#NEXUS
[SS DNA, Triticeae, short locus, Diploids only - polymorphisms - edited JAN. 93
hordeum vulgare exluded because probably not homologous; large unique duplications omitted]
begin data;
	dimensions ntax=13 nchar=530;
	format datatype=dna interleave missing=- equate="1={A-} 2={C-} 3={G-} 4={T-}";
	matrix
Aeg_sears	-TTTTTAATT-TTTTTTA---CGCCG-CGTG-CAAAA-CAAA--ACGCACGTGCGCGA-CATAT----GCTTAGCACGTTTTATT-----------AGTTT-GCACGTTTGC-G
Aeg_shar	-TTTTTAATWTTWTTTT44G-CGCTG-CGTG-CAAAA-CAAA--ACGCACGTGCGCGA-CATAT----GTTTAGCACGTTTTAYT-----------ATATT-GCACGTTTGC-G
Aeg_tau		4TTTTTAATT-TTTTTT--G2CGCCG-CGT3-CAAAA1CAAA--ACGCA2GTGCGCGA-CATAT----GTTTAGCACG444TATT-----------ATTTT-GCACGTTTAC-G
Aeg_umb		TTTTTCAATT-TTTTTT--G-CGCCG-CGTG-CAAAA-CAAA--ACGCACGTGCGCGA-CATAT----GTTTAGCACGTTTTATT-----------ATTTTTGCACGTTTGT-G
Aust_vel	-TTTTTAACATTTTTTTT-G-CGCGT-CRTGACAAA--CAGAAT-C-----------------------------CGTTTTCTT------------ATTTT-GCACGTTGGC-G
Pse_spic	TTTTTTAATT-TTTTTT--G-CGCGT-CGTGACAAA--CAAA--ACGCACGYGCGTGA-CATAT----ATTAACCCCGTTT-TCTT----------ATTTT-CCATGTTTGC-G
Sec_cer		-TTTTWAATWATTTTKT--G-YGTCT-CGTGACAAG-TAYA4141CGCACGTGCARGA-TATAT----RTT3RCCVCRTTTA4TTTTCTTCTTCYRRTTTT-YCACGTTTRY1G
Sec_mon		-TTTTWAATWATTTTTT--G-CGTCT-CGTGACAGG-TAT--A4ACGCACGTGCARGA-TATRT----ATTGACCCCGTTTATTTTTCTTCTTCTGMTTTT-CCACGTTTGC-G
Sec_syl		-TTTTTAATTATTTTTT--G-CGTCT-CGTGACAAG---KATA4ACGCACGTGCAAGA-TAT14----ATTGA2CMCRTTTMTTTTTC4TCTTCTGATTT4-CCACGTTTGC-G
Sec_vav		-TTTTTAATTATTTTTT--G-CGTCT-CGTGACAAG141KATA4ACGCACGTGCAAGA-TAT14----ATTGACCMCGTTTM4TTTTCTTCTTCTGATTTT-CCACGTTTGC-G
Thino_el	-TTTTAAATT-TTTTTTT-G-CGCGT-CGTGA-AAAA-GAAA--ACGCACGTGCGTGA-CATATA---TTTCCCCCCATTTTATT-----------ATTTT-CCACGTTTGC-G
Trit_mon	-TTTTTAAWTATTTTT---G-CGTGA2CGTG-CRAAW-MAAA--ACRCACGTGCGCGG-CATATA----TTTACCACGTTTCATT-----------ATTTT-GCAYGTTTGC-G
Trit_mon2	-TTTTTAATTATTTTTT--G-TGACGACGTG-CGAAA-CAAAA--CGCACGTGCGCGG-CATATA----TTTACCACGTTTCATT-----------ATTTT-GGACGTTTGCCG


Aeg_sears	GTAAGTTTT-AGCTCGCTGCTCATTATTCACGC-GTCTA--------------------------GCGTGTT-CTGAAAGGGGTCGAAACCA-TGGTAAATA
Aeg_shar	GTAAGTTTT-AGCTCACTACTCATTATTCACGC-GTCCA--------------------------GCGTGTT-CTGAAA3GGGTCGAAACCA-TGGTAAATA
Aeg_tau		GTAAGTTTT-AGCTCGCTGCTCATTATTCACGC-GTCTA3CGSSGSS--------------AA--GCGTGTT-CTGAAAGGGGTCGAAACCA-TGGTAAATA
Aeg_umb		GTAAGTTTT-AGCTCGCTGCTCATTATTCACGC-GTCTA--------------------------GCGTGTT-CTGAAAGGGGTCGAAAGCA-TGGTAAATA
Aust_vel	----------------------------------------CGGCAAG3TTC-----------------------TGAAAGGGGTGGAGACCG-TGGWAAATA
Pse_spic	GTACGTTTT-CGCTCGCTGCTCATTATTCACGC-GTCTAGCGGCGGCGTT-GTGGCGCGGCAA----SSGTT-CTGAAAGGGGTCGAGACCG-TGGTAAATA
