P1             P10 P1'        P2                P2' P2.1                              P2.1'        P3        P4        P5                           P5'     P4'  P6     P6a                          P6a'  P6'      P7              P7.1                         P7.1'             P7.2                                 P7.2'                    P3'      P8                            P8'                 P7'
RB3.v.nrdB,1        ucuuuugcgu--AAA--------AUGCGCCUU---UAAACG---GUAA----CGUUUA-----------------------------------------UCGAAAACUCCUUUAAU-UGCUGGAAAGUCCU------------UUAU---------AGGAAAACUAGCAGCCAAGGUUUUGCUUGCA-(837)------UGCAAAGCAA--GGUUCAACGACUA------------GUC----------UUCG-------------GAC-----------GUAGGGUC---------------AAGC-------------GACUC-----------------GA-AAUGGGGAGAAUCC----------UCUG----------GGAUU--------GUGAUAUAGUCUGGU-CUGCAUAGUAAUAUGUAGCAGUUC----AUAAGA-----GAACGGGUUGAGAAUUAGCGAGCUCAAUCGAACA-UAACG--guaccuuuaa
                    ......<<<<--<..--------[^>>>>...---<<<<<<---....---->>>>>>-----------------------------------------.......<<<.<<<...-<<<<<<....<<<<------------....--------->>>>...>>>>>><<<......<<<<<<<<<-~~~~~------>>>>>.>>>>-->>>...[.[[[[[------------<<<----------....------------->>>-----------...<<<<<---------------....------------->>>>>-----------------.>->>.>>>...<<<<<----------....---------->>>>>--------......]]]]]][<<-<<<<<<<....>>>>>>>..<<<<----......----->>>>.<<<<<<<..........>>>>>>>...].-..>>.--]]........
T4.v.nrdB,1         ucuuuugcgu--AAA--------AUGCGCCUU---UAAACG---GUAA----CGUUUA-----------------------------------------UCGAAAACUCCUUUAAU-UGCUGGAAAGUCC------------UUUAU----------GGAAAACUAGCAGCCAAGGUUUUGC------(352)-------GCAAAACAA--GGUUCAACGACUA------------GUC----------UUCG-------------GAC-----------GUAGGGUC---------------AAGC-------------GACUC-----------------GA-AAUGGGGAGAAUCCC---------UCC----------GGGAUU--------GUGAUAUAGUCUGGA-CUGCAUGGUAACAUGCAGCAGUUC----AUAAGA-----GAACGGGUUGAGAAUUAGCGAGCUCAAUCGAAC--AUACG--guaccuuuaa
                    ......<<<<--<..--------[^>>>>...---<<<<<<---....---->>>>>>-----------------------------------------.......<<<.<<<...-<<<<<<....<<<------------.....---------->>>...>>>>>><<<...<<<<<<<------~~~~~------->>>>>>>..-->>>...[.[[[[[------------<<<----------....------------->>>-----------...<<<<<---------------....------------->>>>>-----------------.>->>.>>>...<<<<<<---------...---------->>>>>>--------......]]]]]][<<-<<<<<<<....>>>>>>>..<<<<----......----->>>>.<<<<<<<..........>>>>>>>...]--.>.>.--]]........
T4.v.td,1           uuucuugggu--UAAUUG-----AGGCCUG-----AGUAUAAGGUGAC-UUAUACUUG---------------------------------------------UAAUCUAUCUAA--ACGGGGAACCUCU------------CUAGU----------AGACAAUCCCGUGCUAAAUUGUAGGACUG--(758)------UCUACAUAAA--UGCCUAACGACUA------------UCCC---------UUUG------------GGGA-----------GUAGGGUC---------------AAGU-------------GACUC--------------GAAAC-GAUAGA--CAACUUG--------CUUUAA--------CAAGUUG-------GAGAUAUAGUCUGCU-CUGCAUGGUGACAUGCAG--CUGGA---UAUAAU----UCCGG-GGUAAG--AUUAACGACCUUAUCUGAACAU-AAUG--cuaccguuua
                    ......<<<<--<.....-----[^>>>>.-----<<<<<<<<<....->>>>>>>>>---------------------------------------------...<<<<<<...--<<<<<<....<<<------------.....---------->>>...>>>>>><<<....<<<<<<<<<<--~~~~~------>>>>>>>>>>-->>>...[.[[[[[------------<<<<---------....------------>>>>-----------...<<<<<---------------....------------->>>>>--------------.....->>>>>>--<<<<<<<--------......-------->>>>>>>-------......]]]]]][.<-<<<<<<<....>>>>>>>--<<<<<---......---->>>>>-<<<<<<--.........>>>>>>....]..-.>..--]]........
