUUC----------------GAAA-----------GAA------GAGACUGGUUGACUGCGAAUAAUU--------AAUUA---------AAUUAGCGUAUAGAAUCGGUAACACGUCAG--CACUCAA---------(903)---------UUGAGUUG-AAGGUAUAGUCUAAUCCAAUAU-----GAAA-----AUAUUGG-----------------------------------------------------------------------------------------------------------------UAUAAAUG--cagcaaguua
.......<<<--<<.---------[[[[^>>>>-----..<<<<<<<-....->>>>>>>--..<<<.<<<<<<<..<<....>>...>>>>>>>.>>>------....-<..<.<<--...<<<<<<..-<<<...-------<<<<<----------...------------>>>>>------..>>>..>>>>>><<<-..<<<-----------------~~~~---------------->>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<...<<<<..<<<<<--------.....--------->>>>>.>>>>...>>>>>>>...>>.>..>--<<<<<<<---------~~~~~--------->>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--.]]]]]....
Ceu.cL730 ucuuggaggu--CAUCAGUUCAA-UGACGGGCCUUC----UUACGCG-GCGA-CGCGUA-----------------------------------------UAAUAAAAA-UCUGGCUC-AUAUCGGUGAAC-CCUC--------UAUAACU--AAAACGUGUAAACAAAAA-AGUUAUG-------UGGCGAUACCGAGGG-AAGGUUUUG------------(160)------------CAAAACCCCCGUAACGACUG-----AAUC----------------GAAA-----------GAU------GAGAGUUUAAGA---------------------UUUU--------------------UCUUAAGCUAAUACGCCAG--CACUGCUGUG------(225)------UACUGCAGUUG-AAGGUAUAGUCUAAACUUACAA-----GAAA-----UUGUAAG-----------------------------------------------------------------------------------------------------------------AGUAAUUG--ccgaacccac
....<<<<<<--<.<<<......->>>[[^>>>>>>----.<<<<<<-....->>>>>>-----------------------------------------.........-.<<<<<..-...<<<<<<...-<<..--------<<<<<<<--..................->>>>>>>-------.>>...>>>>>><<<-..<<<<<<<------------~~~~~------------>>>>>>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<<<---------------------....-------------------->>>>>>>>>.....>>>>>--<<<<<<.<<<------~~~~~------>>>.>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--]]].......
Hla.cL730 uaguggaggu--UUUCAACUCA--UGACGGGCCUCC---UUCUCGUG-GCAA-CAUGAGA------------------------------------------UAAAAAG--CUGACUC-AUAUCGGGGGACCCCUUAC------CUUAUUUG------(38)---------CAAAUAAG------CAGGAAAUCCCGAGGG-AAGUUUUUA------------(254)------------UAAAAACCCCGUAACGACUG-----AUUC----------------GAAA-----------GAA------GAGAGUUUAGAU---------------------AACA--------------------AUCUAAGCUAACACGUCAG--AUCUAC----------(148)----------GUAGAAU-AAGGUAUAGUCUAAACUACCUA-----GAAA-----UAGGUAG---------GGAAGA--------AAAGCGC--------UCUUCC--UAGGAGCACUUU---------(149)--------AAGGUGCUCU----------------------GAAAUAUUG--ccgaaccgac
....<<<<<<--<.<<<.....-->>>[[^>>>>>>---.<<<<<<<-....->>>>>>>------------------------------------------.......--<<<<<..-...<<<<<<....<<<...------<<<<<<<<------~~~~--------->>>>>>>>------.>>>...>>>>>><<<-..<<<<<<<------------~~~~~------------>>>>>>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<<<---------------------....-------------------->>>>>>>>>.....>>>>>--<<<<<<----------~~~~~---------->>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>---------<<<<<<--------.......-------->>>>>>--..<<<<<<<<<<---------~~~~~-------->>>>>>>>>>----------------------......>>.--]]].......
She.cL730 uuguggaggu--U--CAACUCAUUUA-UCGGCCUCC----UUGCGCG-GUGA-CGCGCAA---------------------------------------UAAAAAAAAU--CUGGCUC-AUAUCGGUGAA-ACCU-ACAUUAAGACGCGUAUG-----AUUA---------UAUACCGUAUUUUUAAGGUAAUACCGAGGG-AAGUUUAAUAAGUAG-------(38)-----UUGCUUAUUAUAACCCCGUAACGACUG-----AUCC----------------GAAA-----------GGA------GAGAGCUUAAGU--------------------UAUAAU--------------------ACUAAGCUGAUACGCCAG--CACUACAAG-------(321)-------UUUGUAGUUG-AAGGUAUAGUCUGAACUAAGAA-----UAAA-----UUCUUAG------------------------------------------------------------------------------------------------------------------AAUAUUG--ucgaacggac
....<<<<<<--<--...........-[[^>>>>>>----<<<<<<<-....->>>>>>>---------------------------------------..........--<<<<<..-...<<<<<<..-<<<<-........<<<.<<<<<-----....--------->>>>>>>>.......>>>>..>>>>>><<<-..<<<<<<<<<<<<<-------~~~~----->>>>>>>>>>.>>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<.<<--------------------......-------------------->>>>>>>>.....>>>>>--<<<<<<<<<-------~~~~~------->>>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>------------------------------------------------------------------------------------------------------------------....>>.--.]]]......
Cha_vu.mL779 ggcuaggggu--AAAUAA(54)-GCCUUUUGCCCC----AUAGGCGC-GUGA-GCGCUUA-----------------------------------------UAGAAAAA--CUGGCUC-AUAACGGUGGAA-CCGUUA------GUUCUU-----AUUUAUACAAACA-----AAGAAC-----CAUGGCAAUACCGUGGG-AAGUCGGUGGA-----------(41)----------UUCAUAGACCCCGUAACGACUG-----ACUC----------------GAAA-----------GAG------GAGAGCAUGA-----------------------UUGAUU--------------------UCAUGCUAAUACGCCAG--UACUCACC--------(114)--------GGUGAGAUA-AAGGUAUAGUCUAACCUCUAGU-----GAAA-----ACUAGAG------------------------------------------------------------------------------------------------------------------AUGAUUG--gaaaggccaa
.....<<<<<--<.....~~~~-[[[[[[^>>>>>----.<<<<<<<-....->>>>>>>-----------------------------------------........--<<<<<..-...<<<<<<...-<<<<..------<<<<<<-----.............----->>>>>>-----.>>>>...>>>>>><<<-..<<<.<<<<<-----------~~~~---------->>>>>.>>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<-----------------------......-------------------->>>>>>>.....>>>>>--<<<<<<<<--------~~~~~-------->>>>>>.>>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>------------------------------------------------------------------------------------------------------------------....>>.--]]]]]]]...
Cbu.bL1951 cuugucgggu--AAA----------AAAUUGCCC----CGCUAAACU-GUAA-AGUUUAGUG------------------------------------------AUAAA-GUCAGCUC-AUAUCGGGGGAA-CCCUCC------UGCU----------UUUU-------------AGCA-----AAGGGCAAUCCCGAGGG-AAGUC----------------UUAAAU---------------GACCCCGUAACGACUG-----AUCC----------------GAAA-----------GGU------GAGGCACGC-------------------------AUUU----------------------GUGUGCAAUACGCUGAC-UUCUUGCC--------(501)--------GGUGAGA-AAAUGGUAUAGUCUACUCCCUAUG-----GAAA-----CAUAGG------------------------------------------------------------------------------------------------------------------AAAGAGUG--aaguuccgac
......<<<<--<<.----------[[.^^>>>>----<<<<<<<<<-....->>>>>>>>>------------------------------------------.....-<<<<<<..-...<<<<<<...-<<<<..------<<<<----------....------------->>>>-----.>>>>...>>>>>><<<-..<<<----------------......--------------->>>>>>...[.[[[[[-----<.<<----------------....----------->>>------...<<<<<<-------------------------....---------------------->>>>>>.....>>>>>>-<<<<<.<<--------~~~~~-------->>.>>>>->.......]]]]]]<<..<<<<<<-----....----->>>>>>------------------------------------------------------------------------------------------------------------------.....>>.--]].]].....