Sec_cer		AT1YGTTTT-AKKYCRGTGCTTATTATTYACSC-GTCCAKCRRCRRCGYT-G4GGCACGKCRA3TCAY-GTT-TYGAAASYGGTCGAAACCR-TRRTAA1GA
Sec_mon		ATACGTTTT-AGGCCGGTGCTTATTATTCACGC-GTCCAGCGGCRRYGTT-G-GGCACGKCAA-TCAC-GTT-TYGAAAGTGGTCGAAACCG-TAGTAAATA
Sec_syl		ATACGTTTT-1GGCCGGTGCTTATTATTCACGC3GTCCW32SGCGACGTT-G4GGCRCGGC1AATCRY-GTT-TYGAAAGTGGTCGAAACCG-TRGTAAAGA
Sec_vav		ATACGTTTT-AKGCCRKTGCTTATTATTCACGC-GTCCAKCRGCGACGTT-GTGGCRCGGC-RATCAC-GTT-TYGAAAGTGGTCGAAACCG-TRGTAAAGA
Thino_el	GTGCATTTT-AGCTCGCTGCTCATTATTCACGC-GTCTAGCCGCGGCATT-GTGGTGCGGCAA--GAGCGTT-CTAAAAGCGGTCGAAAAAA----TA----
Trit_mon	RTAAG4TTT-AGCTCGTTGCYCATKATTCACGC-GTGTA3CGRCGGG-------------------------------------------------------
Trit_mon2	-TAAGTTTT-AGCTCGTTGCTCATGATTCACGC-GTGTAGCGGCGGG-------------------------------------------------------

                                                    
Aeg_sears	GGCACTGGCGCGG--TT-G--------------------AACC-GTGGT-AAACTCGTCTCCGTAG-TTGAGCGGGAGCGG-----CCAAAGGAATGTG-CAA-TCGC
Aeg_shar	GGCACTGGTGTGG--TT-G--------------------AACC-GTGGT-AAAYKCGTCTCCGTAG-TTGAGCGGGAGGGG-----CCAAAGSAATGTG-CAA-TCGT
Aeg_tau		GGCACTGGTGCGG--TT-G--------------------AACC-GTGGTAAAACTCG42TCTGTAG4TTGAGCGGGA3CGG-----CCAAAGGAATGTG-CAA-TCGT
Aeg_umb		GGCACTGGTGCGG--TT-G--------------------AACC-GTGGT-AAACTCGTCTCCGTAG-TTGAGCGGGAGCGG-----CCCAAGGAATGTGG-AA-TCGT
Aust_vel	CGTGCTGGTGCGG--TT-G-AGA-GRGAGG--GGTG-GYAACC-GTSGT-AAACTCGTCTCCGTAG-TTGTGCGGGAGAGG-----CCAAAAGAATGTA-CACCTCGT
Pse_spic	CGTGGTGGTGCGG--TT-G-AGA--GGGAGG-GGTG-GAAACC-GTGGT-AAACTCGTCTCCGCAG-TTGAGCGGGAGTGG-----CCAAAAGAATGTG-CAA-TCGY
Sec_cer		Y3CGTTGCTGCRG--YG-R-AGA--GGRAGGT-GTGA3TAAAC1GTGGT-AAAGTCGYGTCCGTRGT-AGAG33R3AGRA3T--GGCCG1AAWAAKGTAG-AA-TCGT
Sec_mon		CGCGTTGCTGCGG--CG-G-AGA--GGGAGGT3GTRM-TAAAC-GTGGT-AAAGTCGCGTCCGWKG4-AGAGGGAGAG-AGT--GGCC3AAAWMAKGTAG-AA-TCGT
Sec_syl		CGCGTTGCTGCGG--CR-G-AGA-3GGGAGGT-GTGA-TAAAC-GYGGT-AAAGTCGYSTMCGTRGT-AGA33GAGWG-AGT--GGCCGAAATAATGTAG-AA-TCGT
Sec_vav		CGCGTTGCTGCGG--CG-G-AGA--GGGAGGT-GTGA-TAAAC-GYGGT-AAAGTCGYGTCCGT13GTAGA33GAGWG-ART--GGCC3AAATAATGTAG-AA-TCGT
Thino_el	CGGCTTGCTGCGG--TT-G-AGAGAGGGAGG-GGTG-GAAACC-GTGGT-AAACTCGTCTCGGTAG-TTGAGCGGGAGCGG-----CCAAAGCAATGTA-CAA-TCGT
Trit_mon	---------------------------------------------------------------------------------------CAAAGCAAAGTG-CAA-CCGT
Trit_mon2	---------------------------------------------------------------------------------------CAAAGCAAAGTG-CAA-CCGT
											

Aeg_sears	GTGTGTAGTGGAGCT--GGGA-GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGA-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Aeg_shar	GTGTGTAGTGGAGCW--GGGA-GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ASTAAA-GCACMG-GAT-CC-CAT-CAGAA-
