#NEXUS [written Fri Jun 28 11:33:51 SGT 2013 by Mesquite version 2.75 (build 566) at 199-153.priv23.nus.edu.sg/172.23.199.153] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=15; TAXLABELS Acholeplasma_palmae_Strain_J233_DQ004923 Candidatus_Phytoplasma_vitis_FN562932 Texas_Phoenix_palm_phytoplasma_AF434989 Malaysia_Bermuda_grass_white_leaf_phytoplasma_EU294011 Psammotettix_cephalotes_Flower_stunt_phytoplasma_HQ589192 Sugarcane_white_leaf_phytoplasma_AY139874 Sugarcane_white_leaf_phytoplasma_JN223448 Sugarcane_white_leaf_phytoplasma_AB646271 Sugarcane_grassy_shoot_phytoplasma_AB243298 Sugarcane_white_leaf_phytoplasma_HQ917068 Acholeplasma_axanthum_DQ400425 Hawaiian_sugarcane_Phytoplasma_JN223447 Aster_yellows_phytoplasma_watercress_AY665676 Russian_potato_purple_top_phytoplasma_EU333399 'Hawaiian sugarcane H87-4094 yellow leaf phytoplasma HQ116554' ; END; BEGIN CHARACTERS; TITLE MUSCLE__Alignments; DIMENSIONS NCHAR=2419; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Acholeplasma_palmae_Strain_J233_DQ004923 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCCGTCAAACCACGAAAGTCAGCAATACCCAAAGCCGGTGGCCTAACCGT----AAGGAGGGAGCCGTTTAAGGTAGGGTTGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------G---AAAGGCATTAAAAATGCAACAACCAAATTACTCATCATATTCAGTTTTGAAAGACTA--------------TAAT---------------------------TAATATTTAGTGTTTCTACGGTGGCAGCAAAGCAAGTTATATAAAT--------AACGGGCCTATAGCTCAGGTGGTTAGAGCGCACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACCATTATTTGGGGCTTTAGCTCAGCTGGGAGAGCGCCTGCCTTGCACGCAGGAGGTCAGCGGTTCGATCCCGCTAAGCTCCACCAAAAGAGAT-CTTTGAAAAGTAGATAAA------A------TTCTGTTAAAAGAA-------------------AAGAAATATAGGTTAAGGAACAAAGGGCGCACAGTGAATGCCTTGGCGCTAAGAGCCGATGAAGGACGCAACTAACAGCGAAATTCCATGGGAAGCGGTAAGTACGCGATGATCCATGGGTGTCCGAATGGGGGAACCCACCATGTGGAAGACATGGTATCCAGCAATGGAAGGGAAACGCAGTGAACTGAAATATCTAATTAGCTGCAGGAAAAGAAAGTAAAAACGATTCTGCTAGTAGCGACGAGCGAACGCGGAGGAGCCAGATACTATAATAGTTACAAAACTTTATGTGAGAAGAATAACTTGGGAAGGTTAACCAAAGAAGGTGAAAGTCCTGTAATCGAAGCGTAAAGACTAGAGTATCAGAAAGTACGGCGAGACACGAGAAATCTTGTCGGAA--GATGCGAGGACCATCTCGTAAGGCTAAATACTACTTAGTGACCGATAGTGAACCA Candidatus_Phytoplasma_vitis_FN562932 ------------------------------------------------ATGCAAGTCGAACGGAGACCCTTCAAA----------AGGTCTTAGTGGCGAACGGGTGAGTAACACGTAAGTAACCTACCTTTAAGACGAGGATAACAATCGGAAACGGTTGCTAAGACTGGATAGGAAACAGAAAGGCATCTTTTTGTTTTTAAAAGACCTTCTTCGGAGGGTATGCTTAAAGAGGGGCTTGCGCCACATTAGTTAGTTGGTGAGGTAAAGGCTTACCAAGATTATGATGTGTAGCTGGACTGAGAGGTTGAACAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCGACGCCGCGTGAACGATGAAGTATTTCGGTATGTAAAGTTCTTTTATTGAAGAAGAAAAAATAGTGGAAAAACTATCTTGACGTTATTCAATGAATAAGCCCCGGCTAACTATGTGCCAGCAGCCGCGGTAAGACATAGGGGGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTAGATAAGTCTATAATTTAATTTCAGTGCTTAACGCTGTCTTGTTATAGAAACTGTCTTGACTAGAGTGAGATAGAGGCAAGCGGAATTCCATGTGTAGCGGTAAAATGTGTAAATATATGGAGGAACACCAGAAGCGTAGGCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGAGTACTAAGTGTCGGGGT--AACTCGGTACTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGATACACGAAAAACCTTACCAGGTCTTGACATAC-TCTGCAAAGCTATAGAAATATAGTGGAGGTTATCAGGGATACAGGTGGTGCATGGTTGTCGTCAGTTCGTGTCGTGAGATGTTAGGTTAAGTCCTAAAACGAACGCAACCCCTGTCGCTAGTTGCCAGCACGTAATGGTGGGGACTTTAGCGAGACTGCCAATTAAACATTGGAGGAAGGTGGGGATAACGTCAAATCATCATGCCCCTTATGATCTGGGCTACAAACGTGATACAATGGCTATTACAAAGAGTAGCTGAAACGCGAGTTTTTAGCCAATCTCAAAAAGGTAGTCTCAGTACGGATTGAAGTCTGCAACTCGACTTCATGAAGCTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTAGCAATACCCGAAAGCAGTGGCTTAACTTCGAAAGAAGAGGGAGCTGTCTAAGGTAGGGTTGATGATTGGGGTTAAGTCGTAACAAGGTATCCTTACCGGAAGGTGAGGATGG-ATCACCTCCTTTCTAAGGA----------C---ATACATATAAAAA------------------TCATCATCTTCAGTTTTGAAAGACTTAG------GTTAAAATAT---------------------------AAGTTTTT--CTTTTTATAAAA------AAAGTGTTTCTCTTATATAAAAGACCAAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCACTTAGGCCCACC----------AATTTTA----------------------------------------------------------TATCAGGAAAATATTTACTTCGAAGAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Texas_Phoenix_palm_phytoplasma_AF434989 ---AGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGTGCTTAATACATGCAAGTCGAACGGAAATCTTTTAGAGAAATCTTTTAGATTTTAGTGGCGAACGGGTGAGTAACACGTAAGCAACCTGCCTTTAAGACGAGAATAACAATTGGAAACAGTTGCTAAGGCTGGATAGGAAATAAAAAGGCATCTTTTTATTTTTAAAAGACCTTCTTCGGAGGGTATGCTTAAAGAGGGGCTTGCGTCACATTAGTTAGTTGGTAGGGTAATGGCCTACCAAGACGATGATGTGTAGCTGGACTGAGAGGTTGAACAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGACGAAGTACTTCGGTATGTAAAGTTCTTTTATTGAAGAAGAAACAATAGTGGAAAAACTATCTTGACGTTATTCAATGAATAAGCCCCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTTAATAAGTCTCTAGTTTAATTTCAACGCTTAACGTTGTCCTGCTAGAGAAACTGT-TTGACTAGAGTGAGATAGAGGTAAGCGGAATTCCATGTGTAGCGGTAAAATGTGTAAATATATGGAGGAACACCAGAGGCGTAGGCGGCTTACTGGGTCTTTACTGACGCTGATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACTATGAGTACTAAGTGTCGGGGTTAAACTCGGTACTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGATCCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGATACACGAAAAACCTTACCAGGTCTTGACATAC-TCTGCAAAACTATAGAAATATAGTGGAGGTTATCAGGGATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTAGGTTAAGTTCTAAAACGAGCGCAACCCCTGTCGTTAATTGCCAGCACGTTATGGTGGGGACTTTAGCGAGACTGCCAATGAAAAATTGGAGGAAGGTGGGGATTACGTCAAATCATCATGCCCCTTATGATCTGGGCTACAAACGTGATACAATGGCTATTACAAAGAGTAGCTTAAACGCGAGTTTTTGGCAAATCTCAAAAAAATAGTCTTAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTGGACAATACCCGAAAGCGATAGCCTAACTGCGCAAGCAGAGGGAATCGTCTAAGGTAGGGTCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------------AATTTTTAAAA------------------TCATCATCTTCAGTTTTGAAAGACTTAAATTAATTTAAAAAAAT---------------------------AAGTTTTT--CTTTTTCATTAATTATTCTTATAGTATTTAATTTTT--------TAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCATTTAGGCCCACCAGTCTAAATGAACTGAA-----------------------------------------------------------AATCAAAAAAAAGTT-CTTTGAAAAGTAGATAAA------CAACGTAAATTCTCAAAATAA-------------------TG------------AAGAAAATAAGGG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Malaysia_Bermuda_grass_white_leaf_phytoplasma_EU294011 AAGTGTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGTGCTTAATACATGCAAGTCGAACGGAAATC--------------TTCGGATTTTAGTGGCGAACGGGTGAGTAACACGTAAGTAACCTGCCTTTAAGACGAGGATAACAATTGGAAACAGTTGCTAAGACTGGATAGGAAATTAGAAGGCATCTTTTAATTTTTAAAAGACCTTTTTCGAAAGGTATACTTAAAGAGGGGCTTGCGGCACATTAGTTAGTTGGTAGGGTAAAAGCCTACCAAGACCATGATGTGTAGCTGGACTGAGAGGTTGAACAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGATGAAGTATTTCGGTATGTAAAGTTCTTTTATTGAAGAAGAAAAAATAGTGGAAAAACTATCTTGACGATATTCAATGAATAAGCCCCGGCAAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTTGGTAAGTCTATAGTTTAATTTCAGTGCTTAACACTGTTCTGCTATAGAAACTAT-CAGACTAGAGTGAGATAGAGGCAAGTGGAATTCCATGTGTAGCGGTAAAATGCGTAAATATATGGAGGAACACCAGAGGCGTA?GCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTG?TAGTCCACGCCGTAAACGATGAGTACTAAGTGTCGGGGA--AACTCGGTACTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTG-TTAATTCGAAGATACACGAAAAACCTTA?CAGGTCTTGACATAC-TCTGCAAAGCTATAGCAATATAGTGGAGGTTATCAGGGATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTAGGTTAAGTC?TAAAACGAGCGCAACCCTTGTCACTAGTTGCCAGCATGTTATGATGGGCACTTTAGTGAGACTGCCAATGAAAAATTGGAGGAAGGTGAGGATCACGTCAAATCATCATGCCCCTTATGATCTGGGCTACAAACGTGATACAATGGCTGTTACAAAGAGTAGCTAAAACGCGAGTTTATAGCCAATCTCATAAAAGCAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCGAACCACGAAAGTTGGTAATACTCAAAAACGGTAGCCTAACTTCTTCGGAAGAGGGAACTGTCTAAGGTAGGATCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------AAAGAAAATTTTTTAAA------------------TTTTCATCTTCAGTTTTGAAAGACTTAG------TTC---TAAT--------------------AAGTAGTAAGTTTTT--CTCTTTTAAGAA------AAAG----------------------GAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC----------AACTGAT--------CAATAAGGTCATCTTT-----------------------------CTGATTCTT--AAAAAAAGTT-CTTTGGAAAGTAGATAAA------C-AAAGTAAAATAATAGAAAT-------------------CA------------AAGGAATTAAGGGCGTACAGTGGATGCCTTGGCACTAAGAGCCGATGAAGGACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Psammotettix_cephalotes_Flower_stunt_phytoplasma_HQ589192 -------------------------AACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGGAAATC--------------TTCGGATTTTAGTGGCGAACGGGTGAGTAACACGTAAGTAACCTGCCTTTAAGACGAGAATAACAATTGGAAACAGTTGCTAAGACTGGATAGGAAATTAAAAGGCATCTTTTAATTTTTAAAAGACCTTTTTCGAAAGGTATGCTTAAAGAGGGGCTTGCGACACATTAGTTAGTTGGTAGGGTAAAGGCCTACCAAGACTATGATGTGTAGCTGGACTGAGAGGTCGAACAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGATGAAGTATTTCGGTATGTAAAGTTCTTTTATTGAAGAAGAAAAAATAGTGGAAAAACTATCTTGACGCTATTCAATGAATAAGCCCCGGCAAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTTAATAAGTCTATAGTTTAATTTCAGTGCTTAACACTGTTCTGCTATAGAAACTAT-TAGACTAGAGTGAGATAGAGGCAAGCGGAATTCCATGTGTAGCGGTAAAATGCGTAAATATATGGAGGAACACCAGAGGCGTAGGCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTACTAAGTGTCGGGGG--AACTCGGTACTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGATACACGAAAAACCTTACCAGGTCTTGACATAC-TCTGCAAAGCTGTAGCAATACAGTGGAGGTTATCAGGGATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTAAAACGAGCGCAACCCTTATCGCTAGTTGCCAGCATGTCATGATGGGGACTTTAGCGAGACTGCCAATGAAAAATTGGAGGAAGGTGAGGATCACGTCAAATCATCATGCCCCTTATGATCTGGGCTACAAACGTGATACAATGGCTGTTACAAAGAGTAGCTAAAACGCAAGTTCATAGCCAATCTCAAAAAAACAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTGGTAATACTCGAAAACGGTAGCCTAACTTCTTCGGAAGAGGGAACCGTCTAAGGTAGGATCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A-----AATTTTTTAAA------------------TTTTCATCTTCAGTTTTGAAAGACTTAG------TTCTTATTAT---------------------------AAGTTTTT--CTTTTTTAAGAA------AAAAAG--------------------AAGGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC----------AACTGAA------------AAGGTCTTCTTT-----------------------------CTTGTTCTT--AAAAAAAGTT-CTTTGAAAAGTAGATAAA------C-AAAGTAAAA-TAAAAAAAC-------------------CA------------AAGGAATAAAGGGCGTACAGTGGATGCCTTGGCACT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sugarcane_white_leaf_phytoplasma_AY139874 