Beta-22.v.td,1      guuggagucc--GUUAAUUAGUAGCGGCUUUAGG-GAGUA----AUCC-----CUAUC------------------------------------------GAAUAAAUCUGUGAAU-UCAGGGGAAGCCUGUAGCCACUGUC-UUGAGAUAGGGGUAUGGCAAUCCUGAGCGAAGCCUCU---------UAA----------GGAGGAA--CGUGCAACGACUA------------UCCC---------UUCG------------GGGA-----------GUACACCC---------------AAGC-------------GGGUG--------------GAAGC-GCAGAUU--CCCUAUU-------(122)--------AAUAGGG------UAGUGAUAUAGUCUG-GCCUUCAUGGAAACAUGGAGCAGC-------GUAA--------GCGGGCAGGGAGUA-GCGAACCCUGUUGAACA--UAAG--cgaguaauga
                    .<<<<<<.<<--<<<<....[^^^^>>>>>>>>.-<<<<<----....----->>>>>------------------------------------------......<<<<<<<...-<<<<<<...<<<.<<<.<<.<<<<<-....>>>>>>>.>>>>>>..>>>>>><<<...<<<<<---------...---------->>>>>..-->>>...[.[[[[[------------<<<<---------....------------>>>>-----------...<<<<<---------------....------------->>>>>--------------....>->>>>>>.--<<<<<<<-------~~~~~-------->>>>>>>------........]]]]]][-<.<<<<<<<....>>>>>>>..<<-------....-------->>.<<<<<<<....-.....>>>>>>>...].-->...--]]]]].....
Ceu.c.psbC,1        uccuggaggu--GA--(10)-CAUUGCCUCCAAC-UAGUG----AAAG-----CUAGU---------------------------------------UUUAAAAAGUCUGCCUAA--ACGGAGAAUCUCUCAGCUGU-----(55)-----ACACUGAGACAACUCCGUAUCAACUUACCGUUUU---(588)-----AAAACGUAAGA--GAUCUAACGACUA------------UCCC---------GCAA------------GGGA-----------GUAGGAGUA--------------AAGUU------------ACUCC--------------GAAAC-GGCAGA---GAUCC---------(115)----------GGAUC--------AAGAUAUAGUCUGAU-CUUUACAGUGAUGUAAAG--CGGGUU--UGAAAU---AAGCCGGGGCGA---AUUAACGAAUCGCUU-GAACAUUAAUG--ggugacguuc
                    ...<<<<<<<--<<--~~~~-[[^^>>>>>>>..-<<<<<----....----->>>>>---------------------------------------.........<<<<<<...--<<<<<<....<<<<<<.<<<-----~~~~----->>>>>>>>>...>>>>>><<<...<<<<.<<<<<---~~~~~----->>>>>>>>>..-->>>...[.[[[[[------------<<<<---------....------------>>>>-----------...<<<<<<--------------....>------------>>>>>--------------.....->>>>>>---<<<<<---------~~~~~---------->>>>>--------......]]]]]][<<-<<<<<<<....>>>>>>>--<<<.<<--......--->>.>>><<<<<<---.........>>>>>>-...]....>>.--]]]]......
Cre.c.psbA,3        uccuggaggu--GGU-(119)-GCUACCUCCUGAAGGUGAUGAAGACAAUUCCUUACU--------------------------------------------AAAUUCUGAAAAUA-AGGCAAAUGGUAUU----------(447)---------AGUGGCAGUUGCCUGCCAAC-------------(200)--------------AA--UGUCUAACGACCA------------UCUC---------GCAA------------GAGA-----------GUAGGUGC---------------AAGC-------------GCACCGAAACGACGAUUAUCCUGU-UUCAUAAUAUAUCCCCGUAAGGGA(94)UCCCGUCAGGGGAUG(14)----CGGAGAUAGUCUAG-CGAGCUAUCUUG--------------------------------------------------------AACAUA--AAUG--aucucuggua
                    ....<<<<<<--<<<-~~~~~-^>^>>>>>>....<<<<<.<<<.....>>>.>>>>>--------------------------------------------....<.<<<<<...-<<<<<<....<<<<----------~~~~~--------->>>>....>>>>>>......-------------~~~~~--------------..--......[.[[[[[------------<<<<---------....------------>>>>-----------...<<<<<---------------....------------->>>>>..................>->>>>.>...<<<<<<<....<<<<~~~~>>>>....>>>>>>>~~~~----......]]]]]][<-............--------------------------------------------------------....].--..>.--].].......
