Cyanobacterial/Plastidial tmRNA Alignment 15-Feb-2006 by Kelly Williams for The tmRNA Website, with base-pairing color-coded as in home page diagram. Underline marks the predicted reading frame for the proteolysis-inducing peptide tag. Lowercase marks segments not homologous to tmRNA, intervening segments that are absent in the mature tmRNA, and portions of the expected 3-prime CCA tail that are not encoded in the genome. CYANOBACTERIA: Gloeobacteria Gloeo_viola GGGGAUG-----UACUGGC--UUCGACAGGGCAAUUAGAGCGUAACUGAAGCC-----------------UGCUC----GGUUA----------------GAGCAAA-----AAACCAAGUGCUACUAACAACGUA---------------------------------------------GUUCCCUUCGCUCGCGCC--CGCGCUACUGUCGCG---GCCUGAGUAA------------------------------------------GGCGGGGUUG-------------------------GUAGA-UAACCUUGUAAACC--------------------------------------------------------------AAAACUACCCAA-AAGGCCCCUUCG--------------------------GGGGCCUU-----------------UUUGCU*******************************************************************************************************ACUAGGGUGCGUGAUCGGCUGUUCUGGAC-AGGGGUUCGAUUCCCCU-CAUCUCCACCA Gloeo_viola CYANOBACTERIA: Prochlorales Proch_mari1 GGGGUUG-----UAAUGGU--UUCGACGGGGCGUAAGGAAGAUGACUGAAGCC-----------------UGCUC----GGUUA----------------GAGCAAA-----AACACAAACGCUAACAAAAUCGUU---------------------------------------------AGUUUCUCCCGUCAAACA-----GCACCAGUUGCU---GCUUGAUCUCAAA---------------------------------------GGAGAUGGGGUGA----------------------UAUCA-GCCUUAUCAACC----------------------------------------------------------------AAA-UGAUCCAA--GGAGCCUGGAA--------------------------GGGCUCC------------------ACCAUU*******************************************************************************************************ACUAGGUGAUCUCAACCGAUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAACUCCAuuu Proch_mari1 Proch_mari2 GGGGCUG-----CAAUGGU--UUCGACGGGGUAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUAA----------------GAGCAAA-----UCCGUAACUGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCAGCCU-----GCCCUCGUGGCU---GCCUGACCCUAAUAAG------------------------------------GGAGAUGGGGUGA----------------------GGUCA-GCCUUAUCACCC----------------------------------------------------------------AAA-UGACCCAU--GGGGGCUGCGA--------------------------GGCCCCU------------------UUAACU*******************************************************************************************************ACUAGGUGAUCCACACCAGUGUCUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Proch_mari2 Proch_mari3 GGGGCUG-----CAAUGGC--UUCGACGGGGUUCUAGGAGUUUGACUGAAACC-----------------UGCUC----GGUUA----------------GAGCAAA-----ACCAUAACUGCUAACAAAAUCGUU---------------------------------------------AGUUUCUCCCGUCAAACA-----GCACCUGUUGCU---GCUUGACC-UUAUAAA------------------------------------GGAGAUGGGGUUA----------------------GAUCA-GCCUUAUCAACC----------------------------------------------------------------AAA-UGAUCCAU--UGGGCUUGGAA--------------------------GAGCCCU------------------UUUCAU*******************************************************************************************************ACUAGGUGAUUCACACCAUUAUCUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAucu Proch_mari3 Proch_mari4 GGGGCUG-----CAAUGGU--UUCGACGGGGUAUCAGGAGAGUGACUGAAGCC-----------------UGCUC----GGUCA----------------GAGCAAA-----ACCAUAACUGCUAACAACAUCGUU---------------------------------------------AGUUUCUCCCGUCAAACA-----GCCCCUGUUGCU---GCUUGAUC--UUUUA-------------------------------------GGAGAUGGGGUCA----------------------GGUCA-UCCUUAUUACCC----------------------------------------------------------------AAU-UGAUCCAU--GGAGCCUGGAA--------------------------GGGCUCC------------------UUUUUA*******************************************************************************************************ACUAGGUGAUUCACACCAGUAUCUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuaa