>petA:cemA >outgroup GTTCAATTATTAGTTCCAAATCATTTTTC------GGGTGAGAGTAGGTAGCTATCATAGTTACCTGTCAAAAATTCTGCTACTATATTGATTTAACCAAACGTAAAAGTAAGAAATGGGAAGTCTCGCACTAGGAGAAGAATGAGGGGTAGGAATAGCTAATTCCTGAACATGGAAAACACTTTCTGATCTTGTTTCGGTCGGAGAAAACAACCTATTCT >sequoia_sempervirens GTTCAATTTTTTGTTACAATTCTTTTATTTAAAATAAATAGTAGTAGGTAACTATCATAGTTACCTGCCTGCAATTCTGCTACTATATT---------AAACCTAAAGCTAAAAAATAAGAAGTATCGCCCTAAAAAAAGTAAAAAAGGTGGGATTTG--------------------------------------------------------------- >metasequoia_glyptostroides GTTCAATTTTTTGTTACAATTCTTTTATTTAAAATAAATAGTAGTAGGTAACTATCATAGTTACCTGCCTGCAATTCTGCTACTATATT---------AAACCTAAAGCTAAAAAATAAGAAGTATCGCCCTAAAAAAAGTAAAAAAGGTGGGGACCATTGTTATTTG----------------------------------------------------- >cemA:ycf4 >outgroup GATTGATCTATTGTGTAATTGTTTGATTCCGAAAAAAAAAAAAAAAAAAAGATCCTCGGAGGAAAAGTAAAAGGTTCGCTCCAAATGAGTGAGACGGAGCATAAGGAGATCATTCCCAGATATCCGATAATTCCAGATCATTTCTATCTGGACCAATTATCTATTCATTTTTTCTATCTTTTTCCTTTTTAAAATAATCACTTGACGTAACATAAGTCTTATTCATTGCCAAGATCCTTTGAATCCTGATTGATCACTGGATCGATCCTTTACGAATCTTTCCCCAGTTATTTCCAAATATAAAAAATGCTCTTTAAAAATGAGAGAACAACGAAATAAATCATATAAGAATAAATTGGATCGTGATGAAGAATCGGGACGAGAGGAAAGAAAAAACGTTCTGGTTTTCCTAAAACCAGACCACTATATCTAGTAATTGTTCTTTCTGATACATTCATATTAATCTACTGGCTTTATAAGCTCACCCTCTCTAGGATAGGAAATGAAAAGATATGGCGTGTTCGGGAACTACCAAAAGAATCTTGTTCTGATTCATTCCATAAGTATCAT-TTAGTAGGAATAAACTGCACGATCTTTTTCCCGGACAAAAAACAACCAGTTCTATTGTAATTTATGCTCTTTCTATATTACCTCTTCTTATACTATTTAATCAAAATAGTATATTGTTCATAAAGACCCTATATCGTTCCATTTCCAATCAATTATATTTCAATATAAATATTGAAATATAATTGATTGGATATTGATTCATGTTCCTTGCTTTGATCAATATTAAAATGTCTCAAAATTTGAATGTATGTGGAGGATAAAGAACTCTCCGGTTCATT >sequoia_sempervirens GAATGATCTTATGCGTAATTCTTCGA---------------------AATATCTTTCGGATGAGGGAT----GGTTTGTTCGGAAGGAG--AAGTGGAGTAAAAA-GGAAGGATCA-----ATCC------TTAAAATCGCTTTGATCTGGACTCATTTTCTATTTGTTCTTT---------TCTTATTTAA------CTCTTGACCCGA--------------------AGAATCGCTTCAATTC-GAGCGGCAAATAAATTGAAGTTT---AAGTCT-------AATAATACCAAATTTG-----TACTCTTTGGTA----------------------CATATAGCAG---ATCGAATTATTTCGGGCACATATGTCAAAAAGTGTAAAAAA--------------CTAGAGTCAT-TTACTTCATT--GTATTCTTTTGAGATGTTATATCCGTATTTATTTATTAGACCTTT----TGTCCCTATCTA--ATAGATAAAGAAT-GATATCGAGTGTTTGCGAAGTGCCGAAGAATACCGGTATGCTTCTATAAGTAACATTTCGTGTTAGTGTAAATAAACTG-ACTATACTTCCCCTCCAGACAAA-----------TGTTATG--TCAAACTTTTTCTGG--TATCTACTAATACGAGATCTATCCAT--TTGTATATTATAAAAGAGGACTTTCCCCC--CCCATT--------------------------------------------------------------------------------------------------------------------------------------- >metasequoia_glyptostroides