Msp-1.cL1951 cuugucgggu--GA-----------AACUUGCCCGG---UUAAUUUG-GCGA-CAAAUUA------------------------------------------UUGUAAA--CCAGCUC-AUAACGGUGGA-GUCUAAA------AAGC----------UUUGU------------GCUU-----CAUGAUAAUACCGUGGG-AAGAUUUC-------------UUAA--------------GAAAUCCCCGUAACGACUG-----AUCC----------------GAAA-----------GGU------GAGGACUGAGG-----------------------(35)--------------------CCUUGGUCAAAACGCUGG--CACUUG----------(615)----------CAAGUUG-AAUGUAUAGUCUGAUCAAUAUG-----GAAA-----CGUAUUGCAUAACAUCGACAUUC-------UGUAAAU-------GAAUGUC---------------------------------------------------------------------AAAAUUUG--aaguuccgac
....<<<<<<--<<-----------[[[^^>>>>>>---.<<<<<<<-....->>>>>>>------------------------------------------.......--<<<<<..-...<<<<<<..-<<<....------<<<<----------.....------------>>>>-----...>>>..>>>>>><<<-..<<<<<<-------------....-------------->>>>>>>>>...[.[[[[[-----<.<<----------------....----------->>>------...<<<<<<<<-----------------------~~~~-------------------->>>>>>>>.....>>>>>--<<<<<<----------~~~~~---------->>>>.>>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>.........<<<<<<<-------.......------->>>>>>>---------------------------------------------------------------------.....>>.--]]]]].....
Msp-2.cL1951 cuugucgggu--AAACU-------GAACUUGCCCGG---UUAAUUUG-GCGA-CAAAUUA------------------------------------------UAGCACU--CCAGCUC-AUAACGGUGGA-AUCUAAA------GAGAG---------UAA-------------UUCUC-----CAUGAUAAUACCGUGGG-AAGAUUUAUUU----------UAUA-----------AAAUAAAUCCCCGUAACGACUG-----AUCC----------------GAAA-----------GGU------GAGGGCUCGGAAAAGAAAUCCAACAGAAAAGAUAUAAUCCGAACUGUGGAUUUUAUUUUCUUGGCCAAAACGCUGG--CACUCG----------(523)----------CGAGUUG-AAGGUAUAGUCUGAACAAUAUG-----GAAA-----CAUAUUGCAUAAC---UUUGAC----------(50)---------GUCAGA-------------------------------------------------------------------------AUUG--aaguuccgac
....<<<<<<--<<...-------[[[[^^>>>>>>---.<<<<<<<-....->>>>>>>------------------------------------------.......--<<<<<..-...<<<<<<..-<<<....------<<<<<---------...------------->>>>>-----...>>>..>>>>>><<<-..<<<<<<<<<----------....----------->>>>>>>>>>>>...[.[[[[[-----<.<<----------------....----------->>>------...<<<<.<<<<<<<<<<<<<<.<<<.................>>>>>>>>>>>.>>>>>>.>>>>.....>>>>>--<<<<<<----------~~~~~---------->>>>.>>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>......---<<<<<<----------~~~~--------->>>>>>-------------------------------------------------------------------------.>>.--]]]]]]....
Cbr.cL1951 cuugucgggu--GAAC--------AAUAUUGCCCGA----AUGACGU-GUGA-ACGUUA------------------------------------------AAAGCAAA--CCAACUC-AUAACGGUG-AACCCUAA-------AUACAA--------CAAU-----------UUGUAU-----CAUGGGAAUACCGCGGG-AAUCUUAUGUAAAUUUG-----(56)--CAUAGUUUACAUUUGAACCUGUAACGACUG-----AUCU----------------GAAA-----------AGA------AAGGUGACA-----------------------AAAAAA----------------------UGUCACAACACGUUGG--CACUUUCC--------(540)--------GGAAAGUUG-AAGGUAUAGUCUGAUCAAUAUG-----GAAA-----CAUAUUG-------------------------------------------------------------------------------------------------------------UUAACAUAUAUG--aaguuccgac
....<<<<<<--<<..--------[[[.^^>>>>>>----.<<<<<<-....->>>>>>------------------------------------------........--<<<<<..-....<<<<<-..<<<...-------<<<<<<--------....----------->>>>>>-----...>>>..>>>>>.<<<-..<<..<<<<<<<<<<<-----~~~~-->>.>>>>>>>>>..>>.>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<-----------------------......---------------------->>>>>>.....>>>>>--<<<<<<<<--------~~~~~-------->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-------------------------------------------------------------------------------------------------------------.........>>.--]].]]]....
Chl_vu.mL1951 cuugucgggu--UUUUAU------------GUUGGAC-----------------------------------------------------------------UAGUAAA--UCGACUC-AUAACGGGGGAAGCCUAAA------AUUUGU------AAAACACAA--------ACGAAU-----CAUGGUAAUCCCGUGGG-AAGUGUGAUA------------(31)-----------UAUCACACCCCGUAACGACUG-----AUCC----------------GAAA-----------GGA------GAGGCUUUCU-----------------------UUUUU---------------------AGAAGGCAACACGUCGA--CCCUUAU---------(524)---------AUAAGGUG-AAGGUAUAGUCUGAUCUUUAUG-----GAAA-----CAUAAAGC------UAA-------------CACACAA-------------UUA---------------------------------------------------------------------AAUAUG------------
...<<<.<<<--......------------>>>.>>>-----------------------------------------------------------------.......--<<<<<..-...<<<<<<...<<<....------<<<<<<------.........-------->>>>>>-----...>>>..>>>>>><<<-..<<<<<<<<------------~~~~----------->>>>>>>>>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<-----------------------.....--------------------->>>>>>>.....>>>>>--<<<<<<<---------~~~~~--------->>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>.------<<<-------------.......------------->>>---------------------------------------------------------------------...>>.------------
Aca.mL1951 cuugucgggu--AGAAUUGGA-----ACUUGCCCGAU---UAACGCA-GUAA-UGUGUUA------------------------------------------UAGCAAA--UCAGCUA-AUAACGGUGAAACCCUAA-------GUUUUAA------UUUUGUU--------UUAAAAU------AUGGCAAUACCGUGGG-AACGAUUAUUCUA----GAACUACAAGA------UGAAUAAUUGACCCGUAACGACUG-----AAUC----------------GAAA-----------GAU------GAGAUUUGUUUU---------------------CUGA--------------------AAGACAAAUAAAACGCUGA--CCCCU-----------(603)-----------AGGGUG-AUGAUAUAGUCUAAACUUUUUU-----GAAA-----GAAAAAG-------------------------------------------------------------------------------------------------------------AUUAAGUUUUUG--gaguuccgac
...<<<<<<<--<<.......-----[[^^>>>>>>>---<<<<<<<-....->>>>>>>------------------------------------------.......--<<<<<..-...<<<<<<....<<...-------<<<<<<<------.......-------->>>>>>>------..>>...>>>>>><<<-..<<<<<<<<.<<----...........------>>>>>>>>>>.>>>...[.[[[[[-----.<<<----------------....----------->>>------...<<<<<<<<<---------------------....-------------------->>>>>>>>>.....>>>>>--<<<<<-----------~~~~~----------->>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-------------------------------------------------------------------------------------------------------------.........>>.--]]]]......
Cha_vu.mL2533 gagcuggaga--AAACGU-------AACCUUCUCU----CCUCUAUG-GAAA-CUUAGAGG-----------------------------------------UAAUAAA--CGAGCUC-AAAACGGUGAA-GGC-------------------AUAAAUUACAAGGUCAA-----------------GUUAACGCCGUGGUAAGAACCUAUUCU---------(116)--------AGAAUAUGUUCUCCGUAACGACUGAUUCACAAC----------------(47)-----------GUUGUGA-UGAGAAUGAUGUGU-----------CUGACUCUUUGUCUUUCUUGC----------ACACAUCAUUCAUACGGCUCG--UACCUAAGUUCUUACAGGUGACUGUAGUGAAUAUGGUG-AAGGCAUAGUCUUACCCCAUCA-----GUAA-----UGGUGG-------------------------------------------------------------------------------------------------------------------AAGGUCG--agguuccaag
.....<<<<<--<.....-------[[[[^>>>>>----<<<<<<.<-....->.>>>>>>-----------------------------------------.......--<<<<<<.-...<<<<<<..-<<<-------------------.................----------------->>>..>>>>>><<..<<<<<.<<<<<<---------~~~~~-------->>>>>>.>>>>>>>...[.[[[[[..<<<<<<<----------------~~~~----------->>>>>>>-...<<<<<<<<<<<-----------.....................---------->>>>>>>>>>>....>>>>>>--<<<<...<<<<<<<<<<....>>>>>>.>>>>..>>>>-......]]]]]].<<.<<<<<<-----....----->>>>>>-------------------------------------------------------------------------------------------------------------------...>>..--]]]]].....