Proch_mari4 CYANOBACTERIA: Chroococcales Cyanbi_6307 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUCA----------------GAGCGAA-----CCCGUAACAGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCAAGCC-----GCCCCCGUGGCU---GCCUGACACUCUUAAC------------------------------------GGAGACGGGGUGA----------------------GGUCA-GCCUUGUCACCC----------------------------------------------------------------AAA-UGACCCAU--GGGGCCUGGAA--------------------------GGGCCCU------------------UCCCAU*******************************************************************************************************ACUAGGUGGUCCACACCAGUGUCUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Cyanbi_6307 Syncoc_9311 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUAAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUAA----------------GAGCAAA----UCCCGUAACUGCGAACAACAUCGUA---------------------------------------------CGUUUCUCCCGUCAAGCA-----GCCCCUGUUGCU---GCCUGACC-CUAUUAA------------------------------------GGGAGAUGGGGUGA---------------------AGUCA-GCCUUAUCACCC----------------------------------------------------------------AAG-UGACUCGU---GGGGGUGGAAU-------------------------GCCCCC------------------UUAAAUC*******************************************************************************************************ACUAGGUGGUCCACACCGGUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_9311 Syncoc_9902 GGGGCUG-----CAAUGGU--UUCGACGGGACAUAAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUUA----------------GAGCAAA----UCUCGUAACUGCGAACAACAUCGUA---------------------------------------------CGUUUCUCCCGUCAAGCA-----GCCCCUGUUGCU---GCCUGACC-CUUUUAA------------------------------------GGGAGAUGGGGUGA---------------------AGUCA-GCCUUAUCACCC----------------------------------------------------------------AAA-UGACUGCUU--GGGGGUGGAA--------------------------GCCCCC------------------CUUCAAC*******************************************************************************************************ACUAGGUGAUUCACACCAGUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_9902 Syncoc_7009 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUAA----------------GAGCGAA-----CCCGUAACAGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCAAGCC-----GCCCCCGUGGCU---GCCUGACACUCUUAAC------------------------------------GGAGACGGGGUGA----------------------GGUCA-GCCUUGUCACCC----------------------------------------------------------------AAA-UGACCCAU--GGGGNNNNNNN--------------------------NNNNNNN------------------NNNNNN*******************************************************************************************************NNNNNNNNNNNNNNNNNNGUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_7009 Syncoc_6904 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUCA----------------GAGCGAA-----CCCGUAACAGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCAAGCC-----GCCCCUGUGGCU---GCCUGACACUCUUAAC------------------------------------GGAGACGGGGUGA----------------------GGUCA-GCCUUGUCACCC----------------------------------------------------------------AAA-UGACCCAU--GGGGNNNNNNN--------------------------NNNNNNN------------------NNNNNN*******************************************************************************************************NNNNNNNNNNNNNNNNNNGUGUCUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_6904 Syncoc_9605 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUGA----------------GAGCAAA-----CCCGUAACUGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCAAGCA-----GCCCCUGUUGCU---GCCUGACC--CUUUAA------------------------------------GGGAGAUGGGGUGA---------------------GGUCA-GCCUUAUCACCC----------------------------------------------------------------AAA-UGACUCAU--GGGGGCUGGAA--------------------------GGCCCCC------------------UCAACU*******************************************************************************************************ACUAGGUGAUCCACACCAGUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_9605 