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATCCCYACCGGAAGGWGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ATAATTTTTTAAA------------------TATTCATCTTCAGTTTTGAAAGACTTAG------TTC---TTAT---------------------------AAGTTTTT--CTTTTTTAAGGA------AAAGAA--------------------AATGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC----------AACTGAA----------AAAAGGTCTTTTY------------------------------CTAATTCTT--AAAAAAAGTT-CTTTGARAAGKARATMAA------C-AAAGTATTTTTTTAAAAAT-------------------CA------------AAGGAATCAAGGGCGT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sugarcane_white_leaf_phytoplasma_JN223448 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGTAACAAGGTATCCCTACCGGAAGGCGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ATAATTTTTTAAA------------------TATTCATCTTCAGTTTTGAAAGACTTAG------TTC---TTAT---------------------------AAGTTTTT--CTTTTTTAAGGA------AAAGAA--------------------AATGGGCCTATAGCTCAGTTGGTTAGAGCACACGCCCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sugarcane_white_leaf_phytoplasma_AB646271 -AGAGTTTGATCCTGGCTCAGGATAAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGGAAATC--------------TTCGGATTTTAGTGGCGAACGGGTGAGTAACACGTAAGCAACCTGCCTTTAAGACGAGGATAACAATTGGAAACAGTTGCTAAGACTGGATAGGAAATAAAAAGGCATCTTTTTATTTTTAAAAGACCTTTTTCGGAAGGTATGCTTAAAGAGGGGCTTGCGTCACATTAGTTAGTTGGCAGGGTAAAAGCCTACCAAGACTATGATGTGTAGCTGGACTGAGAGGTTGAACAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGATGAAGTATTTCGGTATGTAAAGTTCTTTTATTGAAGAAGAAAAAATAGTGGAAAAACTATCTTGACGATATTCAATGAATAAGCCCCGGCAAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCGAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTTAATAAGTCTATAGTTTAATTTCAGTGCTTAACACTGTCCTGCTATAGAAACTAT-TAGACTAGAGTGAGATAGAGGCAAGTGGAATTCCATGTGTAGCGGTAAAATGCGTAAATATATGGAGGAACACCAGAGGCGTAGGCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTACTAAGTGTCGGGAT--TACTCGGTACTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGATACACGAAAAACCTTACCAGGTCTTGACATAC-TCTGCAAAGCTATAGCAATATAGTGGAGGTTATCAGGGATACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTAGGTTAAGTCCTAAAACGAGCGCAACCCTTGTCATTAGTTGCCAGCATGTCATGATGGGCACTTTAATGAGACTGCCAATGAAAAATTGGAGGAAGGTGAGGATCACGTCAAATCATCATGCCCCTTATGATCTGGGCTACAAACGTGATACAATGGCTGTTACAAAGAGTAGCTGAAACGTAAGTTTATAGCCAATCTCATAAAAGCAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTGGTAATACTCAAAAACGGTAGCCTAACTTCTTCGGAAGAGGGAACCGTCTAAGGTAGGATCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ATAATTTTTTAAA------------------TATTCATCTTCAGTTTTGAAAGACTTAG------TTC---TTAT---------------------------AAGTTTTT--CTTTTTTAAGGA------AAAGAA--------------------AATGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC----------AACTGAA----------AAAAGGTCTTTTTT-----------------------------CTAATTCTT--AAAAAAAGTT-CTTTGAAAAGTAGATAAA------C-AAAGTATTTTTTTAAAAAT-------------------CA------------AAGGAATCAA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sugarcane_grassy_shoot_phytoplasma_AB243298 -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CAAAG------------------------------------------------------------------------------GAAGTTGGAATCGCTAGT-ATCGCGAATCAGAATCGGCGAGGAGAGGATACAGTTCTCGGGGTTTGTATCACACCGCCCGTCAAACCACGAAAGTTGGTAATACTCAAAAACGGTAGCCTAACTTCTTCGGAAGAGGGAACCGTCTAAGGTAGGATCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA--------------ATAATTTTTTAAA------------------TATTCATCTTCAGTTTTGAAAGACTTAG------TTC---TTAT---------------------------AAGTTTTT--CTTTTTTAAGGA------AAAGAA--------------------AATGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC----------AACTGAA---------AAAAAGGTCTTTTTT-----------------------------CTAATTCTTAAAAAAAAAGTT-CTTTGAAAAGTAGATAAA------C-AAAGTATTTTTTTAAAAAT-------------------CA------------AAGGAATCAAGGGCGTACAGTGGATGCCTTGGCACTAAGAGCCGAATGAAGGGACGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Sugarcane_white_leaf_phytoplasma_HQ917068 