Chl_vu.cL2593 uucagaacgu--AAACA--------UCACUGCGUUU----AUCAAUA-GUAA-UAUUGAU-------------------------------------------UUAGUA--UCGACUU-AUAUCGGUGAAA-CCUUCA------CUAGUUC----AUAAAGACCAA------GAACUGG-CUAGUAUGGCAAUACCGAGGG-AAGAUUUUAUUACACUCUAAACAUC(486)UCAGUGAAUAAUUUCCCCGUAGAGACUU----AGGGA-AAACCAUUGAAAAAAAUUUUUCAUCAC---UCCCU-----AGAUAUCAAUCU--------------------GUUA-------------------AGAUUGAUAUAACACGUCGA--CUCCUU----------UUUAG----------AAGGAUG-AAGAUAUAGUCCAUGCCUUAUG-----GAAA-----CAUAGGGAUUU---ACUUUAGAAGAG------UUUU----UUCUUCCUAAAGU-------------------------------------------------------------------UCACCAUG--cgugagacag
....<<<<<<--<....--------[[[[>>>>>>>----<<<<<<<-....->>>>>>>-------------------------------------------......--<<<<<.<-...<<<<<<...-<<....------<<<<<<<----...........------>>>>>>>-.......>>...>>>>>><<<-<<<...<<<<<.<<<<.........~~~~~..>>>>>>>>>>>>>>>....[.[[[[[----<<<<<-...........................--->>>>>-----..<<<<<<<<<<--------------------....------------------->>>>>>>>>>...>.>>>>>--<<<<<<----------.....---------->>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>....---<<<<<<<<<<<<------....---->>>>>.>>>>>>>-------------------------------------------------------------------.....>>.--.]]]].....
Sdu.cL2593 uucagaacgu--AGA---------UUCACUGCGUUU----AUUUUCA-GUAA-UGAAAAU-------------------------------------------UUAGUA--UUGGCUU-AUAUCGGUGAA-ACCUUCA------UUC-----------AUUAAA------------GAA------AAGGUAAUACCGAGGG-AAGAAUUU-------------(477)-------------AAAUUCCCUGUAGAGACUG---AAACCU----------------GAAA-----------AGGUU----GAGAUCAUUUUUCU-------------------GGUA------------------AGCGAGAUGAUCAGACGCCAA--CUCCAAAG------AAAACAAA-------CUUUGGAUG-GAGAUAUAGUCCGUG-CCUUUG-----GAAA-----CAAGGG------------------------------------------------------------------------------------------------------------------AAGACACG--cgugagacag
....<<<<<<--<<.---------[[[[^>>>>>>>----<<<<<<<-....->>>>>>>-------------------------------------------......--<<<<<.<-...<<<<<<..-<<<<<..------<<<-----------......------------>>>------>>>>>..>>>>>><<<-..<<<<<<-------------~~~~~------------->>>>>>>>>...[.[[[[[---.<<<<<----------------....----------->>>>>----..<<<<<<<<<.<<-------------------....------------------>>.>>>>>>>>>..>.>>>>>--<<<<<<<<------........------->>>>>>>.>-......]]]]]]<<.-<<<<<<-----....----->>>>>>------------------------------------------------------------------------------------------------------------------.....>>.--.]]]]]....
Nol.mL2593 uuuaaaacgu--AGAAUA--------CACUGCGU----GUACACGUG-GUAA-CACGAUGUA------------------------------------------AAGCA--CUCGCU--AUAUCGGUGAAA-UCUAAC------AUUCAA---------GAGU----------UUGAAU-----UAUGACAAUACCGAGGG-AAGAUUGAAAAA----AAGUAGAAACUU(461)--UUUAUCAAUCCCCGUAGAGACUG--AAGCUAA----------------(61)-----------UUAGCU---GAGAAGAAAGUG--------------------UACAG---------------------CACUUCUUCAUACGCGAG--CUCCUAG-------ACUGUGAG--------CUAGGAUG-AAGAUAUAGUCCAUGCAUUAUG-----GAAA-----CAUAAUG----------------------------------------------------------------------------------------------------------------AUUAUCAUG--cgugagacag
......<<<<--<<....--------[[^>>>>>----.<<<<<<<<-....->>>>.>>>>------------------------------------------.....--<<<<<.--...<<<<<<...-<<....------<<<<<<---------....---------->>>>>>-----...>>...>>>>>><<<-..<<<<<<.<<<----............~~~~~-->>>.>>>>>>>>>...[.[[[[[--.<<<<<<----------------~~~~----------->>>>>>---..<<<<<<.<<<--------------------.....--------------------->>>>>>>>>....>>>>>--<<<<<<<-------........-------->>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>----------------------------------------------------------------------------------------------------------------......>>.--.]]]......
Msp-1.cL2593 uucagaacgu--AAACA--------UCAUUGCGUUU---AGUUAGGA-GUAA-UCCUUACU-------------------------------------------UAGUA--UUGGCUU-AUAUCGGUGAAC-CCUAAA------GAGU-----------AAAA------------ACUC-----CAAGGCAACGCCGAGGG-AAGACUU------UUUAGAUUAUUCGACAU(492)-----UCGUCCCCGUAGAGACUG--AGGGAGG---------------UUUUA-----------CCUCUCC----GAUAUCUUUUUU-------------------GUUU------------------AAAAAAGAUAUAAUACGCCAA--CUCCAACA---------GAAAA-------UGUUGGAUG-AAGACAUAGUCCAUGCCCUUAU-----GAAA-----AUUUGGG----------------------------------------------------------------------------------------------------------------AAUCACAUG--cgugagacag
....<<<<<<--<<...--------[[[^>>>>>>>---<<<.<<<<-....->>>>.>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<<...------<<<<-----------....------------>>>>-----..>>>...>>>>>><<<-..<<<..------.................~~~~~-----..>>>>>>...[.[[[[[--.<<<<<<---------------.....----------->>>>.>>----.<<<<<<<<<<<-------------------....------------------>>>>>>>>>>>...>.>>>>>--<<<<<<<<---------.....------->>>>>>>.>-......]]]]]]<<.<<<..<<-----....----->>..>>>----------------------------------------------------------------------------------------------------------------......>>.--.]]]].....
Msp-2.cL2593 uucagaacgu--AAACA--------UCAUUGCGUUU---AGUUAGGA-GUAA-UCCUUUCU-------------------------------------------UAGUA--UUGGCUU-AUAUCGGUGAAC-CCUAAA------GAGC-----------AUAA------------GCUC-----CAUGGCAACGCCGAGGG-AAGACUUUU------CAGAUU(497)----------AGAAUCGUCCCCGUAGAGACUG--UGAAGGA----------------(70)-----------UCCUUC----CGAUAUCUCUUUU-------------------GGUU------------------AAAAGAGAUAUAAUACGCCAA--CUCCAACAA--------GCAAA------UUGUUGGAUG-AAAACAUAGUCCAUGCCCUUUU-----GAAA-----AAUUGGG----------------------------------------------------------------------------------------------------------------GACAACAUG--cgugagacag
....<<<<<<--<<...--------[[[^>>>>>>>---<<..<<<<-....->>>>..>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<....------<<<<-----------....------------>>>>-----...>>...>>>>>><<<-..<<<<<<<------......~~~~~---------->>>>..>>>>>>...[.[[[[[--.<<<<<<----------------~~~~----------->>>>>>----..<<<<<<<<<<<-------------------....------------------>>>>>>>>>>>...>.>>>>>--<<<<<<<<<--------.....------>>>>>>>>.>-......]]]]]]<<.<<<..<<-----....----->>..>>>----------------------------------------------------------------------------------------------------------------......>>.--.]]]].....