Syncoc_8102 GGGGCUG-----CAAUGGU--UUCGACGGGGCAUGAGGAGGGUGACUGAAGCC-----------------UGCUC----GGUGA----------------GAGCAAA-----CCCGUAACUGCGAACAACAUCGUU---------------------------------------------CGUUUCUCCCGUCACGCA-----GCCCCUGUUGCU---GCCUGACC--CUUAGG------------------------------------GGAGAUGGGGUGA----------------------AGUCA-GCCUUAUCACCC----------------------------------------------------------------AAA-UGACUCAU--GGGGGCUGGAA--------------------------GGCCCCU------------------CAAACC*******************************************************************************************************ACUAGGUGAUCCACACCAGUGUUUCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuc Syncoc_8102 Synco_elong GGGGCUG-----UAAUGGU--UUCGACGUGUUGGUGAA--UCCUUCACCGUGAUUCAGGC--CGAGAG-GGAGUCCA-CUCUCGUAAAU-CC-------AGGCUCAA--CCAAAAGUAACUGCGAACAACAUCGUU---------------------------------------------CCUUUCGCUCGUAAGGCU-----GCUCCUGUAGCU---GCUUAAAC----------------GCCACAAACUUUCUGGCUCGAGC-----GUCUAGUCGUAGAC--------------------UCCGUUAAUACGCCUAGAC---------------------------------------------------------UUAAACCCCC-AACGGAUGCUCGAGU-GGCGGC-------------CUCAGGU-CCGUCCUCUCGCU-AAGCAA-AAACCUGAGC----------------AUC-CCGCCAACGGGGAU--AAUCGUUGGCUCCCGCACAGUGGGUC-AACCGUGCUAAGCC-UGUGA----------------------ACGAGCGGAAAGUU-ACUAGUCAAUGCGGAC-AGCGGUUCGAUUCCGCU-CAGCUCCAuuu Synco_elong Syncoc_7002 GGGGCCG-----CAACGGU--UUCGACAGGUUGGCGAA-AGCUUCCACUGUGAUGCAGGU--CGAGAG-UGGGUCUC-CUCUCGCAAAU-CA-------AAGAUCCAAACAAAAUGUAACUGCGAACAACAUCGUU---------------------------------------------CCUUUCGCUCGCAAAGCU-----GC---UGCUGUA---GCUUAAUAAGAAC-----------ACCUUAA---CUUAGGUUCGAGC-----AUUCAUAAUUCGAC--------------------UCCGUUAAGGAUUAUGA-----------------------------------------------------------CUAAACCCCC-AACGGAUGCUCUCUAGGAAUAC-------------AUCUGGUU-UGCACUAGAGCU-AAGACU-AGACCAGAGA----------------UUCUUGG-CGACUCGGAACAAGCAGUC-GUUCCCGUUCUGAGGAUU-AGAAGAACUAAACC-UGUGA----------------------AUGAGCUAGGGGUG-AAUACCCAGUUUGGAC-AGCAGUUCGACUCUGCU-CGGCUCCAuuu Syncoc_7002 Syncys_6803 GGGGCCG-----CAAUGGU--UUCGACAGGUUGGCGAA--AGCUUGCCCGUGAUACAGGU--CGAGAG-UGAGUCUC-CUCUCGCAAAUCAA-------AGGCUCAA--AAAAAAGUAACUGCGAAUAACAUCGUC---------------------------------------------AGCUUCAAACGGGUAGCCAUAGCAGCCUAGUCUGUAAAAGCUACAUUU--------------UCUUGU-----CAAAGACCGUUU-----ACUUCUUUUCUGAC--------------------UCCGUUAAGGAUUAGAGGU------------------------------------------------------------UAACCCC-AACGGAUGCUUUGUUUGGCUCUU------------CUCUAGUU-AGCUAAACAAUC-AAGACUCAGACUAGAGC----------------AUC-CCACCAUCAGGGAU--AAUCGAUGGUCCCCGUCCU-AGGGCU-AGAAGGACUAAACC-UGUGA----------------------AUGAGCGGAAAGUU-AAUACCCAGUUUGGAC-AGCAGUUCAAUUCUGCU-CGGCUCCAuuu Syncys_6803 Croco_watso GGGGCCG-----CAACGGC--UUCGACAGGCUGGCGAA--AUCCAAAUUGUGAUUCAGGU--CGAGAG-UGAGUCUC-CUCUCGUAAAUACA-------AGACUCAA-AACAAUAGUAACUGCGAACAACAUCGUA---------------------------------------------AGCUUCAAGCGCGUAGCA-----------GUAGCU---GCGUAGAA----------------CUCUCU----CAUAGAGUCGCUU-----ACCUCUGACCUGAC--------------------UCCGUUAAGGACUCGGAGGU---------------------------------------------------------ACCAACCCC-AACGGAUGCCCUUAAUAGCUAC-------------CUCUGGUUG-GCUGUUGAGCU-AAGACU-ACACCAGAGC----------------AUC-CCACCGUUCGGGAG--AAUGAGCGGUUCCCGUCUG-AGGGUC-AGAAAGACUAAGCC-UGUGA----------------------AUGAGCGGUAGGUC-AAUACCCAGUCUGGAC-AGCAGUUCGACUCUGCU-CGGCUCCAuuc Croco_watso Thsyn_elong