Phi-E.v.DP,1        uaaugagccu--AAAGAAA---GUUGGGCACC---GCUAUG---GUAA----CAUAGCGUGUU--------------(60)-------------GACAC---UAGGGAGUAUGCUA-ACAGGGGAACUGAGUAGG------GAUGAGCG--CCUACACAGCAAUCCUGUGCCAAGACCC----------UUGU----------GGGUAA--GGUGCAACGACUAUCGAAA------CCACUCA------GAAA-------UGAGGAAGG-------------GAGUAGAGUACUCUACAGGUGAAACUCCUGUGGGGGAAGCGCU-----(494)--------U-AUACUG---GAGUG----------(70)----------CACUCAACGGUUGAAGAUAUAGUCUAGU-GGGUAGCAUAAUUAGGGAAUUAUAUACUACCC-------------------------------------------AUAG--aacgcucaac
                    ......<<<<--<<.....---[^^>>>>...---<<<<<<---....---->>>>>><<<<<--------------~~~~------------->>>>>---.....<<<<<<...-<<<<<<...<<<.<<<<<------........-->>>>>.>>>...>>>>>><<<...<<<<----------....---------->>>>..-->>>...[.[[[[[......------<<.<<<<------....------->>>>...>>-------------.<<<......<<<<<<<<<.......>>>>>>>>>.....>>>-----~~~~~-------->->>>>>.---<<<<<----------~~~~---------->>>>>..............]]]]]].<<-<<<<<<.<<<<<<....>>>>>>...>>>>>>------------------------------------------->>..--]]].......
LL-H.v.terL,1       cagugugguu--UAACA----UUCGGGCCACACU----------------------------------------------------------------AUAAUAAACUCCUUGAAU-UCGGUAAACCUCUCAACGAAU-----AAA-----GUUCGCAGACAAUACCGAGCUAAGCUUAAUAUGCUAA(545)--UUAGCAGAAAAGAA--AGUGUAACGACUAUCGAAACA---CAAAAAGCAUCAGCUGAUUAGCUGAUGCUUUUUGAAUGGAGUAGAGUAGUCCCC--------------AAGC------------GGGGGC--------------GAAGC-AGGGAG---CAUCA---------GCAAUA---------UGAUG--------AAGAGCUAGUCUGAA-CUUGAUAGAAAUAUCAAG-AGCAUGUAUGGACGCGAUACAUGC------------------------GCAACAACAUUA--cgaagaauuu
                    .<<<<<<<<<--<....----[[[^>>>>>>>>>----------------------------------------------------------------........<<<<<<<...-<<<<<<....<<<...<<<<<-----...----->>>>>.>>>...>>>>>><<<...<<<....<<<<<<~~~~~-->>>>>>...>>>..-->>>...[.[[[[[........---<<<<<<<<<<<<<<<....>>>>>>>>>>>>>>>..............<<<<<<--------------....------------>>>>>>--------------....>->>>>>>---<<<<<---------......--------->>>>>--------......]]]]]][<<-<<<<<<<....>>>>>>>-.<<<<<<<<.......>>>>>>>>------------------------....]....>>.--]]]]......
SPO1.v.DP,1         uaaugagccu--AAAGAA----GUUGGGC------ACCGCUAUGGUAACAUAGCGUGU--------------------------------------------UAAACCCAGUG(69)ACAGGGGAACUGAGUAGG------GAUGAGCG--CCUACACAGCAAUCCUGUGCCAAGACCCU---------UUG----------AGGGUAA--GGUGCAACGACUA------------UCGAAACCACUCAGAAAUGAGGAAGGGAGUAGA-----------GUACCUUA---------CAGGUGAAACUCCUG--------UAGGG--------------GAAGC-GCUGGG--CAACCGUUGAG----(543)----CUCAACGGUUG--------AAGAUAUAGUCU-AGCAGGUAGUAUAA----------UCGGGGAAUU---------------------------------UUAUACUACUUGUAG--aacgcucagc
                    ......<<<<--<<....----[^^>>>>------<<<<<<<<<....>>>>>>>.>>--------------------------------------------....<<<<<<<~~~~<<<<<<...<<<.<<<<<------........-->>>>>.>>>...>>>>>><<<...<<<<<---------...---------->>>>>..-->>>...[.[[[[[------------<<.............................>>-----------...<<<<<---------...............-------->>>>>--------------....>->>>>>>--<<<<<<<<<<<----~~~~~---->>>>>>>>>>>--------......]]]]]]-.<<<<<<<<<<<<<----------..........--------------------------------->>>>>>>>>>>>>..--]]].......