Naq.cL2593 uucaaaacgu--AAAA----------UACUGCGU----GGAUUUGUA-GCAA-UACAAAUC----------------------------------------AAAAAUAA--UUGGCUU-AUAUCGGUGAAC-CCUAAAA-----UCUAU----------CUU------------AUAGA----AUAUGGCAACGCCGAGGG-AAGAUUUAUAA----------(693)----------UUAUAAAUCCCCGUAGAGACUU-----AUUU----------------UUUA-----------AAAU------AGAUAUUUGUU--------------------(176)--------------------AACAAGUAUAAUACGCCAA--CAUCUU----------AAU-------------AAGAUG-GUGACAUAGUCCAUGCCCUAAU-----GAAA-----GUUUGGG-----------------------------------------------------------------------------------------------------------------AGUUCAUG--cgugagacag
......<<<<--<...----------[[[>>>>>----.<<<<<<<<-....->>>>>>>>----------------------------------------........--<<<<<.<-...<<<<<<...-<<.....-----<<<<<----------...------------>>>>>----....>>...>>>>>><<<-..<<<<<<<<<----------~~~~~---------->>>>>>>>>>>>...[.[[[[[-----<<<<----------------....----------->>>>------..<<<<<<<<<--------------------~~~~~-------------------->>>>>>>>>...>.>>>>>--<<<<<<----------...------------->>>>>>-......]]]]]]<<.<<<.<<<-----....----->>>.>>>-----------------------------------------------------------------------------------------------------------------.....>>.--.]]]......
Cca.cL2593 uucaaaacgu--AAAUAA--------CACUGCGU----GUAGUUGUA-AAAA-UACAACUA------------------------------------------AAAGAU--UUGGCUU-AUAUCGGCGAAA-CCUUA-------CUAUC-----UUUUUAACUGUAC-------GAUAG------AUGGCAAUGCCGAGGG-AAGUUCUUAUUCUA------AAUUAA-------UAGAUUAAGACACCUGUAGAGACUUUAUAAGUUU-----------------AUA-----------AAACUUAUA-AGAUACUUCCU---------------------ACAA-------------------AGGAAAGUAUAAUACGCCAA--CCCCUACUUU-------(30)------AAAGCGGGGAG-GAGAUAUAGUCCAUGCUCUUAU-----GAAA-----AUAGGAGGGAA---GGUUUAACAA--------UAU--------UUGUUAAACU----------------------------------------------------------------------GCAUG--cgugagacag
......<<<<--<.....--------[[[>>>>>----.<<<<<<<<-....->>>>>>>>------------------------------------------......--<<<<<.<-...<<<<<<...-<<...-------<<<<<-----.............------->>>>>------..>>...>>>>>><<<-....<<<<<.<<<<------......------->>>>.>>>>>..>>>...[.[[[[[<<<<<<<<<-----------------...----------->>>>>>>>>-..<<<<<<<<<---------------------....------------------->>>.>>>>>>...>.>>>>>--<<<<<.<<<<-------~~~~------>>>>.>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>....---<<<<<<<<<<--------...-------->>>>>>>>>>----------------------------------------------------------------------..>>.--.]]]......
Ciy.cL2593 uucaaaacgu--AAA----------UCACUGCGU----GUGCACCCC-UAAA-GGGGUAGCA-----------------------------------------AAAUUA--UUGGCUU-AUUUCGGUGAAACCCUA--------CUAU--------AACUGUCAC----------AUAG------CAGGCAAUACCGAGAGUAU--AUUU-------------(688)-------------AAAUUACUUGUAGAGACUUUAUAAGUGCCAA------------AAAGA-------UUGAACACUUAUA-AGAUACCUCCG---------------------AUAU-------------------UGGAGUGUAUAAUACGCCAA--CCCCCAU----------UAA----------AUGGGGUG-AAGAUAUAGUCCAUGCUUUUAC-----UAAA-----GUAAAGGGUA---AGCUUUAAC---------AAUCU--------GUUAAAGCU-----------------------------------------------------------------------CAUG--cgugagacag
......<<<<--<..----------[[[[>>>>>----.<<<<<<<<-....->>>>>.>>>-----------------------------------------......--<<<<<.<-...<<<<<<....<<<.--------<<<<--------.........---------->>>>------.>>>...>>>>>><<<<<.--<<<<-------------~~~~~------------->>>>>>>>>...[.[[[[[<<<<<<<<.<<<------------.....------->>>..>>>>>>>>-..<<<<<<<<<---------------------....------------------->>>>>.>>>>...>.>>>>>--<<<<<<<----------...---------->>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>...---<<<<<<<<<---------.....-------->>>>>>>>>-----------------------------------------------------------------------.>>.--.]]]].....
Cag.cL2593 uucaaaacgu--UGACUG(58)-UUUAACAGCGU----GUGUUUGCA-GUAA-UGUAAACA-------------------------------------------AAGAA--UUGGCUU-AUAUCGGUGAAA-CCU-AC------GUAAUUGUA------(92)-------UACCAUUAU------UUGGCAACGCCGAGGG-AAGACUUUCUGUAAAAA----(787)-----UUUUUAACAAAGUCCCCGUAGAGACUUCUAACUAGUAAAUGU--------GUUUUUA-----ACAUUACCAAGUGG-AGAUAUCCAUA--------------------AAUUG--------------------UAUGGAUAUAAUACGCCAA--CCCCUGUA--UAAAUUACAAAAAAUAAC-UACAGGGUG-GAGACAUAGUCCGUGCUUUGUC-----GAAA-----GACGAAGGCU----UGUUUAGAAU-----AAAUAAACAGA---AUUCUAAACA----------------------------------------------------------------------UCAUG--cgugagacag
......<<<<--<<....~~~~-[[[.[^>>>>>----.<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<.-..------<<<<<.<<<------~~~~------->>>.>>>>>------..>>...>>>>>><<<-..<<<<<<...<<<<<<----~~~~~----->>>>>>..>>>>>>>>>...[.[[[[[<<.<<<.<<<<.<<<--------.......----->>>>>>>..>>>>>-..<<<<<<<<<--------------------.....-------------------->>>>>>>>>...>.>>>>>--<<<<<<<<--..................->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>...----<<<<<<<<<<-----...........--->>>>>>>>>>----------------------------------------------------------------------..>>.--.]].]]]...
Cpe.cL2593 uucagaacgu--UG------------UAGAGC------------------------------------------------------------------------UAGUA--UUGGCUU-AAAACGGCGAA--AACUUC------ACAGCU---------(26)----------GGCUGU-----AUGUU-AACACCGUGGGUAAGAGUUGUAUU---------(128)---------AAUACAGCAUCCCGUAGAGACUU---GGGUUUA--------------AACUC----------UAAACUC----GGAUAUAAGCUUU-------------------(53)------------------AAAGCUUGUAUAAGACGCCAA--ACCCUUCUAU-----GCUGCAA-----AUAGAAGGGA-AAAGACAUAGUCCAUACCUAUAU-----GAAA-----AUAUAGGAUU----GUUAAGAAAA--------(57)-----UUUUACUUAAC-----------------------------------------------------------------------GUAUG--cgugagacag
........<<--<.------------[[[>>>------------------------------------------------------------------------.....--<<<<<.<-...<<<<.<..--<<<...------<<<<<<---------~~~~---------->>>>>>-----..>>>-..>.>>>><<<.....<<<<<<<<---------~~~~~--------->>>>>>>>..>>>...[.[[[[[---<<<<<<<--------------.....---------->>>>>>>----..<<<<<<<<<<<-------------------~~~~------------------>>>>>>>>>>>...>.>>>>>--.<<<<<<<<<-----.......----->>>>>>>>>.-.......]]]]]]<<.<<<<<<<-----....----->>>>>>>...----<<<<<<<<<<--------~~~~----->>>>.>>>>>>-----------------------------------------------------------------------..>>.--].]]......