GGGGCUG-----AAACGGC--UUCGACGUCCUAGUGAA--AGUUGGGCUGUGAUGCAGGU--CGAGAG-UGGACUAU-CUCUCGUUAAUCCA-------GAGUCCAA-GCCAAAAGUAACUGCGAACAACAUCGUU---------------------------------------------CCUUUCGCUCGUAAAGCUGC------UGCG-----GUAGCCUAAG-----------------ACCUCUA---AACAGGUUCGAGC-----ACUCGUUGUCCGAC--------------------UCCGUUAAGGGCAGCGGGU------------------------------------------------------------UAACCCC-AACGGAUGCGCUAGACAGUUCU-------------CUCUGGU-GGGCUGUUUAGCA-AAGACU-CGACCAGAGC----------------AUC-CUACUGUUCGGGAU--AAGGAACAGUCCCCGCCUG-AGGGUC-AAAAAGGCUAAGCC-UGUGA----------------------AAGAGCAGUCGAUG-AAUAGCUAGGGCGGAC-ACGGGUUCGACUCCCGU-CAGCUCCAuua Thsyn_elong CYANOBACTERIA: Pleurocapsales Chrooc_6712 NNNNNNN-----NNNNNNN--NNNNNNAGGUUGGCGAA--AGCUAAUCUGUGAUGCAGGU--CGAGAG-UGAGUCGC-CUCUCGGAAAU-AC-------AGGCUCAAAUCUAAAUAUAGAUGCAAACAACAUCGUA---------------------------------------------AAAUUCGAGCGUCAAGCA-----------GUAUUU---GCUUAA------------------GCCCAA----CUGAGGCUUGCUC-----GCUUUUAGUCCGAC--------------------UCCGUUAACGGCUAAAACG------------------------------------------------------------AAACCCC-AACGGAUGCACCUUUUAGUUAC-------------UUUCGGU-UGACUAAUUGCGUAAAGACU-UCACCGAAAC----------------AUC-CUACUAUCAGGGAU--AAUUGAUAGUUCCAGUUCUUGGGAUU-AUAAGAACUAAACC-UGUGA----------------------AUGAGCAGAAUGUC-AUUAUCCAGUCUGGAC-AGCANNNNNNNNNNNNN-NNNNNNNNNNN Chrooc_6712 CYANOBACTERIA: Oscillatoriales Oscill_6304 NNNNNNN-----NNNNNNN--NNNNNNAGUGGAGUGAA--AGCUGCUCCGUGAUUCAGGC--CGAGAG-UGAGUUGU-CUCUCGUCAAUCCC-------CAACUCAA-AAAAAAAGUAAAUGCGAACAACAUCGUU---------------------------------------------CCUUUCGCUCGUAAAGCG-----GCUCCUGUAGCU---GCCUAAAA----------------ACCUCU----AGCAGGUUUGAGCG----GUCUAUAGCUUGAC--------------------UCCGUUAAAGGCUACAGAC-----------------------------------------------------------AAACCCUC-AACGGAUGCUCUAGUAAGGUUU-------------CUCUGGUU--ACUUGCUAGUU-AAGACU-CAACCUGAGU----------------AUC-CUGUCAUCCGGGAU--AAUGGAUGGUCCCCGCCCAGAGGGUU-AAAUGGGCUACGCC-UGUGA----------------------AUGAGCGGUAGGCG-AAUACCUCUGCUACAC-AGCANNNNNNNNNNNNN-NNNNNNNNNNN Oscill_6304 Oscill_7515 NNNNNNN-----NNNNNNN--NNNNNNAGGGUGGUGAA--AUCUGCUUUGUGAUGCAGGU--CGAGAG-UGAGUCUU-CUCUCGCAAAUACC-------GGGCUCAA--CAAAUAAUAAGUGCAAACAACAUUGUA---------------------------------------------CCUUUUGCUCGUAAGCAA-----GUAGCUGUAGCUUAAUUGCCGAAAC--------------GCCUCU----UAUAGGUUCGAGC-----GUCUGUGAUUUGAC--------------------UCCGUUAAGGAUUGCAGAC-----------------------------------------------------------UUAACCCC-AACGGAUGCACUAGCUCACUGC-------------CUCUGGU-CGGCU-GCUGGUU-AAGACU-UCACCGGAGA----------------AUC-CCGCCAUCUGGGAU--AAUGGAUGGUCCCCGCCUUCAGGGUUAAGAUAGGCUAAACC-UGUGA----------------------AUGAUCGAAGAGUG-AAUAGCCACUUUGGAC-ACGGNNNNNNNNNNNNN-NNNNNNNNNNN Oscill_7515 Trchd_eryth GGGGCAU-----UAACGGU--UUCGACAGGGUGGUGAA--AUCUGCUUUGUGAUGCAGGC--CGAGAG-UGAGUCUU-CUCUCGAAAAUCCU-------GGACUCAA--AAAAUAAUAAGUGCAAACAACAUUGUA---------------------------------------------CCUUUUGCUCGUAAGCAA-----GUAGCUGCUCUA---GCUUAAUUGCAAAAAC--------ACCUCU----UAUAGGUUCGAGC-----GUCUGUGGUUUGAC--------------------UCCGUUAAUAAUUGCAGAC-----------------------------------------------------------UUAACCCC-AACGGAUGCUCUAGCAAUUUUU-------------CUCUGGUUA--CCUGCUAGUU-AAGAUU-UAACCAGAGC----------------AUC-CCACUAUCCGGGAU--AAUGGAUAGUCCCAGCUCUGAGGGUUAAGAAGGGCUAAACC-UGUGA----------------------AUGAGUGAAGGGUG-AAUAGCCAUUUUGGAC-AUGGGUUCGACUCCCAU-AUGCUCCAuac Trchd_eryth Leptl_borya NNNNNNN-----NNNNNNN--NNNNNNAGGUUGGCGAA--CGUUCCAUCGAGAUGCAGGU--CGAGAG-GGAGUCCA-CUCUCGUAAAU-CU-------AGGCUCAA----AAAAAUAGAUGCAAACAACAUCGUA---------------------------------------------CCUUUCGCUCGUAAAACU-----GCACCUGUUGCA---GCAUAAAAC---------------ACCUCUAA--UUCAGGUUCGAGC-----GCUUACCGUCUGAC--------------------ACCGUUAAAGAUAGUAAGC-----------------------------------------------------------ACAACCCC-AACGGUUGCUCUAGAAUUUCGC-------------CUUUGGU-CGGCAUUCUAGCU-AAGACA-AUACCAAAGC----------------AUC-CUAUUGUCCGGGAC--AAAGGACAGUUCCCGCUUCGAGGAUU-AGAGAAGCUAAACC-UGUGA----------------------AUGAUUGAUAGAGCUAAUACCCAGUUUGGAC-ACGGNNNNNNNNNNNNN-NNNNNNNNNNN