SP82.v.DP,1         uaaugagccu--AAAGAA----GUUGGGC------ACCGCUAUGGUAACAUAGCGUGU--------------------------------------------UAAACCCAGUG(69)ACAGGGGAACUGAGUAGG------GAUGAGCG--CCUACACAGCAAUCCUGUGCCAAGACCCU---------UUG----------AGGGUAA--GGUGCAACGACUA------------UCGAAACCACUCAGAAAUGAGGAAGGGAGUAGA-----------GUACCUUA---------CAGGUGAAACUCCUG--------UAGGG--------------GAAGC-GCUGGG--CAACCGUUGAG----(576)----CUCAACGGUUG--------AAGAUAUAGUCU-AGUGGGUAGUGUAA----------UUAGGGAAUU---------------------------------AUAUACUACCCAUAG--aacgcucaac
                    ......<<<<--<<....----[^^>>>>------<<<<<<<<<....>>>>>>>.>>--------------------------------------------....<<<<<<<~~~~<<<<<<...<<<.<<<<<------........-->>>>>.>>>...>>>>>><<<...<<<<<---------...---------->>>>>..-->>>...[.[[[[[------------<<.............................>>-----------...<<<<<---------...............-------->>>>>--------------....>->>>>>>--<<<<<<<<<<<----~~~~~---->>>>>>>>>>>--------......]]]]]]-.<<<<<<<<<<<<.----------..........---------------------------------.>>>>>>>>>>>>..--]]].......
T4.v.nrdD,1         gcuuaugagu--UAACGUAAGUCAAGCUCAUG---------------------------------------------------------------------UAAAAUCUGCCU-AA-AACGGGAAACUC-------------UCACU---------GAGACAAUCCGUUGCUAAAUCAGC---------AGUA--------GCUGUAAA--UGCCCAACGACUA------------UCCCU-----GAUGAAUGUA--------AGGGA-----------GUAGGGUC---------------AAGC-------------GACCC--------------GAAAC-GGCAGA--CAACUC----------UAA----------GAGUUG--------AAGAUAUAGUCUGAA-CUGCAUGGUGACAUGCAG----------------(825)---------------------------CUGAACAC-AUUG--augaagugaa
                    ...<<<<<<<--<........[[[>>>>>>>>---------------------------------------------------------------------.....<<<<<<.-..-<<<<<<...<<<-------------.....--------->>>....>>>>>><<.....<<<<---------....-------->>>>....--.>>...[.[[[[[------------<<<<<-----..........-------->>>>>-----------...<<<<<---------------....------------->>>>>--------------.....->>>>>>--<<<<<<----------...---------->>>>>>--------......]]]]]][<<-<<<<<<<....>>>>>>>----------------~~~~~---------------------------.....]..-.>>.--.]]]......
Ban.b.recA          guucggaaau--C--(41)---UGGGUUUCCCU--UGCUA----GUGA-----UAGCAUGUUAAAAAACCUUGUGAACCUUAUUGCCUAAGGGUGUAACUAUUCAUAUAGUUGCUA-ACGGUGAAGCCC---------ACCAUUAUUCA--------GGGUAAUACCGUGCCAAGCUCCAUA-------GUGA-------UAUGGGGAA--GGUGUAGAGACUACCG---------AAAA---------GGAC------------UUUU-----------------------------------------------------------------------AGUU-AACUGA(43)UCUCU---------GUAA----------AGAGA------UGAAGAGAUAGUCCGGA-CUAUAGAGAUGGAAAAUCUAUAG-----------------------------------------------AUA---GUG--ccagaaacaa
                    ....<<<<<<--<--~~~~---[[^>>>>>>..--<<<<<----....----->>>>>.<<<<.....<<<<<<<<......>>>>..>>>>...>>>>........<<<<<<...-<<<<<<..<<<<---------...........-------->>>>..>>>>>><<<...<<<<<<<-------....------->>>>>>>..-->>>...[.[[[[[...---------<<<<---------....------------>>>>-----------------------------------------------------------------------...>->>>>>.~~~~<<<<<---------....---------->>>>>------........]]]]]][<.-<<<<<<<.........>>>>>>>-----------------------------------------------.].---.>.--]]].......