Cme.cL2593 uucagaacgu--UAAACU(25)-CUAAACUGGCGUU---GAUUUAUA-GUAA-UAUAAAUC-------------------------------------------UAGCA--UUGGCUU-AAAACGGUGAAC-GCUUC-------ACAACC---------(22)----------GGUUGU------AUGCCAACGCCGUGGGUAAGAAUUCUUUUU---------(81)--------AAAAAGAAUUCCCUGUAGAGACUU---GAGCUUA--------------AUCUC----------UAAGCUC----GGAUAUCAA-----------------------(63)----------------------UUGGUAUAAUACGCCAA--AUCCAAUUAU-----GCUACUA-----AUAAUUGGAAU-AAGACAUAGUCCAAGCCUAUAU-----GAAA-----AUAUGGG------------------------(156)------------------------------------------------------------------------------------GUGUACCA--cgugagacag
.....<<<<<--<<....~~~~-[[..[[>>>>>>>---<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<...-------<<<<<<---------~~~~---------->>>>>>------..>>...>>>>>><<<...<<<<<<<<<<<---------~~~~-------->>>>>>>>>>>>>>...[.[[[[[---<<<<<<<--------------.....---------->>>>>>>----..<<<<<<<-----------------------~~~~---------------------->>>>>>>...>.>>>>>--<<<<<<<<<<-----.......----->>>>>>>>>.>-......]]]]]].<.<<<<<<<-----....----->>>>>>>------------------------~~~~~------------------------------------------------------------------------------------...>....--.]].]]....
Cni.cL2593 uucaaaacgu--AAACA--------UCAUUGCGU----GUGCUUAUA-GGAA-UAUAAGCA-------------------------------------------AAGUA--UCGGCUC-AUAUCGGAGAAC-CCUUC-------UUAUUAUAA----AUAUCCCA-----UUAUAAUAA-------UGGCAACCCCGAGGG-AAGAUUUAACUUU--------UUAA---------AAGGUUAUUUCCCCGUAGAGACUU--CAAAUUUU--UUCUUAAUUAAAAUUAAUUUAAUUA--AAAAUUUG---AGAUAUAAUUUCAU------------------AACU-----------------AUGAAAUUAUAUAACACGCCGA--CCCCUAAGUUA----GUUAUAAAUA---UAACCGGGUG-AAGGUAUAGUCCAUGCCCUUAU-----GAAA-----AUAAGGG----------------------------------------------------------------------------------------------------------------AAUAACAUG--cgugagacag
......<<<<--<....--------[[[[>>>>>----.<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<.<...-<<...-------<<<<<<<<<----........----->>>>>>>>>-------.>>...>.>>>><<<-..<<..<<<<<<<--------....--------->>>>>>>..>>>>>...[.[[[[[--<<<<<<<<--.........................-->>>>>>>>---..<<<<<<<<<<<<------------------....----------------->>>>>>>>>>>>...>.>>>>>--<<<<...<<<<----..........--->>>>.>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>----------------------------------------------------------------------------------------------------------------......>>.--.]]]].....
Cre.cL2593 uucaaaacgu--AAAUAA--------CACUGCGU----GUGCUUGCA-GUAA-UGUAAGCA-------------------------------------------AAGUA--UCGGCUU-AUAUCGGUGAAA-CCUUC-------CUAUUG---------(38)----------CAAUAG------AUGGCAACGCCGAGGG-AAGACCAUUUCUUUUU------(506)----AAAAAGAAAUCGUCCCCGUAGAGACUU---UAUAAA----------------(53)-----------UUUAUA----GGAUAUU--------------------UUCUCGAGAGUGGGAA-----------------AGUAUAAUACGCCGA--CUCCUGCCAU------UAACA------GUAGCAGGAUG-AAGACAUAGUCCAUGCCUUUAC-----GAAA-----GUAAAGGGGUU--AGUUUUAAAG-ACCGCAAGUUUUAUUCGG-CUUUAAAAUU----------------------------------------------------------------------UCAUG--cgugagacag
......<<<<--<.....--------[[[>>>>>----.<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<...-------<<<<<<---------~~~~---------->>>>>>------..>>...>>>>>><<<-..<<<.<<<<<<<<<<------~~~~~---->>>>>>>>>>.>>>>>>...[.[[[[[---<<<<<<----------------~~~~----------->>>>>>----..<<<<<--------------------................----------------->>>>>...>.>>>>>--<<<<<<<.<<------.....------>>.>>>>>>.>-......]]]]]]<<<<<<<<<<-----....----->>>>>>>....--<<<<<<<<<<-..................->>>>>>>>>>----------------------------------------------------------------------.>>>.--.]]]......
Col.cL2593 uucaaaacgu--AAAUAA--------CACUGCGU----GUGCACGUG-GUAA-CACGUGCA-------------------------------------------GAGUA--UCGGCUU-AUAUCGGUGAAA-CCUUCCUAUU--UUGAC---------AAACU------------GCAA---UAGAAGGCAACGCCGAGGG-AAGAUCUUUACUU---------(516)-------AAGUAAACGUCCCUGUAGAGACUUCAGAUUUAAUUG-------------(29)---------CAAUUCUG----GGAUACUUUCUCG-------------------UGUG------------------UGUGAAAGUAUAAUACGCCGA--CUCCUGU--------AUUUUCUA-------ACAGGAUG-AAGACAUAGUCCAUGCCCUAGC-----GAAA-----GCCAGGG-GUC--UAAUAGAGGGCU------(106)------GGCCCCUAUUAAACCAUUGACUU--------UUUCCAU--------GAUCAAUGG-------------------------GGCAUG--cgugagacag
......<<<<--<.....--------[[[>>>>>----.<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<<<<.....--<<<.<---------.....------------>>>>---..>>>>>...>>>>>><<<-..<<<.<<<<<<<---------~~~~~------->>>>>>>.>>>>>>...[.[[[[[<<<<....<<<<-------------~~~~--------->>>>>>>>----..<<<<<<<<.<<-------------------....------------------>>.>>>>>>>>...>.>>>>>--<<<<<<<--------........------->>>>>>.>-......]]]]]]<<.<<<<.<<-----....----->>.>>>>-...--<<<<<<.<<<<<------~~~~~------>>>>>>>>>>>..<<<<<<<.<<--------.......-------->>>>>>>>>-------------------------...>>.--.]]]......
Clu.cL2593 uucagaacgu--AAACAA--------CACUGCGUU----UGUCUGUA-GGAA-UACAGACA-------------------------------------------UAGUU--UCGGCUU-AUAUCGGUGAAC-CC-UAA------AGCUU---------CAAAA-----------AAGCU------AUGGCAACGCCUAGGG-AAGAC-----------------(511)---------------GUCCCCGUAGAGACUU----CAGAA----------------GAAACAAA--------UUCUG----GGAUAUAAUCUC-------------------GUGUGG------------------GAGAUUGUAUAAUACGCCGA--CUCCUAUGUAAA-----(36)---UUUACAAUAGGAUG-AAGACAUAGUCCAUGCCCGUGC-----GAAA-----GCAGGGG---------------------------------------------------------------------------------------------------------------AAUUCACAUG--cgugagacag
.....<<<<<--<.....--------[[[>>>>>>----<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<.<<<<...-<<-...------<<<<<---------.....----------->>>>>------..>>...>>>>.><<<-..<<<-----------------~~~~~--------------->>>>>>...[.[[[[[----<<<<<----------------........-------->>>>>----..<<<<<<<<<<-------------------......------------------>>>>>>>>>>...>.>>>>>--<<<<<<<<<<<<-----~~~~--->>>>>.>>>>>>.>-......]]]]]]<<.<<<.<<<-----....----->>>.>>>---------------------------------------------------------------------------------------------------------------.......>>.--.]]]......
Hla.cL2593 uucaaaacgu--CAAA----------GCAGGCGUGUU----AUUGUC-GUAA-GGCAAU-------------------------------------------UUAAGAA--UUAACUG-AUAUCGGUAAAA-CCUUC-------CUAUUUAU------(105)--------GUAAAUAG------AUGGCAAUACCGAGGG-AAGAUUUUAUA-----------(671)---------UAUGUUAUCCCCGUAGAGACUU--CAAAGUGCUU-------------UUA----------AAGCACUUUG--GGAUAUUCUUUC-------------------GUGAGA------------------GGAAGAGUAUAAAACGUUAA--CUCCUAUAUG--GUUUAUAGAAAA---CAUAUAGGAUG-AAGAUAUAGUCCAUG-CCUUGU-----GAAA-----ACAAGG-----------------------------------------------------------------------------------------------------------------AGUGCCAUG--ugugagacag
...<<.<<<<--<...----------[[[>>>>>.>>----<<<<<<-....->>>>>>-------------------------------------------.......--<<<<<..-...<<<<<<...-<<...-------<<<<<<<<------~~~~~-------->>>>>>>>------..>>...>>>>>><<<-..<<<..<<<<-----------~~~~~--------->>>>..>>>>>>...[.[[[[[--<<<<<<<<<<-------------...---------->>>>>>>>>>--..<<<<<<<<<<-------------------......------------------>>>>>>>>>>.....>>>>>--<<<<<<<<<<--............--->>>>>>>>>.>-......]]]]]]<<.-<<<<<<-----....----->>>>>>-----------------------------------------------------------------------------------------------------------------......>>.--]]].......
