NEXUS
[File created by TreeBASE:  7/26/07  21:04:57]
[Matrix accession#: M1859]

BEGIN TAXA;
	TITLE M1859;
	DIMENSIONS  NTAX=19;
	TAXLABELS
		Acholeplasma_brassicae	Aster_yellows_witches_broom	Aster_yellows_phytoplasma_A_isolate_99uw111	Aconitum_proliferation_phytoplasma	Aster_yellows_phytoplasma_Queen_Annes_lace	Clover_phyllody_phytoplasma_operonA	Clover_phyllody_phytoplasma_operonB	Aster_yellows_phytoplasma_bolt_distortion2_operonB	Aster_yellows_phytoplasma_Maryland_strain_AY1	Aster_yellows_phytoplasma_bolt_distortion2_operonA	Aster_yellows_phytoplasma_severe_operonB	Aster_yellows_phytoplasma_severe_operonA	Aster_yellows_phytoplasma_white_bolt	Aster_yellows_phytoplasma_semigeotropism	Aster_yellows_phytoplasma_western_severe_strain	Bermuda_grass_white_leaf_phytoplasma	Tomato_big_bud_phytoplasma	Western_X_disease	Ash_yellows_phytoplasma
	;
END;

BEGIN CHARACTERS;
	TITLE M1859;
	DIMENSIONS NCHAR=280;
	FORMAT DATATYPE = DNA MISSING = ? GAP = -  ;
	MATRIX
		Acholeplasma_brassicae                                   CAAACCAATTCGTAATGAAATCA-TCATATTCAGTTTTGAAAGACTTAAG--AGTTTTTCTTGAAA-------------TAAGTTAAGGTA-------TAAAAACCCTT-------AAAAAAGGGCCTATAGCTCAGCTGGTTA--GAGCGCACGGCTGATAACCGTGAGGTCGATGGTTCGAGTC---CATTTAGGCCCACCATT--------TAACT-TGTGCACTCAGTC--AAATGAGCGTACTTTAATAACCT-ATAA-TATAGGTTGAGAT---
		Aster_yellows_witches_broom                              AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTTTAAAT----TGTTTGCAAATTGTATTTGCAACATTTAAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCAAA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAATGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_A_isolate_99uw111              AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTTTAAAT----TGTTTGCAAATTGTATTTGCAACATTTAAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCAAA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aconitum_proliferation_phytoplasma                       AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTTTAAAT----TGTTTGCAAATTGTATTTGCAACATTTAAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCTACCATA-------ACCAAA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_Queen_Annes_lace               AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTTTAAAT----TGTTTGCAAATTGTATTTGCAACATTTAAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCAAA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Clover_phyllody_phytoplasma_operonA                      AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTATAACTAACTTACTTGCAAATTGTATTTACAATATTTTAATCTTTTT---AATATTAA-GGGCCTATAGATCAGTTGGTTATAGAGTACACACCTAATAATTGTGAGGTCGGTGGTTCAAGTTACACATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATATTAAAA-AAAGCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Clover_phyllody_phytoplasma_operonB                      AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTATAACTAACTTACTTGCAAATTGTATTTACAATATTTTAATCTTTTT---AATATTAA-GGGCCTATAGATCAGTTGGTTATAGAGTACACACCTAATAATTGTGAGGTCGGTGGTTCAAGTTACACATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATATTAAAA-AAAGCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_bolt_distortion2_operonB       AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTCACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_Maryland_strain_AY1            AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTCACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGACCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_bolt_distortion2_operonA       AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTCACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_severe_operonB                 AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTAACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_severe_operonA                 AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTAACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_white_bolt                     AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTAACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_semigeotropism                 AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTAACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Aster_yellows_phytoplasma_western_severe_strain          AAGGA-AAC---------AATTA-TCATCTTCAGTTTTGAGAGACTTAAGAAAGTTTTTCATTGTAACT----TGCTTGCAAATTGTATTTGCAACATTTTAATCTTTTT---AAGATTAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCATA-------ACCACA-AATAGGCAAAATCTTAAAA-AA-GCTCTTTGAAAAGTAGATAAACGAAGGTTAAAAA---
		Bermuda_grass_white_leaf_phytoplasma                     AAAGAAAATT--TTTTAAATTT--TCATCTTCAGTTTTGAAAGACTTAGTTCTAATA------AGTA-----------GTAAGTTTTTCTC-------TTTAAGAT--------AAAAGGAAGGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGATGGTTCAAGTC---CATTTAGGCCCACCAACTGATCAA-TAAGGTCATCTTTCTGATTCTTAAAAAAAGTTCTTTGAAAAGTAGATAAACA-AAGTAAAATA---
		Tomato_big_bud_phytoplasma                               AAGGA-AACC---AATAAAATCAATCATCTTCAGTTTTGAAAGACTTAGGCAA----------------------CT---AAGTTTTTCTT-------CGTGA-CTTC--------ACGAA-GGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCAG------------AGTTATAGGTTTCGTAAGAACACAAA-TTCTTTGAAAATTAGGTAAATAATAGTTATTT----
		Western_X_disease                                        AAGGA-AAA----AATAAAATTA-TCATCTTCAGTTTTGAAAGACTTAGAAAA----------------------TTCATAAGTTTTTCTT-----TTTTTAAGGC----------ATTAA-GGGCCTATAGCTCAGCTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCAGTTTATTTT-AAAAGTTATAAGCACTGTCTTAAAAAAAAGTTCTTTGAAAAGTAGATAAACA-TAG---TAAA---
		Ash_yellows_phytoplasma                                  AAGGTTAATC--ACATAAATTCA-TCATCTTCAGTTTTGAAACACTTAGATTGA---------AAAAA-----------TAAGTTTTTCTT------TTTTAAGC-----------ACCAAAGGGCCTATAGCTCAGTTGGTTA--GAGCACACGCCTGATAAGCGTGAGGTCGGTGGTTCAAGTC---CATTTAGGCCCACCAATAGAT----TAATATAAACGGTCCTGCT-TAAAAGAAAGTTCTTTGAAAAGTAGATAAATA-TAGCTTTTAA---
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 280 ; 
 CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;