NEXUS
[File created by TreeBASE:  7/26/07  20:56:38]
[Matrix accession#: M452]

BEGIN TAXA;
	TITLE M452;
	DIMENSIONS  NTAX=24;
	TAXLABELS
		Lasallia_papulosa	Ramalina_sinensis	Ramalina_paludosa	Ramalina_fastigiata	Ramalina_intermedia	Ramalina_americana_1c	Ramalina_americana_1b	Ramalina_americana_1a	Ramalina_americana_9	Ramalina_americana_2	Ramalina_americana_3d	Ramalina_americana_6b	Ramalina_americana_3c	Ramalina_americana_3b	Ramalina_americana_3f	Ramalina_americana_5b	Ramalina_americana_3a	Ramalina_americana_7b	Ramalina_americana_7a	Ramalina_americana_6a	Ramalina_americana_4b	Ramalina_americana_3e	Ramalina_americana_5a	Ramalina_americana_4a
	;
END;

BEGIN CHARACTERS;
	TITLE M452;
	DIMENSIONS NCHAR=600;
	FORMAT SYMBOLS = " @ * 0 1 2 3 4 5 6 7 8 9 A T G C " MISSING = ? GAP = -  ;
	MATRIX
		Lasallia_papulosa           ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CGGCATTCCGGGGGGCATGCCTGTCCGAGCGTCATTGCACCCCTCAAGCTCCGCTTGGTGTTGGG?CC??C?CC?G?????T???CC?CCCGGGACGCGCCCGAAAGCGATTGGCGGCGCGGTCCGACTTCGAGCGTAGTAGTGACTCCAAACCCGCTCCGGAAGCCGGCAGGTCCGCCCCGGTCAGACAACCCG?GTTGCACAC???T?TC?GAC???????????????????????????????????????????????????????@37
		Ramalina_sinensis           GATCATTAAAGAGAGGGG?CCTGCGCCCCTGGGGACTCCGGTCCCCGCCTCTATACCCTGTGATTATC?TTACCTTTTGTTGCTTTGGCGGGA?AGCCGGCCCCCGGGTCGGTTGGTCCGCAGGGATCACT??TCGCCAGCAGCCCACCGAAACTCGTTTT?ATGCGTGCCA?GTCTGAGT?C?C?AATTTTATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTG??CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCACTCAAGCGTAGCTTGGTATTGGGTTCTTCGCCCGGGG??TC?TCC??CGC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGAGCGACTTTAAGCGTAGTAAATTTTTCT??CCCGCTTCGAAAGCCTCGCCCCGGG?TCCGGCCAGACAACCCCC?????ACA?TAT?ATCTCACGATTGACCTCGGATCAGGTAGG???????????????????????????????*7*26
		Ramalina_paludosa           GATCATTAAAGAGAGGGGC?TCGCGCTCCTGGGGACTCCGG?CCCCGCCTCTACACCCGATGATTACCGT?ACCACTTGTTGCTTTGGCGGGG???TC?????????????????????????????????CCCCGCCAGCAGCCCACCAACAC?GCATCTTATTCATGCCC?GTCTGAGTA?TC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGG?ATGCCTGTTCGAGCGTCATTGCACCACTCAAGCGTAGCTTGGTATTGGGTTC?TCGCCGGGGGCA???TCC?CCC??GGCGTGCCCGAAACGCATTGGCGGTCCGGTGTGACTTTAAGCGTAGTAAATTTT?CC??CCCGCTTTGAAAGCCTCGTACCGCG?G?CGGCCAGACAACCCCCG???????????TATCTCACGATTGACCTCGGATCAGGTA?????????????????????????????????36915
		Ramalina_fastigiata         ??TCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGATTCCGGTCCCCGCCTCTACACCCTGTGATTAC?GTTACCCTTTGTTGCTTTGGCGGGGG?????????????????????????????????CACTCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATGTTC?GTCCGAGT?C??TAATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCACTCAAGCGTAGCTTGGTATTGGGTCCATCGCCCGGG??ATC?TCC?CCGC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTTAAGCGTAGTAAATTTT?CT??CCCGCTTTGAAAGCCTCACGCCGTG?GCCGGCCAGACAACCCCC?????ACA?TATTA??TCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTT???????????????95804
		Ramalina_intermedia         GATCATTAAAGAGAGGGACTTCGCGCCCCAGGGGACTCCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC?????????????????????????????????CCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATACACTGTCCGAGTA???TAATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??AC?TCCCC?GGGGTGCCCGAAAAGCATTG?CGGTCCGGTGTGACT?TAAGCGTAGTAAATCTT?CT??CCCGCTTTGAAAGCCTCGCACCGTG?GCCGGCCAGACAACCCCC?????A???TATT?TCTCACGATCGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAA?????????????84703
		Ramalina_americana_1c       GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC?????????????????????????????????CCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATGCCC?GTCTGAGT?C?C?AATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTT?GTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??TC?ACC?CCC??GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTTAAGCGTAGTAAATCTT?CT??CCCGCTTTGAAAGCCTCGCACCGTG?GCCGGCCAGACAACCCCCC????ATA???TT?TCTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAA??????????????????63602
		Ramalina_americana_1b       GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACCTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC????????????????????????????????T?CCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATGCCC?GTCCGAGT?C?C?AATT?CATAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??TC?ACC?CCC??GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGCGACTTTAAGCGTAGTAAATCTT?CT??CCCGCTTTGAAAGCCTCGCACCGTG?GCCGGCCAGACAACCCCCC????ATA?T?TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACT????????????????73602
		Ramalina_americana_1a       GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC?????????????????????????????????CCCCGCCGGCAGCCCACCGAAACTCGTTTT?ATCCATGCCC?GTCTGAGT?C?C?AATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAACCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGG?TCCTTCGCCGGGGG??TC?ACC?CCC??GGCGTGCCCGAAAAGCATCGGCGGTCCGGTGT?ACTTTA?GCGTAGTAAATCTT?CT??CCCG?TT?GAAAGCCTCG?ACCGTG?GCCGGCCAGACAACCCCCC????ATA?T?TT??CTCACGATTGACCTCG?ATCAGGT??GGATACCC????????????????????????63602
		Ramalina_americana_9        GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC?????????????????????????????????CCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATGCCC?GTCTGAGT?C?C?AATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCGTTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??TC?ACC?CCC??GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTTAAGCGTAGTAAATCTT?CT??CCCGCTTTGAAA?CCTCGCACCGTG?GCCGGCCAGACAACCCCCC????ATA?T?TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA????????63602
