NEXUS
[File created by TreeBASE:  7/26/07  21:00:19]
[Matrix accession#: M1145]

BEGIN TAXA;
	TITLE M1145;
	DIMENSIONS  NTAX=7;
	TAXLABELS
		Hypocrea_nigricans_GJS98.183	Hypocrea_flavovirens_PC4	Trichoderma_virens_GL39	Trichoderma_virens_GL21	Trichoderma_virens_GL20	Trichoderma_virens_GL3	Hypocrea_virens_GJS95.194
	;
END;

BEGIN CHARACTERS;
	TITLE M1145;
	DIMENSIONS NCHAR=1566;
	FORMAT DATATYPE = DNA MISSING = ? GAP = -  ;
	MATRIX
		Hypocrea_nigricans_GJS98.183       ----------------------CCCTCCGTAGGTGAACCTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTTTATAATCTGAGC-CTTCTCGGCGCCTCTCGTA-G--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTGCCTTGGCGGTGGCCGTCT--CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTT-AA-ACACCCAACTT------------------------------------------------------------------------TCGT-A-CGTAC-AATCCTGTTCCCTCACGTCGGCATCATTCGCCGGTCTGAT-TCTCAAACACTTGTGCTAACCAT-CGCCTTCTAGGGGTGCGTATTCCATCAATCATCTTGAATGAGATCGATCGAACACA--ATACTGACTTGC-TATAACAGCCACGTCGACTCCGGAAAGTCGACCACCGTAAGTTG-CACCCTCT----CTTGCTCCGATATCAAACGT---CGTT--TGATGGGGGACACCTAC--TCTAGA-GCACAGGGCTAACCATTCATCATACAGACCGGTCACTTGATCTACCAGTGCGGTGGTATC-GACCGT-CGTACCATC-GAGAAGTTCGAGAAGGTAAGCTTCAACTGATT--TTTCGCCTCGATTCTTTCCTCCTTCACATTCAATT-GTGCCCGACAATT--CTGCAGAGAATTTT-CGTGT-CGACAATTTTT--CATCACCCCG--CTTTCCGTT------ACCCCTCCTTTGCA-GCG-ACGCAAAA-TTTTTTTTGCTGTCG-TCT-GGTTTTT---AGTGGGGTTCTCTGTG---------CAACCCCACTAGCTCACTGCTTTTTCCTGCTTCACTCTCACTTCCTCGTCATCATTCAACACGCTCTGTGTCTTTGGTCATTCAGCGATGCTAACCACTTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATCGACATTGCTCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTTCATCAATCTCATGGTGCAACTGCGAGCTAGTGCTAACATGCAATTTCACAGACGTTTCCCGGGCACCGTGA
		Hypocrea_flavovirens_PC4           ----------------------CCTCCGTAGGGTGAACCTGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGCGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGG-AAAAACAACCAAAACTCTTTTGTATACCCCCTCGCGGGTTTTCTTACT-TCTGAGAACTTCTCGGCGCCCCTTAGCGG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTCCCTTCGCGGGGCGGCCGGCCCCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCAATGCCGT-AAA-ACACCCAACTTT--------------------------------------------------------------CC-ACGTGGTCGTTATCGTATGTATTCACCAGATTCCTTTCGGCATCATTCGCCGATTTGTCGTTTGAAACAATTGTGCTAACTGT-TGCTTTCCAGGGGTGCGTATTCCATC---TATCGTGAAGGACATCGATCGAACACA--TCACTGACCTAC-TACGACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCCATTC--CCTGACATGCCATCAAGCCATAGTGCT--TGATGGGGGACATC-ACCTCTTTGA-ACTCTGCGCTGACCATCTTCTTCACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACCGT-CGTACCATC-GAGAAGTTCGAGAAGGTAAGC-TCAATCAACTGATTCCGACTCTGGTTT---TCCGTTCCCCTTCAATT-GTGACGGACAATTC-TCAACCGGAATTAT-CCTTGTCAACAATTTTG--CATCACCCCG--CTTTCTCTTCCCATTACCCCTCCTTTGCA-GCG-ACGCAAA---TTTTTTTGCAGCC--TC--GAATTTT---AGTGGGGTCGCTTGTGCATCCCCCACCAACCATTCACTGCTTTTGCCCTTGACTGCGTGTACCTGTCATCATTCCACGCTTTTCGTCATC----TCTTTCAGCGATGCTAACCATCTTTCCATCAATAGGAAGCCGCCGAACTCGGCAAGGGTTCCTTCAAGTACGCTTGGGTTCTTGACAAGCTCAAGGCCGAGCGTGAGCGTGGTATCACCATTGACATTGCCCTGTGGAAGTTCGAGACTCCCAAGTACTATGTCACCGTCATTGGTATGTCTACGGATCTCATCCCGTTCCTTGTTCGCCAGCCTGTACTAATGCCAGTTTGACAGACGCTCCCGGC---------------
		Trichoderma_virens_GL39            TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA----------------------------------------CGGCATCGTCCGCCGTTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGCCGACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGAGGTATCTGACAAGGCGTACCATC-GAGAAGTTCGAGAAGGTGAGCCTCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAATTTGTGCTCGACAATTT-TGTTTA-GAATCAT-CGAGGGCAACAATTTTTTTCGTCACCCCGGCTTTTTGTTCCCATTACCCCTCCTTTTGCCAGCGGACGCAAAAATTTTTTTGGCTGCC--TCT-GGGTCTTAT-AGTGGGGGGG-TTGCAC---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		