Ban.b.nrdE          auuccuggau--UAA----UUGGUAGUCCCUC---UACACA---GUAA----UGUGUA----------------------------------------UGAGAAAACCUUGUG(33)ACGGUAUCAGUU-------------(75)------------GGUAAUACCGUGCCAAGCUUGAAAG-----(761)------CUUUCAAGAA--GGUGUAGAGACUAUCGAAC------GCGCGUC------AUUA-------GACGAAAGC----UAGUAGAGUAGGCUGG-----------AAAUAGGUA----------CCAGUC--------------GAAGU-GCAAGG--CAACC----------AGUUACA--------GGUUG--------AUGAUAUAGUCC-AACCUUCAUAGAAAUAUGAAG-----------------------------------------------------ACGAGUUG--accaaaaaaa
                    ......<<<<--<<.----[[[[^>>>>>...---<<<<<<---....---->>>>>>----------------------------------------........<<<<<<<~~~~<<<<<<...<<<-------------~~~~------------>>>..>>>>>><<<...<<<<<<<<-----~~~~~------>>>>>>>>..-->>>...[.[[[[[......------<<.<<<<------....------->>>>...>>----..........<<<<<<-----------.........---------->>>>>>--------------....>->>>>>>--<<<<<----------.......-------->>>>>--------......]]]]]]-<<.<<<<<<<....>>>>>>>-----------------------------------------------------.....>>.--]]]]].....
Twort.v.ORF142,2    cugaaagcau--AAAUAA-----UUGUGC------CUUUAUACAGUAA-UGUAUAUCG--------------------------------------------AAAAAUCCUCUAAU-UCAGGGAACACCUAAACA-----AACUAAGA------UGUAGGCAAUCCUGAGCUAAGCUCUUA--------GUAA--------UAAGAGAA--AGUGCAACGACUA------------UUCC---------GAUA------------GGAA-------------GUAGGGUC-------------AAGU-----------GACUCGA-----------------AAUGGGGAU--UACCCU----------UCU----------AGGGUA--------GUGAUAUAGUCUGAACAUAUAUGGAAACAUAUAGAAGGAUAGGAGUAACGAACCUAUUC------------------------GUAACAUAAUUG--aacuuuuagu
                    ......<<<<--<<....-----^^>>>>------<<<<<<<<<....->>>>>>>>>--------------------------------------------....<<<<<<<...-<<<<<<....<<<..<<<-----........------>>>>>>...>>>>>><<<...<<<<<<--------....-------->>>>>>..-->>>...[.[[[[[------------<<<<---------....------------>>>>-------------.<<<<<<<-------------....----------->>>>>>>-----------------.>.>>>>>>--<<<<<<----------...---------->>>>>>--------......]]]]]][<<..<<<<<<....>>>>>>...<<<<<<<.........>>>>>>>------------------------....]....>>.--]]........
Ceu.mL1931          guucuaaggu--UAAAGGC----UAGCCUUA----GUAAA---AAUAAGUAA-UUUGCU-AGG--------------ACAU--------------CCU----(70)CAGGAUGAAU-UGUCGAGUCGCAUG----------------------------CGACUCGACGAUAGAGAAGCGUCAGUAAAACAAUGUUUUAACGCUUUU(28)UCAUCAACGACUAAAACUUAUUAUAGAAUUGAUAA--UGUAU------UUAUUAGUUUAACGAAGAUAA-CGGCGCUA---------------CGC------------UAGCGU----------------AGC-GGCCUA(20)GGCGCGUCG-----(31)----CGACGCGCC(18)------AAGAUAUAGUCUAG(18)AGUGGCUGCGUGC(59)GCAAGUAAUAUACUUUUUAAUCUUGAAAAAGAGAAGA----------------CAAACUG--agcaaaaccc
                    .....<<<<<--<<.....----^^>>>>>.----<<<<<---.........->>>>>.-<<<--------------....-------------->>>----~~~~<<<<<<<...-<<<<<<<<<<....---------------------------->>>>>>>>>><<<.<<<<<<<<...<<<<<<...>>>>>>>>>>>>>>~~~~>>>...[.[[[[[............<<<<<<<<<<--.....------>>>>>>>>>>...........-..<<<<<<---------------...------------>>>>>>----------------..>->>>>>>~~~~<<<<<<<<<-----~~~~---->>>>>>>>>~~~~------......]]]]]]<<~~~~<<<<..<<<.<<<~~~~>>>.>>>...>>>>.<<<..<<<<....>>>>..>>>----------------....>>.--]]........