Leptl_borya CYANOBACTERIA: Nostocales Nostoc_7120 GGGUCCG-----UAACGGU--UUCGACAGGUUGGCGAA--CGCUACUCUGUGAUUCAGGU--CGAGAG-UGAGUCUC-CUCUCGCAAAU-CA-------AGGCUCAA-AACAAAAGUAAAUGCGAAUAACAUCGUU---------------------------------------------AAAUUUGCUCGUAAGGAC-----GCUCUAGUAGCU---GCCUAAAUA---------------GCCUCU----UUCAGGUUCGAGC-----GUCUUCGGUUUGAC--------------------UCCGUUAAGGACUGAAGAC------------------------------------------------------------CAACCCCCAACGGAUGCUCUAGCAAGUGUU-------------CUCUGGUU-GGCUUGCUAGCU-AAGAUU-UAAUCAGAGC----------------AUC-CUA-CGUUCGGGAU--AAUGAACGAUUCCCGCCUUGAGGGUC-AGAAAGGCUAAACC-UGUGA----------------------AUGAGCGGGGGGUC-AAUACCCAAUUUGGAC-AGCAGUUCGACUCUGCU-CGGAUCCACua Nostoc_7120 Nosto_punct GGGUCCG-----UCACGGU--UUCGACAGGUUGGCGAA--CGCUGCUCUGUGAUUCAGGU--CGAGAG-UGAGUCUC-CUCUCGGAAAUCAA-------AGGCUCAA-ACAAAAAGUAAAUGCGAAUAACAUCGUU---------------------------------------------AACUUUGCUCGUAAGGAU-----GCUCUAGUAGCU---GCCUAAAC----------------ACCUCU----UAUAGGUUCGAGC-----GUCUUUAGUUUGAC--------------------UCCGUUAAGGACUGAAGAC-----------------------------------------------------------CAAACCCC-AACGGAUGCUCUAGUAAGCGUU-------------CUCUGGUU-GGCUUGCUAGCU-AAGAUU-AAAUCAGAGA----------------AUC-CUA-CGUUCGGGAU--AAUGAACGAUUCCCGCCUUGAGGGUC-AGAAAGGCUAAACC-UGUGA----------------------AUGAGCGGGGGGUC-AAUACCCAAUUUGGAC-AGCAGUUCGACUCUGCU-CGGAUCCACua Nosto_punct Anaba_varia GGGUCCG-----UAACGGU--UUCGACAGGUUGGCGAA--CGCUACUCUGUGAUUCAGGU--CGAGAG-UGAGUCUC-CUCUCGCAAAU-CA-------AGGCUCAA-AACAAAAGUAAAUGCGAAUAACAUCGUA---------------------------------------------AAAUUUGCUCGUAAGGAC-----GCUCUAGUAGCU---GCCUAAUUA---------------GCCUCU----UACAGGUUCGAGC-----GUCUUCGGUUUGAC--------------------UCCGUUAAGGACUGAAGAC------------------------------------------------------------CAACCCCCAACGGAUGCUCUAGCAAGUGUU-------------CUCUGGUU-GGCUUGCUAGCU-AAGAUU-UAAUCAGAGC----------------AUC-CUA-CGUUCGGGAU--AAUGAACGAUUCCCGCCUUGAGGGUC-AGAAAGGCUAAACC-UGUGA----------------------AUGAGCGGGGGGUC-AAUACCCAAUUUGGAC-AGCAGUUCGACUCUGCU-CGGAUCCACua Anaba_varia Fremy_diplo NNNNNNN-----NNNNNNN--NNNNNNAGGUUGGCGAA--CGCUGCUCUGUGAUUCAGGU--CGAGAG-UGAGUCUC-CUCUCGCAAAUCCA-------AGGCUCAA-AACAAAAGUAAAUGCGAACAAUAUCGUA---------------------------------------------AAAUUUGCUCGUAAGGAA-----GCCCUAGUUGCU---GCCUAAUA----------------GCCUCU----UAUAGGUCCGAGC-----GUCUUUAGUCCGAC--------------------UCCGUUAAGGGCUAGAGAC------------------------------------------------------------CAACCCC-AACGGAUGCUCUAGCAAGUAUU-------------CUCUGGUU-GACUUGCUAGCU-AAGACU-UAAUCAGAGC----------------AUC-CUA-CGUUCGGGAU--AAUGAACGAUUCCCGCCUUGAGGGUC-AGAUAGGCUAAACC-UGUGA----------------------AUGAGCGGAGGGUC-AAUACCCAAUUUGGAC-AGCANNNNNNNNNNNNN-NNNNNNNNNNN Fremy_diplo PLASTIDS: Viridiplantae Mesos_virid GGGGUUG-----AAAUGGU--UUCGACGUUUUAGUAU-AUAUC--UUCUUACAAGCAAGU--CGAGA-AUGAACCAA--UCUCGUAAAC--------UUGAGUUCA--AUUGCAAAUAAAUGCUAACAAUAUUUUA------------------------------------------CCUUUUAAUCGUAAGACAGCCGUAGCUGUUUAAAAGUUUUUUGAUAACUUCGAGCAUUUUUGAUUUGUUAAAUACAAUUGUUA--UAAAACAAAUUAAAUAAUAGUU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUGUUUCUUUACAAAUAAUGUAGAAAUAAUUUUUUUUAGCUUUUCAAGCUCCAGCUUUGUGGAUUAGCAAAGCUAAACU-UGUGAAUA-----------------------CAAAGAAGAGAUCAAACUAAAGCGGAC-GCGGGUUCAAAACCCGC-CAGCUCCAuaa Mesos_virid Nephr_oliva GGGGUUG-----UCAUGGA--AUCGACGUCUCUUCUA-AGAACGAAAGGUUAAAGCAGGU--CGAG-GUCGAAGAUGGA-CUCGUACUC--------UCCACUUCA-UUGCUUGAUUGCAUGCUAAUCAGAUUCUU------------------------------------------CCUUUCUCUCGCCGGGUAGCCGUUGCUGCUUAAGCGAGUUUCUAGUGCCACUUUGUCACUAGUUUGUAUUAUGAGUUUCACACUCACUUCAAUGACGGUGAUAGAUA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUACAUAUCACUCCUGCUUAGAGGGUCAUCUAAGCUAAACCAUGUGAAUA-----------------------UAACCUUUCGGGCCUCGAGAGACGGAA-GUGAGUUCAAUUCUCAC-CAACUCCACCA