Trichoderma_virens_GL21            ---------------------GGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTC-------------------------------------------------------------------------------------------------------------GTCCGCCGCTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAG-TAACCATACGCCATACAGACTGGTCACTTGATCTACCAGTGCGGGGGTATC-GACAAG-CGTACCATCCGAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCAT-AATTT----CCCCTTCACATTCAATTGGTGCTC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		Trichoderma_virens_GL20            TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA--------------TTCCTAT-TATCCCAC-CACTTTCGTCGGCATCGTCCGCCGCTCTGAC-TCTGGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCCGCATCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAAT--GTGCTCGACAATTC-TGGTCA-GAATCAT-CGAGGGCAACAATTTTTT-CGTCACCCCG--CTTTCGGTTCCATTTACCCCTCCTTTGCA-GCG-ACGCAAAAAATTTTTTTGCTGCCCTTT--GGGTTTTTTAAGTGGGGGGG--TGCACC--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		Trichoderma_virens_GL3             TGGAAGTAAAAGTCGTAACAAGGTCTCCGTTGGTGAACCAGCGGAGGGATCATTACCGAGTTTACAACTCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTCTGAAATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAATAAGCGGA------------------TAT-TATCCCA--CCGTTTCGTCGGCATCATCCGCCGCTCTGAC-TCTGGAATCTTTGTGCTAACAAC-CGTCCTCTAGGGGTACGTATTCCGTCAATCATCATGAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCGACGTCAAACGTTGCCGTT--TGATGCGGGGTGTCTACGCTTTTGA-ACACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATCAGACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTAAGCT-CAATCAACTGGTTTCGCATCAATTT----CCCCTTCCCATTCAATT-GTGCTCGACAATTT-CTGTTCAGAATCAT-CCGATGCAACAATTTTTT-CGTCACCCCG--CTTTTCGTTCCCATTACCCCTCCTTTGCA-GCG-ACGCAAAAA-TTTTTTTGCTGGCCTTCT-GGGTTTTT--AGTGGGGGGG--TGCAACCAAG---CCAACCCCCACCACTTGCCTTTTTTTGCTTTTTG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
		Hypocrea_virens_GJS95.194          T---------------------------------------GCGGAGGGATCATTACCGAGTTTACAA-TCCCAAACCCAATGTGAACGTTACCAAACTGTTGCCTCGGCGGGATCTCTGCCCCGGGTGCGTCGCAGCCCCGGACCAAGGCGCCCGCCGGAGGACCAACCAAAACTCTTATT---GTATACCCCCTCGCGGGTTTTTT-ACTATCTGAGCCAT-CTCGGCGCCCCTCGT-GG--------GCG-TTTCGAAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTTCAACCCTCGAACCCCTCCGGGGGGTCGGCGTTGGGGATCGGCCCTTTACGGGGCCGGCC-------CCGAAATACAGTGGCGGTCTCGCCGCAGCCTCTCCTGCGCAGTAGTTTGCACACTCGCATCGGGAGCGCGGCGCGTCCACAGCCGTTAAACACCCCAAACTTC--------------------------------------------------------------------------------TAT-TATCCCAC-CACTTTCGTCGGCATCGTCCGCCGCTCTGAC-TCTAGAACATTTGTGCTAACCAC-CGTCCTCTAGGGGTGCGTATTCCGTCCATCATCATAAATGAGATCGATCGAACACA--ATACTGACTTGC-GACAACAGCCACGTCGACTCCGGCAAGTCGACCACCGTGAGTTA-CACCCTCTGCCTCTCGCCTCGACGTCAAACGTTGCCGTT--TGATGCGGGGAGTCTACGCTTTTGA-ATACACAGCTAACCATTCGCCATACAGACTGGTCACTTGATCTACCAGTGCGGTGGTATC-GACAAG-CGTACCATC-GAGAAGTTCGAGAAGGTGAGC-TCAATCAACTGCTTTCGCATCAATTT----CCCCTTCACATTCAATT-GTGCTCGACAATTC-TGTTCAAGAATCAT-CGAGG-CAACAATTTTTT-CGTCCCCCCG--CTTTCG-TTCCATTACCCCCTCCTTTGCAAGCG-ACGCAAAAA--TTTTTTGCTGCC--TCT--GGTTTTTT-AGTGGGGGG--TTGCACCAG------CAACCCCCACCCACTTTCCTTGGTGGCTCTTTGCC-CCTTCGTCTTACCCAACTTT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
	;
END;

BEGIN CODONS;
CODONPOSSET * CodonPositions = 
 N: 1 - 1566 ; 
 CODESET * UNTITLED = Universal: all ; 
 END;

BEGIN ASSUMPTIONS;
CHARSET ITS = 1 - 658 ; 
 CHARSET TEF = 659 - 1566 ; 
 CHARSET EXON1 = 659 - 676 ; 
 CHARSET INTRON1 = 677 - 823 ; 
 CHARSET EXON2 = 824 - 857 ; 
 CHARSET INTRON2 = 858 - 953 ; 
 CHARSET EXON3 = 954 - 1026 ; 
 CHARSET INTRON3 = 1027 - 1566 ; 
 
 charpartition itstef = 1: 1 - 658 , 2: 659 - 1548 ; 
 OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 END;