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ATAATTTTTTAAA------------------TATTCATCTTCAGTTTTGAAAGACTTAG------TTC---TTAT---------------------------AAGTTTTT--CTTTTTTAAGGA------AAAGAA--------------------AATGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Acholeplasma_axanthum_DQ400425 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCCCGTCAAACCACGAAAGTCAGCAATACCCAAAACCGGTGGCCTAAC--CTGCAAAGGAGGGAGCCGTCTAAGGTAGGGTTGATGGTTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGAGCATAACAGTAAGAATAACTTACAAAAACTCTACTCTC-------TCGTCATATTCAGTTTTGAAGGATTTTC-----CTTC---TAAT---------------------------AATATTTA----------------------------------------------TTAGGGCCTATAGCTCAGCTGGTTAGAGCGCACG-CCTGATAAGCGTGAGGTCGATGGTTCAAGTCCATTTAGGCCCACCATTATAAGGCTGCTATA------------GTAGTCTGGT-------------------------------------------AAATGAGAT-CTTTGAAAAGTAGATAAATTCTGTCGTAACAAATAATAAAAAAGTTTAATTAGCAATAATTAAGCGCGTAAAAAGGTTAAGAAAGTAAGGGCACACAGTGAATGCCTAGGCACTAAGAGCCGAAGAAGGACGCAACTAACGGCGAAACGCCACGGGAAGCAGTAAGTATGTGAAGATCCGTGGGTATCCGAATGAGGGAACTCGGCATGTAGAAGACATGTCACGTCGAAAGACGAGGGAAACGCAGTGAATTGAAATATCTTAGTAACTGCAGGAAAAGAAAGTAAAAACGATTCTGCGAGTAGCGACGAGCGAAAGTGGAGGAGCCCGATACCATAATAGTTACAAAACTTTATGTGAGAAGAACAACCTGGGAAGGTTGACCAAAGAAGGTGAAAGTCCTGTAAACGAAGCATAAAGACTAGGGTATCAAAGAGTACAGCGGGACACGAGAGATCTTGCTGGAACTATAAGGAGGACCATCTCCTAAGGCTAAATACTACTTAGTGACCGATAGTGAACCA Hawaiian_sugarcane_Phytoplasma_JN223447 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGGCATCACCTCCTTTCTAAGGA----------A---ACAA---------------------------TTATCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTT---TCATTGTCACTTGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTTAAGAT--------------------------------TAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCATTTAGGCCCACC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Aster_yellows_phytoplasma_watercress_AY665676 ----GTTTGATCCTGGCTCAGGATTAACGCTGGCGGCGTGCCTAATACATGCAAGTCGAACGGAAGTT--------TAAGCAATTAAACTTTAGTGGCGAACGGGTGAGTAACGCGTAAGCAATCTGCCCCTAAGACGAGGATAACAGTTGGAAACGACTGCTAAGACTGGATAGGAGACAAGAGGGCATCTTCTTGTTTTTAAAAGACCT--AGCAATAGGTATGCTTAGGGAGGAGCTTGCGTCACATTAGTTAGTTGGTGGGGTAAAGGCCTACCAAGACTATGATGTGTAGCCGGGCTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGATGAAGTATTTCGGTACGTAAAGTTCTTTTATTAGGGAAGAATAAATGATGGAAAAATCATTCTGACGGTACCTAATGAATAAGCCCCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTAAATAAGTTTATGGTCTAAGTGCAATGCTCAACATTGTGATGCTATAAAAACTGT-TTAGCTAGAGTAAGATAGAGGCAAGTGGAATTCCATGTGTAGTGGTAAAATGCGTAAATATATGGAGGAACACCAGTAGCGAAGGCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTACTAAACGTTGGGTA--AAACCAGTGTTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGGTACCCGAAAAACCTCACCAGGTCTTGACATGCTTCTGCAAAGCTGTAGAAACACAGTGGAGGTTATCAGTTGCACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTACCAGCACGTAATGGTGGGGACTTTAGCAAGACTGCCAGTGATAAATTGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGATACAATGGCTGTTACAAAGGGTAGCTGAAGCGCAAGTTTTTGGCGAATCTCAAAAAAACAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTGGTAATACCCAAAGCCGGTGGCCTAACTTCGCAAGAAGAGGGAACCGTCTAAGGTAGGGTCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ACAA---------------------------TTATCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTT---TCATTGTAACTTGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTTAAGAT--------------------------------TAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCATTTAGGCCCACCAT--------AACCACA----------AATAGG-------------------------------------CAAAATCTT---AAAAAAGCT-CTTTGAAAAGTAGATAAA------CGAAGG------TTAAAAAAT-------------------CA------------AAGGAACTAAGGGCGCACAGTGGATGCCTTGGCACTAAGAGCCGATGAAGGACG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Russian_potato_purple_top_phytoplasma_EU333399 -------------------------AACGCTGGCGGCGCGCCTAATACATGCAAGTCGAACGGAAGTT--------TAAGCAATTAAACTTTAGTGGCGAACGGGTGAGTAACGCGTAAGCAATCTGCCCCTAAGACGAGGATAACAGTTGGAAACGACTGCTAAGACTGGATAGGAGACAAGAAGGCATCTTCTTGTTTTTAAATGACCT--AGCAATAGGTATGCTTAGGGAGGAGCTTGCGTCACATTAGTTAGTTGGTGGGGTAAAGGCCTACCAAGACTATGATGTGTAGCCGGGCTGAGAGGTTGAACGGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATTTTCGGCAATGGAGGAAACTCTGACCGAGCAACGCCGCGTGAACGATGAAGTATTTCGGTACGTAAAGTTCTTTTATTAGGGAAGAATAAATGATGGAAAAATCATTCTGACGGTACCTAATGAATAAGCCCCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGGGGCAAGCGTTATCCGGAATTATTGGGCGTAAAGGGTGCGTAGGCGGTTAAATAAGTTTATGGTCTAAGTGCAATGCTCAACATTGTGATGCTATAAAAACTGT-TTAGCTAGAGTAAGATAGAGGCAAGTGGAATTCCATGTGTAGTGGTAAAATGCGTAAATATATGGAGGAACACCAGTAGCGAAGGCGGCTTGCTGGGTCTTTACTGACGCTGAGGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAGTACTAAACGTTGGGTA--AAACCAGTGTTGAAGTTAACACATTAAGTACTCCGCCTGAGTAGTACGTACGCAAGTATGAAACTTAAAGGAATTGACGGGACTCCGCACAAGCGGTGGATCATGTTGTTTAATTCGAAGGTACCCGAAAAACCTCACCAGGTCTTGACATGCTTCTGCAAAGCTGTAGAAACACAGTGGAGGTTATCAGTTGCACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTACCAGCACGTAATGGTGGGGACTTTAGCAAGACTGCCAGTGATAAATTGGAGGAAGGTGGGGACGACGTCAAATCATCATGCCCCTTATGACCTGGGCTACAAACGTGATACAATGGCTGTTACAAAGGGTAGCTGAAGCGCAAGTTTTTGGCGAATCTCAAAAAAACAGTCTCAGTTCGGATTGAAGTCTGCAACTCGACTTCATGAAGTTGGAATCGCTAGTAATCGCGAATCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTGGTAATACCCAAAGCCGGTGGCCTAACTTCGCAAGAAGAGGGAACCGTCTAAGGTAGGGTCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ACAA---------------------------TTATCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTT---TCATTGTAACTTGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTTAAGAT--------------------------------TAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCATTTAGGCCCACCAT--------AACCACA----------AATAGG-------------------------------------CAAAATCTT---AAAAAAGCT-CTTTGAAAAGTAGATAAA------CGAAGG------TTAAAAAAT-------------------CA------------AAGGAACTAAGGGCGCACAGTGGATGCCTTGGCACTAAGAGCCGATGAAGGA---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 'Hawaiian sugarcane H87-4094 yellow leaf phytoplasma HQ116554' -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAGCAT-GTCGCGGTGAATAC---GTTCTCGGGGTTTGTA-CACACCGCCCGTCAAACCACGAAAGTTGGCAATACCCAAAGCCGGTGGCCTAACTTCGCAAGAAGAGGGAACCGTCTAAGGTAGGGTCGATGATTGGGGTTAAGTCGTAACAAGGTATCCCTACCGGAAGGTGGGGATGG-ATCACCTCCTTTCTAAGGA----------A---ACAA---------------------------TTATCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTT---TCATTGTMACTTGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTTAAGAT--------------------------------TAAGGGCCTATAGCTCAGTTGGTTAGAGCACACG-CCTGATAAGCGTGAGGTCGGTGGTTCAAGTCCATTTAGGCCCACCAT--------AACCACA----------AATAGG-------------------------------------CAAAATCTT---AAAAAAGCT-CTTTGAAAAGTAGATAAA------CGAAGG------TTAAAAAAT-------------------CA------------AAGGAACTAAGGGCGCACAGTGGATGCCTTGGCACTAAGAGCC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- ; END; BEGIN