Nephr_oliva PLASTIDS: Glaucocystophyceae Cyanp_parad GGGGCUG-----UUUAGGU--UUCGACGUUUUUUUCUAAUUAU--GUUUGUUAAGCAAGU--CGAGGAUUUGUUCUA--UCUCGAAAAUCA---------AGAAC-UCUCAAAAUUUAAACGCAACUAAUAUUGUA------------------------------------------CGUUUUAACCGUAAAGCAGCUUUCGCUGUUUAAUAAUUACUUUUAAUUUAAAAACCUAAUUUUUUUAGGAAUUUAUUUAUUUAUUGUUUAUCCUGCUUAAUGAAUUAAAAAAAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAUACU-UGUGA--------------------------AUAAACGCAUAAUUUAAAAAAACGGAC-GUGGGUUCAAAUCCCAC-CAGCUCCACuc Cyanp_parad PLASTIDS: stramenopiles Ampho_coffa NNNNNNN-----NNNNNNN--NNNNNNAUCUAAAAUUAAUUAC---UAUAUGAAUCAGGU--CGAAG--CUUGUACU--CUUCGAAAAAAU-------CUACAAAC---UAUAAUAUAAAGGCUACUAUUAUAACA------------------UGGUUUAUUUCAAAAAUUAUAAAUCGUAAUGCUUGUUCAUUACAAUUUGUAGUUUAA------------------------UUAACUUUAUUUCUACACAAACAAAUUAUUCACUAGAUCU-AU-CAUUUUUCAGAAUUUUAGUUUAGAAUAACAAUACUUUUU------UUUGUUC------UUUAAAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAUGCC-UGUGAACG----------------------AGUAUAUUAAAUC--AUUUUAGAUGGAC-AUGGNNNNNNNNNNNNN-NNNNNNNNNNN Ampho_coffa Thala_weiss GGGGCUG-----AUUUGGU--UUCGACAUUUAAAACUUCUUUC-----UAUGUGUCAGGU--CAAAG--UUUGUAUU--CUUUGUAAAAAA-------AUACUAAA---AUACUAAUAAAUGCUAAUAAUAUAAUA------------CCGUUUAUUUUUAAAGCAGUAAAAACAAAAAAAGAAGCAAUGGCUUUAAAUUUUGCUGUAUAG------------------------UUCAUUAACUUAGGUUAUUAAAUAUUUUUUCAUUAUAACU-GGACUUUUCUCUAGUUUAUAGUUUAGAAUAAAUUUAAAUUUUGCAAAACUCGUUCGAAAAUUUUCGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAAACC-UGUAAACGCA--------------------AAUAC--UAAGAAA--UUUUAGAUGGAC-AUGGGUUCAAUUCCCAU-CAGUUCCAauc Thala_weiss Thala_pseud GGGGCUG-----AUUUGGU--UUCGACAUUUAAACACUAUUUC-----UAUAUGUCAGGU--CAAAG--UUUGUAUU--CUUUGUAAAAA--------AUACUAAA---UUAUUAAUAAAUGCUAACAAUAUAAUG------------CCUUUUAUGUUUAACGUAGUAAAAACAAACCGUUCAUUAACUACUUUAAAUUUCGCUGUUUAA------------------------UCACUUAACUUAGGUUAUUAAAUAUUUUUUCAUUAUUGCU-AGACUUUUAUCUAGUAUAUAGUUUAGAAUAAGUUUAAAUUUUAAAAA--UUGUUC-AAGUUUUUUGAACUAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACC-UGUAAAUGAG--------------------UAUAU--UAAUAAA--CUUUAGAUGGAC-AUGGGUUCAAUUCCCAU-CAGCUCCAaua Thala_pseud Odont_sinen GGGGCUG-----ACUUGGU--UUCGACAUUUAAAAAUUG---UUACAGUAUGAUGCAGGU--CGAAG--UUUCUAAU--CUUCGUAAAAAA-------AGAGAAA----UUUAUAAUAAAUGCUAAUAAUUUAAUU------------UCUUCUGUGUUUAAAAGUUUAUCAACUAAGCAAAAUAGUUUAAAUUUAAGUUUUGCUGUUUAAGUUUUAUGCACAUUUAAUGAUCUAGUAAAUAACUUUG-UUCGCUA-UAAUUUAUAUUUAUAACU-AGACUUUUGUCUUUUUUAUAGUUUAGAAUAACUUUAUCAUUU-CAAACCUCGUUC-----CAUC-UAGUUGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAAACC-UGUGAACG----------------------AAUACUAUAAUAAAAUUUUUAGAUGGAC-GUGGGUUCGACUCCCAU-CAGCUCCAuau Odont_sinen Skele_costa NNNNNNN-----NNNNNNN--NNNNNNAUUUAAAAGUUAUUUA-----UAUAAGCCAGGU--CAAAG--UUUGUACU--CUUUGUAAAAA--------AGACUAAAUU-AUUAUAAUAAAUGCUAACAACAUAAUG------------UCUUUUAUUUUUAAAACAGUAACUCCAAAAAAUCAUUUAAAUGUUUUAAGUUUCGCUGUUUAA------------------------UUAUUUAAUGUAGUUUAUUAAAUAUUUUUUCAUUAUAGCU-AGACUUUUUUCUAGUAUAUAGUUUAGAAUAAAUUUAAAUUUU--AAAGAUUGUUC------AAAUCAUUUGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAAGCC-UGUAAACG----------------------CGUGU--AUAAAUAAGCUUUAGAUGGAC-AUGGNNNNNNNNNNNNN-NNNNNNNNNNN Skele_costa Frgla_pinna NNNNNNN-----NNNNNNN--NNNNNNAUUUGAAAAUAACUAA---AGUAUGAUGCAGGU--CGAAG--CUUGUAUU--CUUCGUAAAAAU-------CUACAAA----UUUAACAUAACUGCUAAUAAUAUAAUU---------------CCUUUUCACUUUAAAACAGUAAAUUUCAAUAACUCAAAUUUAUUACAAUUUGCUGCUUAA----------------------AUAAAAACGAACUUUUAGUAACAAAAUUGGUACUCUAU-UCUGAGACGUUUC-GUUUUAGAUAGUUUUGAAUAAUUUUAACA---------GUUGUUC--------ACUUAUCGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAUGCC-UGUGAACG----------------------AAUAC--UUUAAUUAAAUUUAGAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Frgla_pinna