		Ramalina_americana_2        GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTTGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG?AGTC?????????????????????????????????CCCCGCCAGCAG?CCACCGAAACTCGTTTT?A?CCAT?CCC?GTCCGAGT?C?C?AATT?CAT?A?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACG?AGCGA?ATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T?GACC?CCC??GGCGA??CCGAAAAGCATTGGCGG?CCGGTGTGACTTTAAGCGTAGTAAATTTT?CT??CCCGCTTTGAAAGCCTCGCACCGTG?GCCGGCCAGACAACCCCCC????ATA?T?TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGA???????????????????63502
		Ramalina_americana_3d       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCG?CTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGATTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGG?C?T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC???T?TCTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAA??????????????????00400
		Ramalina_americana_6b       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GCC????????????????????????????????CCCCCGCCAGCAGCCCATCGAAACTCGTTTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAA??????????????????50000
		Ramalina_americana_3c       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCTCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG??GTC????????????????????????????????CCCCCGCCAGCAG?CCACCGAAACTCGTTTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAG10000
		Ramalina_americana_3b       GATCATTACAGAGAGGGGCTCCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTACTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAAATTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAA?00000
		Ramalina_americana_3f       GATCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?CTC?????????????????????????????????CCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATTCATGCCT?GTCTGAGT?CAC??ATT?TATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATC??????42000
		Ramalina_americana_5b       ??TCATTAAAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGG???GTC?????????????????????????????????CCCCGCCAGCAGCCCCCCGAAACTCGTTTT?ATTCGTGCCT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GG?GTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACT????????????????30000
		Ramalina_americana_3a       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTT????????????????????????????????CCCCCGCCAGCAGCGCACCGAAACTCGTTTTTATTCATGCTT?GTCCGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGAGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGCATTGGGTCCTTCGCCGGGGG?TT??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAAC?TAAGCATA????????20300
		Ramalina_americana_7b       ???CATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCTCCGCCTCTAAACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATCCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGCCCTTCGCCGGGGG?TT??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGCGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG??CCGGCCAG?CAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAA?????????????00300
		Ramalina_americana_7a       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGCTTT?ATTTATGCTT?GTCTGAGT?CAC??ATT?CATAA?CGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAG?AAATTTT?CT??CCCGCTTTG?AAGCCTCGGGCCGTG?GCCGGCCAGACAACCCCC?????ATA???TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAAC?TAAGCATATCAATAA?00001
		Ramalina_americana_6a       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCTCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATTCATGCCT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG?TT??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTCT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG??CCGGCCAGACAACCCCC?????ATA???TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCC????????????????????????00301
		Ramalina_americana_4b       GATCATTACAGAGAGGG?CTTCGCGCTCCAGGGGACTTCGGTCTCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGG??GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATTCATGCTT?GTCTGAGT?CAC??A?T?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAG?GGAATGCGATAAGTAATGTGAATTACAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTA?TGGGTCCTTCGCCGGGGG??T??ACCCCCCC?GG?GTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?CCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCC????????????????????????10200
		Ramalina_americana_3e       ??TCATTACAGAGAGGGGCTCCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGTTTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTACTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAAATTT?CT??CCCGCTTTGCAAGCCTCGCGCCGTG?GCCGGCCAGACAACCCCC?????ATA???TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAG00001
		Ramalina_americana_5a       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGATTT?ATTCATGCTT?GTCTGAGTT?AC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCATTGCACCATTCAAGCGTAGCTTGGTACTGGGTCCCTCGCCGGGGG??T?G?CCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGCGCCGCG?GCCGGCCAGACAACCCCC?????ATAC??TT??CTCACGATTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATA????????01100
		Ramalina_americana_4a       GATCATTACAGAGAGGGGCTTCGCGCTCCAGGGGACTTCGGTCCCCGCCTCTACACCCTGTGATTACC?TTACCTTTTGTTGCTTTGGCGGGGG?GTC????????????????????????????????CCCCCGCCAGCAGCCCACCGAAACTCGATTT?ATTCATGCTT?GTCTGAGT?CAC??ATT?CATAA?TGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGG?CATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCTCGGTATTCCGGGGGGCATGCCTGTTCGAGCGTCTTTGCACCATTCAAGCGTAGCTTGGTATTGGGTCCTTCGCCGGGGG??T??ACCTCCCC?GGCGTGCCCGAAAAGCATTGGCGGTCCGGTGTGACTTGAAGCGTAGTAAATTTT?CT??CCCGCTTTGCAAGCCTCGC??????????????????????????????????????????????????????????????????????????????????????????????????0000?
	;
END;