GAATGATCTTATGCGTAATTCTTCAA---------------------AATATCTTTCGGATGAGGGAT----GGTTTGTTCGGAAGGAG--AAGTAGAGTAAAAAAGGAAGGATCA-----ATCC------TTAAAATCGCTTTGATCTGGACTCATTTTCTATTTATTGTTT---------TCTTATTGAA------CTCGTGACCCGA--------------------AGAATCGCTTCAATTC-GAACGGCAAATAAATTGAAGTTT---AAGTCT-------AATAATACCAAATTTG-----TACTCTTTGGTA----------------------CATATAGGAG---ATCAAATTGTTTCGGACACATATGT-AAAAAGTGTAAAAAA--------------CTAGAGTCAT-TTACTTCATT--GTATTCTTTTGAGATGTTATATCCGTATTTAT------AACCTTT----TGTCCCTATCTA--ATAGATAAAGAAT-GACATCGAATGTTTGCGAACTGCCGAAGAATACCGGT--------------------------TAGTGTAAATAAACTG-ACTATACTTCCCCTCCAGACAAA-----------TGTTATG--TCAAACTTTTTCTGG--TATCTACTAATATGAGATCTATCCAT--TTGTATATTAAAAAAGAGGACTTTCCCCC--C--ATT--------------------------------------------------------------------------------------------------------------------------------------- >rpl33:psaJ >outgroup -AACTTACTCTGGATATTGGGTCTACT---TTGCTTTTAAATCTGAAAAAGA---AAGAGGGAAAAAGGGATAGAAGTTGATAGCCGGAGATCCCACGATAAAACATTTGAA--AGTAAAAAAATTAA-TTATTGATCAGGAGTTTTCAGTTTTACTTACAAAATTAAATGTGAAAG-AACCTTTGGATCTAAATTTCTACTTTAATTCTACCCCCCCCCCCCATTCCATCCCTAAAATTAGATCTATTTTTAGGTTAAATCAACTAATTCATCCAATAGGTAGGAGAAGTAAATCCAGCACAATCTTTTTTCCATTGAAGGGGAGGACAAAAA-- >sequoia_sempervirens TAACTTACTTTGGATATTGTATCTACTTCTTTTCTTTTCAATTTGGAAAAAAGAGAAGAAAGAGAAAGGGATAGAAGTTTTCGAAGAATGATTAAAGATTTTATTACGAGAATGAATTAAGTAATAAAATCTTTAATTAAGAGTTTTCAGTAGT--TTAC-----TATTTGTGGAAGCAACTTTTGGATCTAGATTTCTATTTTG-TCTTATTCTAACTTCAC----CCTCCCTTGAATTCTAAAGAGATTGAATTTCATTTATTTTCTTTATCCAAGAAGAAAAGGAAATAAATCTAACATCATTTTTTTCTTTCGGGTTCGCAGGAGAGGAAAA >metasequoia_glyptostroides TAACTTACTTTGGATATTGTATATACTTCTTTTCTTTTCAATTTGGAAAAAAGAGAAGAAAGAGAAAGGGATAGAAGTTGTCGAAGAATGATTAAAGATCTTATTACGAGAATGAATCAAGTAATAAAATCTTTAATTAAGAGTTTTCAGTAGT--TTAA-----TATTTGTGGAAGGAACTTTTGGATCTAGATTTCTATTTTG-TCTTATTCTAAGTTCAC----CCTCCCTTGAATTCTAAAGAGATTGAATCTAATTTATTTTCTTCATCGAACAAGAAAAGGAAATAAATCTAACATCATTTTTTTCTTTCGGGTTCGCAGGAGAGGAAAA >petG:petL >outgroup -------TCGATTCAACGGAATAAGTAGGGATA-ATAGTTATCTTGGATAGTACCCTGAATTTGCTATGAATCTCAATGATCAGAAATTGATATAGAGAGAATCAATTCAATTATTGAAATTGAAATAGTGAACTGAGAAGGTTTCATT >sequoia_sempervirens