Sob.cL2593 uucagaacgu--AAAUAA--------UACUGCGUUU----AUCUGUA-GUGA-UAUAGAU-------------------------------------------AUAGUA--UUGGCUU-AUAUCGGUGAAA-CCUUC-------CUAUAGU-------UG-AACU-------GCUGUAG------AUGGCAACGCCGAGGG-AAGACUCCAAUAUUU-------(570)-----AAAUAUUGUCGUCCCCGUAGAGACUU----CAGCA---------------UUCGAU-----------UGCUG----GGAUAAAACUUUG-------------------UGUG------------------UAAAGUUUUAUAAUACGCCAA--CUCUUUGAAUU------CUUUG----AGUUCAAAGAUG-AAGACAUAGUCCAUGCCUCCAU-----GAAA-----GUGGGGGGGUAA-AAUUACC----------AAAAAA----------GGUAAUU-----------------------------------------------------------------------CAUG--cguaagacag
....<<<<<<--<.....--------[[[>>>>>>>----<<<<<<<-....->>>>>>>-------------------------------------------......--<<<<<.<-...<<<<<<...-<<...-------<<<<<<<-------..-....------->>>>>>>------..>>...>>>>>><<<-..<<<..<<<<<<<<-------~~~~~----->>>>>>>>..>>>>>>...[.[[[[[----<<<<<---------------......----------->>>>>----..<<<<<<<<<<<-------------------....------------------>>>>>>>>>>>...>.>>>>>--<<<<<<<<<<<------.....---->>>>>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>.....-<<<<<<<----------......---------->>>>>>>-----------------------------------------------------------------------.>>.--.]]]......
Pbi.cL2593 uucaaaacgu--AAA----------UUACUGCGU----GUGCUUUUA-GAAA-UGAAAGCA----------------------------------------GCAAUAAU--UUGGCUU-AUAUAGGUAAAC-CCUUC-------UGAAAGCU------UCAAACU------GGCUUUCA------AUGGCAAUGCCUAGGG-AAGAUUUAUAUCUAA-------(61)------UUAGAUAUAAAUCCCCGUAGAGACUU-CUUUAGUAA---------------UUU------------UUGCUAAAG-AGAUACUGCAA---------------------(56)--------------------UUGUAGUAUAAUACGCCAA--CUUCCCUUU-----UUUUAUUUUU-----AAAGGGAAG-AAGACAUAGUCCAUGCUUUAGU-----GAAA-----ACUAGAG-GUA-AAAUCUAUUUUAA-UAUUAAAGAAGAAU-UUAAGAUAGAUUU----------------------------------------------------------------------CAUG--cgugagacag
......<<<<--<..----------[[[[>>>>>----.<<<<<<<<-....->>>>>>>>----------------------------------------........--<<<<<.<-...<<<<<<...-<<...-------<<<<<<<<------.......------>>>>>>>>------..>>...>>>>>><<<-..<<<<<<<<<<<<<-------~~~~------>>>>>>>>>>>>>>>>...[.[[[[[-<<<<<<<<<---------------...------------>>>>>>>>>-..<<<<<<<<<---------------------~~~~-------------------->>>>>>>>>...>.>>>>>--<<<<<<<<<-----..........----->>>>>>>>>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-...-<<<<<<<<<<<<<-..............->>>>>>>>>>>>>----------------------------------------------------------------------.>>.--.]]]].....
Pak.cL2593 uucagaacgu--AGA----------UCACUGCGUU----GGUUAAUA-GUAA-UAUUAGCC-------------------------------------------UAGCA--CCGGCUU-AUAUCGGUGAAA-CCUUA-------UUUAGUU-------UAAAACU-------GGCUAAA------AAGGCAAUACCGAGGG-AAGAGCAA--------------(508)------------UUGUUCCCUGUAGAGACUG---AAACUUAAAAA----------AGAAAAC------UUUUUAAGUU---CGAUGGUCAGAAA-------------------GGUU------------------UUUCUAACCAUAAUACGCCGG--CCCUG------------(37)-----------CAGGUG-AAGAUAUAGUCCAUGCCUUUUA-----GAAA-----UAUUAGGAUUC-GGACUUUGCU---------GCAGA--------AGCAAAGUUU--------------------------------------------------------------------UACAUG--cgugagacag
.....<<<<<--<<.----------[[[^>>>>>>----<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<<<.-------<<<<<<<-------.......------->>>>>>>------>>>>...>>>>>><<<-..<<<<<<--------------~~~~~------------>>>>>>>>>...[.[[[[[---.<<<<<<<<<<----------.......------>>>>>>>>>>---..<<<<<.<<<<<-------------------....------------------>>>>>.>>>>>...>.>>>>>--<<<<<------------~~~~----------->>>>.>-......]]]]]]<<.<<<..<<-----....----->>..>>>....-<<<<<<<<<<---------.....-------->>>>>>>>>>--------------------------------------------------------------------...>>.--.]]]].....
Tmu.cL2593 uucagaacgu--AGA----------UCACUGCGUU----GGUUGCUA-GUAA-UAGUAGCC-------------------------------------------UAGCA--UCGGCUU-AUAUCGGUGAAA-CCUUC-------UUUAGUU-------UUUAACU-------GGCUAAA------AAGGCAAUACCGAGGG-AAGAAC----------------(512)--------------GUUCCCUGUAGAGACUG---AAACUUAGAAA-----------GGAAAC------UUUUUAAGUU---CGAUGGCCAGAAA-------------------GGUU------------------UUUCUAGCCAUAAUACGCCGG--CCCUAGCCCC-----GAACACA----GGGGUUUAGGUG-AAGAUAUAGUCCAUGCCUUUUA-----GAAA-----UAUUAGGAUUC-AGACGCUCAAC---------UUU---------GUUGACGUUU--------------------------------------------------------------------AACAUG--cgugagacag
.....<<<<<--<<.----------[[[^>>>>>>----<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<...-<<<<.-------<<<<<<<-------.......------->>>>>>>------>>>>...>>>>>><<<-..<<<<----------------~~~~~-------------->>>>>>>...[.[[[[[---.<<<<<<<<<<-----------......------>>>>>>>>>>---..<<<<<.<<<<<-------------------....------------------>>>>>.>>>>>...>.>>>>>--<<<<<<<<<<-----.......---->>>>.>>>>>.>-......]]]]]]<<.<<<..<<-----....----->>..>>>....-<<<<<.<<<<<---------...--------->>>>>>>>>>--------------------------------------------------------------------...>>.--.]]]].....
Afo.cL2593 uucagaacgu--AGACAA--------CACUGCGUU----GGUUGGCA-GUAA-UGUCAACC-------------------------------------------UAGCA--UCGGCUU-AUAUCGGUGAA-GCCUUC-------UUUAGUUG-------CGAAC-------CGACUGAA------AUGGUAAUACCGAGGG-AAGACUCUAU------------(427)----------AUAGAGUCCCCGUAGAGACUG---AGACCU-----------AAUUUAACAAC-----------GGGUCG--AGAUAGCUGCAG--------------------AUUUCA-----------------CUGCAGGUAUAAAACGCCGA--CUCCUAUA--------CUUUCA-------UAUAGGAUG-AAGAUAUAGUCCAUGCCUAUUG-----AAAA-----CAGUAGG-----------------------------------------------------------------------------------------------------------------AAAACAUG--cgugagacag
.....<<<<<--<<....--------[[^>>>>>>----<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<..-<<<...-------<<<<<<<<-------.....------->>>>>>>>------..>>>..>>>>>><<<-..<<<<<<<<------------~~~~~---------->>>>>>>>>>>...[.[[[[[---.<<<<<-----------...........----------->>>>>.--..<<<.<<<<<<--------------------......----------------->>>>>>.>>>...>.>>>>>--<<<<<<<<--------......------->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--.]]]......