BEGIN ASSUMPTIONS;
USERTYPE 3_1 STEPMATRIX = 4 
 A T G C 
 . 3 1 3 
 3 . 3 1 
 1 3 . 3 
 3 1 3 . 
 ; 
 
 USERTYPE 100_1 STEPMATRIX = 4 
 A T G C 
 . 100 1 100 
 100 . 100 1 
 1 100 . 100 
 100 1 100 . 
 ; 
 
 USERTYPE 2_1 STEPMATRIX = 4 
 A T G C 
 . 2 1 2 
 2 . 2 1 
 1 2 . 2 
 2 1 2 . 
 ; 
 
 USERTYPE 1_0 STEPMATRIX = 4 
 A T G C 
 . 1 0 1 
 1 . 1 0 
 0 1 . 1 
 1 0 1 . 
 ; 
 
 USERTYPE 5_1 STEPMATRIX = 4 
 A T G C 
 . 5 5 5 
 5 . 5 1 
 5 5 . 5 
 5 1 5 . 
 ; 
 
 OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; 
 CHARSET recodes = 93 - 134 182 - 192 405 - 419 474 - 479 521 - 540 ; 
 CHARSET inform = 9 21 27 30 38 44 158 165 167 171 - 172 177 369 387 393 401 451 457 470 - 472 486 488 498 502 505 596 - 598 600 ; 
 CHARSET nonITS = 1 - 8 204 - 362 544 - 595 ; 
 TYPESET * saved = unord: 1 - 600 ; 
 WTSET * saved = 1: 1 - 600 ; 
 END;