Bolidom_OLI NNNNNNN-----NNNNNNN--NNNNNNAUUAUAAAAAUUUUAA---AUUAUGAUGCAAGU--CGAAA---AAUAUUA--UUUCGUUAAAA--------AAUAUACC---UUUAAAAUAAAUGCAAAUAACAUUUUA------------------------------------------GCUUUUAACCGUAAAUCUUUAAGUUUCGCUUAAAAUUAUUUAUGGAAAUUUUUAAGAGUGUCCAUCUCUUAAAAAUUUGAAAACUUUAUGGACAUUAUAAAACUAGACUUUUCUAGAUCUUUUAAGUUAAAUUAUUACUUAAUUCCUUUUAAUUUGUUCAUUUUAAAUGAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAAACU-UGUGAACG----------------------AUUAAUUUAUCAC--UUUUAUAAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Bolidom_OLI Pylai_litto NNNNNNN-----NNNNNNN--NNNNNNAUUUAAAAUUAUAAU-------------AGUUA--CUAAG-CAGAUUUAAGUCUUAGAAUA------------UAAA-----------AUAAUUGCAAACAACAUUAUG---------------------------------------------AGCUUUAAUAAAAACCAAGUUUUUGCAUAAAAUACUUGAGUUUUAAUAUCAAUCAAUUUUAUAAUUGUUGAUUGAAAUAGGUAGAAGAUUAUUUUUUCUCUUAAAUUUUAGUUUUGGUAAUUUUACUAUCAGUAAAAUAUAAUAUUUAUAAAAUAAAUAUAAAUCGAU---------------------------------------------------------------------------------------------------------------------------------CCAUAUUUUUGCUACCAAUCUGUUUUUAAUAGUUUUAAGCUUAUUUUAGCUAAGCAGAUUGAUAA-CUAAAUCUGUGAUUU-----UAGUACUUAGUUUGAUAAUU------UUUUAAAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Pylai_litto PLASTIDS: Haptophyceae Pavlo_luthe GGGGCUG-----UUUAGGU--UUCGAUCCUAAAAAAAACUAAUA--AGUGUGAUGCAAGU--AGAGG----AAAC----CCUCUUAAAAAA--------------AAAGCAAACAAUAAAUGCAAACAAUAUUUUA------------------------------------------------UCUUUUAAUCGAGUAGCUGUAGCCCCGUAUAGUUAUAUAGCAUUAACUCCUUAUGGUCAAAAAAUCUAGAAAGUUUGAUCGUAAAGCAAACCUUAGCUAGAAGCACACAAGAAUAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NNNNNNNNNNNNNN-------------NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-NNNNNNNNNNNNNNNNN-NNNNNNNNNNN Pavlo_luthe Prymn_parvu NNNNNNN-----NNNNNNN--NNNNNNAUUUAGGUCUGGA----AGUUUUUAA--AAUAU--UCCU----AAUUUA----AGGAUAAUCUC----------------------AAAUAGUUGCAAAUAAUAUUUUA---------------------------------------------UCUUUUAAUACUAAACUAGCACUAGCUUAAGUUUUUAGUAUAAUCAGUUAUGGUAUUUUACUCUUUUAACCUUUCUGAUAAACAUAAAAAAGAGGCGCAUUUUUGCAAAGAAAUUUAG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAAAUG-UUUUCU-------------AUGGUUGUAAAUAAAGAACUUUUUUAGGGCUAAAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Prymn_parvu Emiln_huxle GGGGCUG-----UUUUGGA--AUCGACAUUAAAAUUUUUA------GGACAUU--UUGUU--AUAACUU--AUA---AAGUUAUUUACUUU---------------------AGAACAAAUGCAAACAACAUCUUA---------------------------------------------AACUUUAAUUCAAAGUUAGCUAUCGCUUAAAAUUUUUGAAUUACCAAUGAAAUUGGUCACUUAUUUUAUUGGUUCGAUUUAUAGUGAAUGCUGUAUUACGUAUACAAAGAAAUUUUC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUCUCGAAU-AAAACG--------------CCGUAGUUGACAAAGGUUCAAUUUAAAAUUGAAUGGAC-GUGGGUUCAAAUCCCAC-CAGCUCCAaaa Emiln_huxle PLASTIDS: Rhodophyta Cydum_calda GGGGCUG------AAAGGAUAUUCGACAUAUUAAUUUCGUGCG----CUAUGAUGCAAGC--CGAGA---AUGCUUA--UCUCGUAAAA-----------AAGCA-GACAAAGAAAUAAAUGCAAACAAUAUUAUU------------------------------------GAAAUUAGCAAUAUUAGAAAACCAGCUCUAGUAGUCUAGCCUGAUUCAGUUAUUUCUAAAUUAUUUAUGUUAUGUUAU----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUAAGCU-UGUAGU------------------------AACUAUCUAGUGUACAAUUUCUAUGGAC-GUGGGUUCAAUUCCCAC-CAGCUCCACaa Cydum_calda Cysch_merol GGGGCUG------UAAGGU-GUUCGACAUAAGUUGUU------------------GUUAU----------------------------------------------------UCAAUAAUUGCAAAUCAAAUUCUA---------------------------------------CCUUUUUCUAUUCCCGUUAAACAUCUAGCUGUUUAAAUUUAAAGACAAUUUAAAGACAAUCUAAAGACUCAAGAGACAAAAAUUUUAGGUAUUUAGGUAACUUUUAGGUAACUAAGUAAGGAAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UAAGUA-ACGAA---------------------------------------AACAACUUAUGGAC-GUGGGUUCAAUUCCCAC-CAGCUCCAaug Cysch_merol Rhoso_marin