TREES; Title Single_Linkage_cluster_analysis; LINK Taxa = Taxa; TRANSLATE 1 Acholeplasma_palmae_Strain_J233_DQ004923, 2 Candidatus_Phytoplasma_vitis_FN562932, 3 Texas_Phoenix_palm_phytoplasma_AF434989, 4 Malaysia_Bermuda_grass_white_leaf_phytoplasma_EU294011, 5 Psammotettix_cephalotes_Flower_stunt_phytoplasma_HQ589192, 6 Sugarcane_white_leaf_phytoplasma_AY139874, 7 Sugarcane_white_leaf_phytoplasma_JN223448, 8 Sugarcane_white_leaf_phytoplasma_AB646271, 9 Sugarcane_grassy_shoot_phytoplasma_AB243298, 10 Sugarcane_white_leaf_phytoplasma_HQ917068, 11 Acholeplasma_axanthum_DQ400425, 12 Hawaiian_sugarcane_Phytoplasma_JN223447, 13 Aster_yellows_phytoplasma_watercress_AY665676, 14 Russian_potato_purple_top_phytoplasma_EU333399, 15 'Hawaiian sugarcane H87-4094 yellow leaf phytoplasma HQ116554'; TREE Single_Linkage_tree_1 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(10,(9,(6,8))))))))))); TREE Single_Linkage_tree_2 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(9,(10,(6,8))))))))))); TREE Single_Linkage_tree_3 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,((6,8),(9,10)))))))))); TREE Single_Linkage_tree_4 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(10,(8,(6,9))))))))))); TREE Single_Linkage_tree_5 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,((6,9),(8,10)))))))))); TREE Single_Linkage_tree_6 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(8,(10,(6,9))))))))))); TREE Single_Linkage_tree_7 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(9,(8,(6,10))))))))))); TREE Single_Linkage_tree_8 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(8,(9,(6,10))))))))))); TREE Single_Linkage_tree_9 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(9,(6,(8,10))))))))))); TREE Single_Linkage_tree_10 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(6,(9,(8,10))))))))))); TREE Single_Linkage_tree_11 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(8,(6,(9,10))))))))))); TREE Single_Linkage_tree_12 = (1,(11,(2,(((12,15),(13,14)),(3,(4,(5,(7,(6,(8,(9,10))))))))))); END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 2419; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 2419; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 2419; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1372390431803; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 2979925152356328595; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4945440097158319768; mqVersion 275; checksumv 0 3 1237957791 null getNumChars 2419 numChars 2419 getNumTaxa 15 numTaxa 15 short true bits 2305843009213693967 states 15 sumSquaresStatesOnly 345107.0 sumSquares -1.3835058055281934E19 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 943 653; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4945440097158319768 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; togglePaleInapplicable on; toggleShowBoldCellText off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;