Apu.cL2593 uucagaacgu--AGACAA--------CACUGCGUU----GGUUGGCA-GUAA-UGUCAACC-------------------------------------------UAGCA--UCGGCUU-AUAUCGGUGAA-GCCUUC-------UUUAGUUG-------CGAAC-------CGACUGAA------AUGGUAAUACCGAGGG-AAGACUCUAUGAA---------(426)-------UUGAUAGAGUCCCCGUAGAGACUG---AGACCU-----------AAUUUAACAAC-----------GGGUCG--AGAUAGCUGCAG--------------------AUUUCA-----------------CUGCAGGUAUAAAACGCCGA--CUCCUAUA--------CUUUCA-------UAUAGGAUG-AAGAUAUAGUCCAUGCCUAUUG-----AAAA-----CAGUAGG-----------------------------------------------------------------------------------------------------------------AAAACAUG--cgugagacag
.....<<<<<--<<....--------[[^>>>>>>----<<<<<<<<-....->>>>>>>>-------------------------------------------.....--<<<<<.<-...<<<<<<..-<<<...-------<<<<<<<<-------.....------->>>>>>>>------..>>>..>>>>>><<<-..<<<<<<<<<<<---------~~~~~------->>>>>>>>>>>>>>...[.[[[[[---.<<<<<-----------...........----------->>>>>.--..<<<.<<<<<<--------------------......----------------->>>>>>.>>>...>.>>>>>--<<<<<<<<--------......------->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--.]]]......
Mvi.mL2593 uuuagaacgu--AAACUG(29)----CACUGCGUU----ACUUUAUG-GUAA-CAUAAAGA------------------------------------------AAAGCA--UUAACUU-AUAUCGGUGAAC-UCUUUC---------------------CAAGC-------------------GAGAGACAAUACCGAGGG-AAAAC--------UAAAAGUAGCAAAAAA(458)-------GUUACCUGUAGAGACUG-AGAAAUC--------------UUCUU---------------GAUUUC--CGAUUCUUGU-------------------AAAAUCCUC-------------------ACAAGAAUAAUACGUUAA--CCCCUAUA----------UAU--------UAUAGGGUG-AAGAUAUAGUCCAUGCUGUAUA-----GUAA-----UAUACAG-----------------------------------------------------------------------------------------------------------------AAAACAUG--cgugagacag
.....<<<<<--<.....~~~~----[[[>>>>>>----.<<<<<<<-....->>>>>>>.------------------------------------------......--<<<<<.<-...<<<<<<...-<<<<<<---------------------.....------------------->>>>>>...>>>>>><<<-..<<<--------................~~~~~------->>>.>>>...[.[[[[[-.<<<<<<--------------.....--------------->>>>>>--..<<<<<<<<-------------------.........------------------->>>>>>>>...>.>>>>>--<<<<<<<<----------...-------->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>-----------------------------------------------------------------------------------------------------------------.....>>.--.]]]......
Aca.mL2593 uuuagaacgu--AGAUAA--------CACUGCGUU----GGUUUGUG-GUAA-CAUAAACC------------------------------------------GUAGCA--UUAACUU-AUAUCGGUGAA-GCCCUA-------CUCUUUU-------UUGAACU-------GGAAGAG-------GGGUAAUACCGAGGG-AAAAUAUAAAUUAUUU------(473)--AAAUAGUUUAUUAUUACCUGUAGAGACUG-AGGAGUAGUUUUUG----------UUA--------UAAAAACUAUUCC-CGAUAAUUCC-------------------AAACUUCCUC------------------GGAAUUAUAAUACGUUAA--CUCCAUAA-------UAAAUUUUU-----UUAUGGAUG-AAGAUAUAGUCCAUG-CCACUA-----GUAA-----UAGUGG-----------------------------------------------------------------------------------------------------------------AUUUUCAUG--cgugagacag
.....<<<<<--<<....--------[[^>>>>>>----<<<<<<<<-....->>>>>>>>------------------------------------------......--<<<<<.<-...<<<<<<..-<<<<..-------<<<<<<<-------.......------->>>>>>>------->>>>..>>>>>><<<-..<<<<<<<<<<<<<<------~~~~~-->>>>>>>>>>.>>>>.>>>...[.[[[[[-.<<<<<<<<<<<<<----------...-------->>>>>>>>>>>>>-..<<<<<<<<-------------------..........------------------>>>>>>>>...>.>>>>>--<<<<<<<<-------.........----->>>>>>>.>-......]]]]]]<<.-<<<<<<-----....----->>>>>>-----------------------------------------------------------------------------------------------------------------......>>.--.]]]......
Tag.cL2596 agaacgucgu--AGAAUA---------UUUGCGAC------CAUUUUAANUGAUUUA------------------------------------------CAUGACAAAA--UCGACUC-AUAACGGUGAAG-CCCAAAGAGU-----------------UGGAC----------------ACCUUUGGGGAAUACCGUGGG-AAGUCGGUUGCUA---------(428)------UAGCAACUUGACCCCGUAACGACUU----CAUUU-----------------GAAA------------AAAUG----GGAUUUCUUAAU---------------------AAU------------------AUUAAGAUAUAAUACGUCGA--UACUCGC----------(28)---------GCGAGAUA-AUGGUAUAGUCUAACCCCUCAA-----GUAA-----UUGAGGGAUU--UUCCU--------------(75)--------------AGGAA---CUCC--------------(59)------------GGAG---------------------------UAGUUG--nagacaguuc
.....<<<<<--<<<...---------^^^>>>>>------................------------------------------------------..........--<<<<<..-...<<<<<<...-<<<<<<<.<<-----------------.....---------------->>>>>>>>>...>>>>>><<<-..<<<<<<<<<<<---------~~~~~------>>>>>>>>.>>>>>>...[.[[[[[----<<<<<-----------------....------------>>>>>----.....<<<<<<<---------------------...------------------>>>>>>>........>>>>>--<<<<<<<----------~~~~--------->>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>...--<<<<<--------------~~~~-------------->>>>>---<<<<--------------~~~~------------>>>>---------------------------...>>.--.]]]......
Cbr.cL2596 agaacgucgu--AGAACA----------UUGCGAC----CUCAC-GAAGNGAA---GUG----------------------------------------CAUGACAAAN--NCGACUC-AUAACGGUGGAG-CCCAAACA------------------ACUGGACA---------------UGUUGGGGGAAUACCGUGGG-AAGUCGGUUGCUAG--------(754)-----CUAGCAACUUGACCCCGUAACGACUU----CAUCU-----------------GAAA------------AGAUG----GGAUAUCUCCGGUUU-----------------UUAU--------------GUAAACAAAGAUAUAAGAUGUCGA--CUCUCGUU---------(26)--------AACGAGAUG-AAGGUAUAGUCUAACCUUUUAA-----GCAA-----UUAGAAGAAU--UUCCUGA------------GAAA------------UCAGGAA---CUCC--------------(54)------------GGAG---------------------------UGGUUG--aagacaguuc
.....<<<<<--<<....----------^^>>>>>----..<<<-........--->>>----------------------------------------..........--<<<<<..-...<<<<<<...-<<<.<<<<------------------........--------------->>>>.>>>...>>>>>><<<-..<<<<<<<<<<<<--------~~~~~----->>>>>>>>>.>>>>>>...[.[[[[[----<<<<<-----------------....------------>>>>>----..<<<<<<...<<<<-----------------....--------------..>>>>..>>>>>>.....>>>>>--<<<<<<<<---------~~~~-------->>>>>>>.>-......]]]]]]<<.<<<<<<<-----....----->>>>>>>...--<<<<<<<------------....------------>>>>>>>---<<<<--------------~~~~------------>>>>---------------------------...>>.--]]........