NNNNNNN------NNNNNN--NNNNNNNNNNNNNNNNNNNNNN-NNNNNNNAAUACAAGU--CGAGAA-UGAGAAU--UUCUCGUUAAAAU---------UUCUCAAAAAAAAUAAUAAAUGCAAAUAACAUUUUA------------------------------------AAAUUCUUUACCAAGUCUCCGGUAGUAGCAUUCGCUUAAAACCUUUGGUUUCACAUUAGUCUAAUCUUAAUUUAAUAUGAAAAUCUUUAAGAUGCAGCUAAAAAAUAAAUUUAGCUAAGAACCCUACGCAAUCAAAUGUAUGUAUAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACU-UGGAAUAC------------------------UAUUGACUAAUACAAUCUAAUUGGAC-GAGGNNNNNNNNNNNNN-NNNNNNNNNNN Rhoso_marin Porpa_purpu GGGGCUG------CAAGGU--UUCUACAUUGUGAAAAAACAAA-UAUAUGAAAGUAAAAC--GAGCUC-AUUAUUA--GAGCUUU---------------UAGU--------UAAAUAAAUGCAGAAAAUAAUAUU------------------------------------------AUUGCUUUUUCUCGAAAAUUAGCUGUUGCAUAAAUAGUCUCAA--------------UUUUU--GUAAUUC-GAAGUGAUAGACUCUUAUACACUAC-GAAUAUUC-UGUUAGAGUUGCUCUUAAUAAAAGAA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAGUAAAAAAAUACAAAUUC-------UUAUGUU-UUUUACCUGAAUUG--AUU-CAAUUUAAGGUUAGUAUUUUUUGAUUUUUACAAUGGAC-GUGGGUUCAAGUCCCAC-CAGCUCCAuca Porpa_purpu Graci_tenui GGGACUG------CAAGGU--UUCUACAUAUAGU-----AUAC-AAUAUA---CAUUGUCAUUAAUA--UAACUU----UAUUAC---------------UAUUA----------GUAAAUGCUAAAAAUAAUAUA------------------------------------------UUAACUUUAUCUAGAAGAUUAAUUUAUGCUUAAACUUUUUGAAAUAAAAGAUUAAGCAGUUACAGAUUGUUACUAGAACUCAAAUAAUAUAAGCCAUAUAGUUAUUUGAUAUAUUGAAUUUGGUUGCUCUUAAAUUAGUCUUAAUCAAAGAAUUAAUUUUAAGAUAAGUAAGAAAUCAUUACA-------------------------------------------------------------------------------------------------------------ACAUCAAAUCGUAUUUUUUAGAUUACAUCUAUAAUAUAUUACUUAUAAUAUAUUAUUUCUAAUGUAAUUAGAC-GA----------------------------------UAUAUAGUAUAUUAUUAUGGAC-GUGGGUUCAAUUCCCAC-CAGUUCCAuac Graci_tenui Mastc_papil NNNNNNN------NNNNNN--NNNNNNAUAUAGU-AUUGUAUG-UAUAAGUAGUAAAGGA--UGAAG-GUAAGCUAAA-CUUCAUUAAUCC---------UAGCUUG-----ACUACAAAUGCAAAACAUCAAAUU------------------------------------------GUUCCUUUUUCUAAAAGAAUUAUAGUAGUAUAAUAU---------------------UUUUUAGAAUAUUA-GAUUAUAAUUUCUC-UAAAUAAUCU-GGUAUUUU-UAUUUGAGAUGCUCUUAAUUAGAUAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUUAUUUUUAAGCAAAGU--UACAAUUUUUAUAU-AUUUUUCC-UUUGUACUUGA----CUUG----UAUAAGUAUACUUUACAUACAGUUUUGAUAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Mastc_papil Prion_lance NNNNNNN------NNNNNN--NNNNNNAUAUAAUUC-CGUCUA-UAUAAGGUUCAGAGAA--UGAAG-GUGAGCUAAA-CUUCAAUAAUCC---------UAGCUUA-----AAAACAAUUGCAAAACAUCAAAUU------------------------------------------UUACCAUUAUCUAGGAAAAUUGCUUUAGCUUAAUAUAAGUAAAAGAAAAUAUGAUUUUUUCUAGGUUAUCAAGAUUGAGA-UUCUAGUAUAUAUCUUGAUUGGUUAUUACACUAGAUGCUCUUAAAUUUAUGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------UUUAAGCUAAGU--UUCAAUCUAUUUAUUGUUUUUUC-UCUUGACUUAGUCAAUAAUUUGAUAAUUGUCAACUUAUUAAGCUGAAUUACUAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Prion_lance PLASTIDS: Cryptophyta Guill_theta GGGGCUG-----AUUUGGA--UUCGACAUAUAAAUUUGCGUGUUUCAUUAUGAAGCAAGU--CAAG---UUUAAUG--AUCUUGUAAAAAA---------CAUUAAA--GUACAAAUAAAUGCAAGCAAUAUAGUU---------------------------------------UCAUUUAGUUCAAAACGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUAACUUUCUUAGUAGAAAUUGGAGAAGUUUACUAAGAUUUAUAUUUACUCCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAUUCAUCAUUUGUAUGUUU--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CUAAACUUUGUGAAAG----------------------AAUAGUGGGCUCC-AUUUAUA-AUGAAC-GUGGGUUCAAAUCCCAC-CAGCUCCAuag Guill_theta Rhomo_salin NNNNNNN-----NNNNNNN--NNNNNNAUUUUGGAAAGAAUAGUA--UUAUGAUGCAAGU--CAAGAU-UGAGCUC--AUCUUGUUAAUAA---------AGCUCAU---CAUAAAUAAAUGCAAAUAAUAUUGUA---------------------------------------------CCUUUUUCUCGUAAGGUCGCUUUAGUUUAAGAUUGUUUUCCUCAUUGGAGACUUGAUUAAUCUAUAAAAAUAAGUUAAAGCUAAAACAUUGGAAGAAAUUUAGCUUAUAAAUAAAAUUCCGUUCUCAUAACUUUAGUGGGUAAAAAAAUACUUUCUUUGAGUAUUGAACAAAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AUAAACU-UGUGAAUG----------------------AGUGUGCUACGUAAG--CUGAAAUGGAC-GUGGNNNNNNNNNNNNN-NNNNNNNNNNN Rhomo_salin