TTTTTATTTATTAAAAAAGAATAGGTAAGGATTCATAGCTAATCTATATAGTACCTCAAATTGACTCGGAATCTCAAT----------TCCTATTTAGGGTTTTATTTTATT------------------------------------- >metasequoia_glyptostroides -TTTTTTTTATTAAAAAAGAATAGGTAAGGATTCATAGCTAATCTACATAGTACCTCAAATTGACTCGGAATCTCAAT----------TTCTATTTAGGGTTTTATTTTATT------------------------------------- >petL:psbE >outgroup GAAGGACTGAATGAAATA---------TGGTTTATACATGTCTTCATGAGACAATTACCTAAATTTTTATTTTTGTAACCTTCAGATCAGAATACAAAAGATTAATTGTCCCAATTAGTACCCAATTAGTACCCAATTCAGGATCCTATATCTACTATAGGATATGTATGAACGAACATGGATGAGAGGAAATCTATGGTAGAAATCTCTTCATTTTCCTAGAAATCCCCACATTAATCGAACAGCTAATGAATAGCACCCGCGAACCCCTTCACAATTTGTTGAACGTAATTTCCTTACAGGGTGAATCAGTACGATTG---GATCACATCCCCTGGCATACCAGTAGCTATCGGTCCAGAGACTGGATCGGAAGAAACCTCTTCTACAGACAAACTAGCCAAAGTTTTGTGAATTTAACGTTTAGTTGTAAGAATATGAATATCCAGTTTGTCCTTTAATTTCTAGATCTTATTGATCCAATCATTCGACCCTCTAAATGGATTAGGTTTTTCTATATTCATTCTTAG---AGCCAGTAGAGCCCGACATTACAAGAATTCCACCTA--TTGTAAGGAATAACTCGTAATTTAACATACCTAAAATTGACT--AGGTTCTATTGCACTATCCACTTGGTTTTATTTAAGTTTTATTTAATGAGTAACGCCT-ACTCGTTAATA--CAAGGTAATATATAA-----TAAGGCCGTGGCATAACTTCACTCCACCTGTACTGGATACTATTGAAAGAACAACATACATCTGCGTAGCACCAAGGATCCCTGAATTACTGGGATCATCTACACGGACATAATGTCATGTTGGAATGAAAAAGGAAGGGGTAAACATATAATATTCTGGATGAGTTGTATTAATAGTGATTTATACCCTTTGTAAGGAAGGGGCACTCATCCTCTTTTTCGGCTCTACAGCCCAGCCACCTGTATGTAGAAGCTAATTCCAATCGAAATTTTCCATGGTCTATGTA----ATTGTTACAACATCGATTGAAGGGGTTCCTTACGCCCG-------GACCTCGGAACATGCAATATTCTATTATTTCTGTTAGGATTCAGTCACCAAACAGAGATGGAATAACTG-------------------------CTGGCAGGAACAGAATCATTCTATCTGGTTCCTTCTCGATACTCATCAAAATTGTATTGCTATGTCAGAAGAAAGCTAGCTATACTGGTCCAGTAGACTTCAAAGAAAAGATACCCTTGGTATAACATTGACAATCGAACAAGGATTGGAGAAGATATCAGTAGTTTTCCATTTCCTGATCTCTCTCTTTCATGGGATCAATTCCCCCTTGACTGAACAATAATATATGGAGCTGAGC >sequoia_sempervirens GAAGGAATCAATGAAAAAAAAAAACAATGATTGATACGTATTTTTGTCAGGCAATTACCTCAATTTTTCTCTA----------GGAACAGAA-AGAAAAAATCATTTCAATAAATAGATACCAATTTA-----TAATTGAATATCTAACAATTGTTA----ATGT-TGTGAAAAAACAT-----GGAGGGAATAGACGATAAAAAGATATTTTTTATATTT----TCTAAAAAAAAAGTGAAAATTCAATC-------CCCCCCAATT-GATTG-AACAAGCCATAAATAAAATGAATACCAATTGTAATTTCACAAATAAATTATCGTTCGTAATAGTCTATTACTAAGTATGAGAT----GAATGAATTTCACAATGATTCTGAT-TAGATAACCTTAC----ATTATCTCTATC----GGTCT-TTAGAACGAAAAAAGCTTTTGCTACAGCCAAGCATAGTAAAAAAGAACTG-TACGCTATAAATAAATGGATTCACTTTTTCCATATGCCTTTTTCATTTTAAGGAAAATAATTGAAGTCAACCCTGCTTGCTATCCTTTCTTTCTTGTAAAACAAAATAGGAATAGTAACATAGTGACTATTTGATCAAGAGAATATTCCACTATTCATCGATTCCTTTTTA---TTCATAAGAGGAATAACACTTCGGTCGTTCACATTCAAAGTGCTATAGAAGTCATTAAGTTCATAGCATAACTTATATTCGCT--------ATACTATTGTAAATACACGAT----ATAAATAATATTAAAA-----CAAAATAGAGAAAGAAACAGTATAATATTTTGGATAAGTTGCATTTATAATGAATGATACTCCTTGATCTTCTTCTTAA--AACGACATGAAT-GTATTCTA--------GCGATAAAG------TCACC-----TGTGGAAGCGAGAGCCATTACAATTATT------TGCTCAAATGAAATTAACTTCCCCATGATCCGTATATCCAATTGTTGCAATAGAGA--GACAGGATTCCTTGCGGAAGCTATTATGAAATTGAAATATGCAAAATTCTTTCATTTCTGTTCAGTGAAAAGAAAGCAAAAAAAGAAAATGAATTAAGTTGATCAAACAGAGCTGGAGTAACTGGCAGTAGCAGAATCGTTCTATCCTACTCCCTTTTCATATTAAGCAAAATTATATTGCTATGTTAGAAGAAGGCTAGCTATACT----TAGTATACTT-----CAAATATACCCTTGGTATCATATTGACAATCAAACAAGGATTGTAGAAGATATCAGTAGTTTTCCATTTCCTGATCTCTTTCTTTCATGGGATCAATTTACCCTTGATTTTACAATAATATAGGGAGCTTAGC >metasequoia_glyptostroides GAAGGAATCAATGAAGAAAAAAA-CAATGATTGATACGTATTTTTGTCAGACAATTACCTCAATTTTTATCTA----------GGAACAGAA-AGAAAAAATAATCTAAATAAATAGATACCAATTTA-----TAATTGAATATCTAACAATTGATA----ATGT-TGTGAAAAAACAT-----AGAGGGAATAAACGATAAAAATCTATTTTTTTTTTTA----TTTTGAAAAAA-GTGAAAATTCAATC-------CCCTTGATTTTGATTG-AGCAACCCATAAATAAAATGAATACCAATTGTAATTTCACAAAT----TATTGTACGCAATAGTCTATAATTAAGTACGAGAT----GAATGAATTTTACAATGATTCTGAT-TAGATCACCTTTC----ATCATCTCTACCTAACGTCCC-CTAGAACAAAAAAAACTTTTGTTGCAGCCAATCATAGTAAAAAAGAACTG-TACGCT--------------------TTTCCATATGCCTTTTTCATTTTAAGGAAAATAATTTTAGTCAAACCTGCT----ATCCTTTCTTTCTTGTAAAACAAAATAGGAATAGTAACATAGTTACTATTCGATCAAGGAAATATTTCACTATTCATCGATTGCTTTTTA---TTCATAAGAGGAATAACACTTCGGTCATTCACATTCAAAGTGCTATAGAAGTAATTAAGTTCATGGCATAATTT-TATTCGCT--------ATACTATTGTAAATACACTATT---ATAAATAATATTAAAA-----CAAAATAGAGAAAGAAACAGTAGAATATTTCTGATGAGTTGCATTTATAATGAATGATACTCCTTGATCTTCTTCTTAA--AACGGCATTAAT-GTATTCTA--------GCGATAAAG------TCACC-----TGTGGAAGCAAGAGCCATTACAATTATTATTTATTACTCAAATGAAATTAACTTCCCCATGATCCGTATATCGAATTGTTGCAATAGAGA--GACAG-----------------------------------------------------------------------------------------------------------------------------------------------------------TATTAAGTAAAATTTTATTGCTATGTTAGAAGAACGTTAGCTATACT----TAGTATACTT-----AAAATATACCCTTGGTATCATATTGACAATCAAACAAGGATTGTAGAAGATATCAGTAGTTTTCCATTTCCTGATCTCTTTCTTTCATGGGATCAATTTACCCTTGATTTTACAATAATATAGGGAGCTTAGC >psbL:psbJ >outgroup AACAATGAGAATATTATCACTCCATTTGAAGAGATCCAATACTCATAATTATCTATGCTATGACTGT--TTATGTG--ACTGTTTATGTCCCGAGCATGACCACTTAAGAAAATGTTAAAAGGAGTAAGAGAA >sequoia_sempervirens ------------AACAGTGAGAAGACTTTCTTTTCTTACCTAATTGAATTTGGTGAGA-TCGAATACTTCTATGTATTATTGTTTATGTCTTGAGCATGACTACTTAAGAAAATGTGAAAGGAAGTAATAGAA >metasequoia_glyptostroides -------------------------------------AACAGTGAGAATATTATATGCCTTGAGCATGACTACCTA--AGAAAATATGCCTTGGGCATGACTACCTAAGAAAATGTGACAGGAGGCAATAAAC >psbI:psbK >outgroup ACGTAATCTTCAAGATCCTGATTATAAGTACAACAGAATAGATCATCAATCTTTGTACCATATATGGATACTTGAATACCAAACAAT------AGTATGATTAATACAAATCACG----AAAT------TATTTCTCCAGATCATGTGTGA--AAATAAAATTGAA--AGAAAGAGAGAATTTATC-----------------TCTTTGTTTTCCAAAGTCTTT---TTTCCCTTCCTCTTTTTTAGATCAAC--------CAGATAT-----TTATTGAATCTTTATGAAAATTTGTCATTCGTGTGACCAAATA--------GCCCAATCCGAAAGTGAGCG------ATGGGATCGAAAGGAATTGACG-AAGGTGAGCGGAAAAGTTTTGAGACGGGAGCAAATAAGGCATC-TGGATCTGGTATCG---------------------------------TCGGATGGAGCA-AGGATATAACTTCTGTCACAATAAAAGAGTGATACAAAAATTGGATCAATGACAGCGATCCAAAACCTCGAAAAAGAAAAAAGAAAAAAAAGGGGGGGGGATACTTT---------------------------------------------------- >sequoia_sempervirens ATGTAATCTCCGGGATTCTTATTAGAATTACAACGGAATAGATCATCAATTTTTGTATCATATATTGGTACTTCAATCCCGAGCAAAGAAGAAAAGAGAAACAGAATAAATTCCATTTTGAAT---CTGTTTTTTTCTTCTTTGCTCGGGGTTGAACAGGAT-AAATAGGAACTCGAGTACTAATTAAACTATCCTAAACAAGTTTAGGATTATCACAATCAACAAATTTATTTATCATCTTTTCAAACAAAAAATAGAAACAAGTCTATAAATTGTCTAAAATAGAAGAAAATTTGGAATGCATAT-ACAAATTCTCATTCTTACTCGTTCTTTAAATAAATATCAAAGATATGTTCTCTCTAAATAGAAACAACATATTCTAATCAATACCTAATAGCCCGAACTCCAACTGCGATGGAGTTGATATTA-------------------------------TAATTGATGTACCGCAAAATAAGCATCAGAACAAGTAAAAAGAGTGTTACATCAATTTGATTAATGAAAGTGATCCAA----TCTAAATAGTTAGAATGTAACTATTGAAACAATCCATTTTTTTTGTATCAAGTGAATACAAAAATGAATCAAAACTTTTTGTCAAATTATCG >metasequoia_glyptostroides ATGTAATCTCCGGGATTCTTATTAGAATTACAACGGAATAGATCATCAATTTTTGTATCATATATTGGTACTTCAATCCCGAGCAAAGAAGAAAACAGATTCAGAATAAATTCAATTTTGAATATCTTTTTTTTTTCTTCTTTGCTCGGGATTGAACAGGGTTAAATAGGAACTCGAGTACTAATTAAACGATCCTAAACAAGTTTAGGATTATCACAATCAACAAATTTTTTTATCATCTTTTCAAACAAAAAATAGAGACAAGTATATAAATTGTCTAAAATAGAATAAAATTTGGAATGCATAT-ACAAATTCTCATTCTTACTCGTTCTTTAAATAAATATCAAACATATGTTCTCTATAAATAGAAATAACATATTCTAATCAATATCTAATAGCCCGAACTCCAACTGTCATGGAGTTGATATTAACTAATCCGGGGTATTTTGATCTGTTGAGAATAATTGATGTACCACAAAATAAGCATCAGAGCAAGTAAAAAGAGTGTTACATCACTTTAATTAATGAAAGTGATCCAA----TCTAAATAGTTAGAATGTAACTATTGAAACAATCCATTTTTTTCATATCAAGTGAATACAAAAATGAATAAAAACTTTTTGTCAAATTATCG