Cpa.cL2596 aaaacgucgu--GAACUG---------CUUGCGAC----CUUGCAAA-GCGA-UUUGCA------------------------------------------UGUAAAAA--UUGCCUC-AUAUCGGAGAAA-CCCUUUUUC------------------(105)----------------GAAAAAGGGCAACCCCGAGGG-AAGUUGAUAC----(752)AAUUCUAG---------AUAUUUAACCCCGUAACGACUC----UGUU------------------(53)-------------GGCA----GGAUAGCA-----------------------(40)-----------------------UGCUAUAACACGGCAA--CUCUUUCUUUUCAUC-AAUAAA-GAUGCAAAAAAGAUG-AUGGUAUAGUCUGAC-CCCUAA-----GUAA-----UUAGGG-AACUU-UCCAAAACCGAAUCUCA-AACGA-UGAGAAAGGUUAAGGA---UUUUUC-------------(78)-----------GAAAAA---------------------------AAUCG--gagacaguuu
.....<<<<<--<<....---------[^^>>>>>----..<<<<<<-....->>>>>>------------------------------------------........--<<<<<..-...<<<<.<...-<<<<<<<<<------------------~~~~~---------------->>>>>>>>>...>.>>>><<<-..<<<<<<<<----~~~~~........--------->>>>>.>>>>>>...[.[[[[[----<<<<------------------~~~~------------->>>>----..<<<<<<-----------------------~~~~----------------------->>>>>>.....>>>>>--<<<<<<.<<<.<<<<-......->>>>.>>>>>>>>.>-......]]]]]]<<.-<<<<<<-----....----->>>>>>-.....-<<<..<<<<...<<<<<-.....->>>>>..>>>>..>>>---<<<<<<-------------~~~~----------->>>>>>---------------------------..>>.--]]].......
Cmo.cL2596 aaaacgucgu--AAA----------GUAUUGCGAC----CUUGCAUU-NGAA-GAUGC------------------------------------------UUGAUAAAU--UUGCCUC-AUAUCGGUGAAC-CCCUCCUUUUUA----------------UUUU---------------UAAAAAAGGGUAACCCCGAGGG-AAGUCAGGAAU-----------(715)---------AUUCUUGACCCCGUAACGACUC----UGUU-----------------(116)-------------GGCA----GGAUAACA-----------------------(54)-----------------------UGUUAUAACACGGCAA--CUCCUUUCACU---AAAAUAA------AGUGAAAGAUG-GUGGUAUAGUCUUAA-CCUUUA-----GUAA-----UUAGGG-AACU------GGGC----------(29)---------GCUU-----GACAACUUA-----------GCAUGCG----------UAAGUUG-GCGUUCUCAAAAGGGGGAGGGCACGUCACG--gagacaguuc
.....<<<<<--<<.----------[[.^^>>>>>----...<<<<<-....->>>>>------------------------------------------.........--<<<<<..-...<<<<.<...-<<<<..<<<<<<----------------....--------------->>>>>>>>>>...>.>>>><<<-..<<<<<<<<<-----------~~~~~--------->>>>>>>>>>>>...[.[[[[[----<<<<-----------------~~~~~------------->>>>----..<<<<<<-----------------------~~~~----------------------->>>>>>.....>>>>>--<<<.<<<<<<<---.......------>>>>>>>>>.>-......]]]]]]<..-<<<<.<-----....----->.>>>>-....------<<<<----------~~~~--------->>>>-----..<<<<<<<-----------.......---------->>>>>>>-<<.<<<<<......>>>>>.>>.....>..--]].]].....
Ceu.cL2596 aaaacgucgu--AAACUGA--------CUUGCGAC----CUUGUAAA-GCGA-UUUACAUG------------------------------------------AUAAAU--UUGCCUC-AUUUCGGAGAAC-CCCUUUU----------------UUUUACCAAACAUUU------------AAAAGGGCAACCCCGAGGG-AAGUCGGGUUAUAUA-------(861)----UGAAAAACCUUGACCCCGUAACGACUC----UGU-------------------(51)--------------GCA----GGAUAAC------------------------(38)------------------------GUUAUAACACGGCAA--CUCUUUAAU------UUUUAUUU-----AUUAAAGAUG-AUGGUAUAGUCUAAC-CCCUAA-----GUAA-----UUAGGG-AAUUAUGUCAAAGCCU--------(25)--------AGGCCAAGACAACUUUCUAAACUUAAUC----ACUC---GAUUAAGCAUGAA-------------------------UUUAAUUG--gagacaguuu
.....<<<<<--<<.....--------[^^>>>>>----<.<<<<<<-....->>>>>>.>------------------------------------------......--<<<<<..-...<<<<.<...-<<<<<<<----------------...............------------>>>>>>>...>.>>>><<<-..<<<<<<<<...<<-------~~~~~---->>...>>>>>.>>>>>>...[.[[[[.----<<<-------------------~~~~-------------->>>----..<<<<<------------------------~~~~------------------------>>>>>.....>>>>>--<<<<<<<<<------........----->>>>>>>>.>-.......]]]]]<<.-<<<<<<-----....----->>>>>>-.....<<<<...<<<<--------~~~~-------->>>>...>>>>...<<<....<<<<<<<----....--->>>>>>>...>>>-------------------------.....>>.--]]].......
Cec.cL2596 aaaacgucgu--AAACUGA--------CUUGCGAC----CUUGUAAA-GUAA-UUUAC------------------------------------------UUGAAAAAU--UUGCCUC-AUUUCGGUGAA-ACCCUUUU-----UC------UUUCUUUCUUUUUUAACCAAAC---GA-UUUUAAGGGUAACCCCGAGGG-AAGUCAGGUU------------(956)---------AACCUUGACCCCGUAACGACUC----UGU-------------------(86)--------------ACA----GGAUAACAACUAUGCCUUU------------UUCU------------GAAGUAACAGUUGUUAUAAUACGGCAA--CUCUUUAAU--UUUUCUUUAUUAAUU--AUUAAAGAUG-AUGGUAUAGUCUAAC-CCCUAA-----GUAA-----UUAGGG-AUUUGUGUUUGGACCUUU----UAAAAAA---AAGGGUUCCGACAA--CGAUCUAAACUUAAUUCAAGGUUUCUUGAUUAAGCAUGAUUG-------------------------AGUUUG--gagacaguuc
.....<<<<<--<<.....--------[^^>>>>>----...<<<<<-....->>>>>------------------------------------------.........--<<<<<..-...<<<<.<..-<<<<<<..-----<<------......................--->>-....>>>>>>..>.>>>><<<-..<<<<<<<<------------~~~~~--------->>>>>.>>>>>>...[.[[[[[----<<<-------------------~~~~-------------->>>----..<<<<<<<<<....<<<<------------....------------>>>>....>>>>>>>>>.....>>>>>--<<<<<<<<<--...............-->>>>>>>>.>-......]]]]]]<<.-<<<<<<-----....----->>>>>>-.....<<<<.<<<<<<<<----.......--->>>>>>>>.>>>>.--<<<<<....<<<<<<.<<<<....>>>>>>>>>>...>>>>>-------------------------...>>.--]]].......
Cre.c.psbA,2 --acaugggu--UUCU------CAUUCGUGGCCCA----ACAAAAAG-GUGA-CUUUUUG---------------------------------------AUUAAAAAAA--CUGACUC1047ACGGUGAACCCUAAA-------UUCGCA----------UAAA---------UGCGAA-----CAUGGCAAUACCGUGGG-AAGAAUUAGCAUU---------(42)--------GAUGCUAAUUCCCUGUAACGACUG-----AUCC-----------------GAAA------------GGA-----GAGAGCGAGUU--------------------AAUAUA--------------------AACUUGCUAACACGUCAG--CACUCGUU---------(76)--------GACGAGUUG-AAGGUAUAGUCUAAACUUAAUA-----GAAA-----UAUUAAG--------------------------------------------------------------------------------------------------------------AUCCACUUUUG--cgugaguggg
--...<<<<<--<...------[[[[[[[^>>>>>----.<<<<<<<-....->>>>>>>---------------------------------------..........--<<<<<..~~~~<<<<<<...<<....-------<<<<<<----------....--------->>>>>>-----...>>...>>>>>><<<-..<<<<<<<<<<<---------~~~~-------->>>>>>>>>>>>>>...[.[[[[[-----.<<<-----------------....------------>>>-----...<<<<<<<<--------------------......-------------------->>>>>>>>.....>>>>>--<<<<<<<<---------~~~~-------->>>>>>>.>-......]]]]]]<<<<<<<<<<-----....----->>>>>>>--------------------------------------------------------------------------------------------------------------.......>>>.--]]]]]]]]..
P1 P10 P1' P2 P2' P2.1 P2.1' P3 P4 P5 P5a P5a' P5' P4' P6 P6' P7 P7.1 P7.1' P7.2 P7.2' P3' P8 P8' P7'P9.0 P9 P9' P9.1 P9.1' P9.2 P9.2' P9.0' P10'