Aeg_tau		GTGTGTAGTGGAGCT--GGGA-GGGGCAAGCAT--AA-GGG-ASSAA-GACGGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA3GCACCG-GAT-CC-CAT-CAGAA-
Aeg_umb		GTGTGTAGTGGATCT--GGGA-GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Aust_vel	CTTTGTAGCGGCGCT--GGGA-GGGGMWAGCAT--AA-GGY-ACGAAGG-CGGGAG-TAACA-TGTCGGATG-YGAT-CATACC-AGC-ACTAAA-GCMM2G-GAT-CC-CWT-CAGAA-
Pse_spic	CTTTGTAGTGGAGCT--RGGA-GSGGCAAGCAT--AA-GGG-ACGAAGG-CAGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Sec_cer		CCTCGTAGCKGGYCT--RGGA-GGGGMAAGCAT--AA-GGA-GSGAAGR-YGGGGA3TAACA3TGTYRGATG-CGAT-CATACC-AGC1ACTAAA-GCACSG-GAT-CC-CAT-CAGAA-
Sec_mon		CCTC3TAGCGGGCCT--GGGA-GGGGCAAGCAT21MA-GGA-GSGAA3GACGGGGA-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Sec_syl		CCTCGTAGCGGGYCY--GGGA-GRGGCAAGCAT--AA-GGA-KSGAA-GACGGGGA-TAACA-TGTCGGATG-YGAT-CATACC-AGC-ACTAAA-GCAYCG-GAT-CC-CAT-2AGAM-
Sec_vav		CCTCGTAGCGGGYCY--GGGA-GRGGCAAGCATMM---GGA-KSGAA-GACGGGGA-TAACR-TGTCGGAT3-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Thino_el	CTTTGTAGTGGAGCT--GGC--GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-GAGAA-
Trit_mon	GTGTGTRGTGGA3CT--GRGA-GGGGCAAGCATM--A-GGG-ACGAA-GACGRGGG-TRACA-TGTCGGATG-CGAT-CATACY-AGC-ACTAAA-GCAYCG-GAT-CC-CAT-CAGAA-
Trit_mon2	GTGTGTAGTGGAGCT--GGGA-GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGG-TAACA-TGTTGGATG-CGAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-


Aeg_sears	CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Aeg_shar	CTCCGAAG4T-AAGCGTGC--TT3GGCGAGAGTA-GTAC-TA3GAT3GGT-GACCTCCTGRGAA1G-TCC-TCGTGTTGCATTCCC
Aeg_tau		CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCYTGGGAA-G2TCC-TCGTGTTGCATTCC2
Aeg_umb		CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCC-
Aust_vel	CTCCGAAGTT-AAGCGTGC--TTGGGYGAGAGTA-GTAC-TAGGATRGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCARTCCC
Pse_spic	CTSCGAAGTT-AAGCGTGC--TTGSGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Sec_cer		YTCCGAAGTT-AAGCRTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTSGGAA-G-TCC4TCRTGTTGCATTCMC
Sec_mon		CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCAYTCCC
Sec_syl		CTYCGAAGTT-AAGCGTKC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TYGTGTTGCAWTCCC
Sec_vav		CTCCGAAGTT-AAGCGTKC--TTGGGCGAGAGTA-GTAC-TAGGATGSGT-GACCTCCKGGRAR-S-TCC-TCGTGTTGYATTCCC
Thino_el	CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Trit_mon	CTYCGAAGTT-AAGCRTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Trit_mon2	CTCTGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
[-CGAGAGTAGTAC-TAGGACAGG insert into gene in psli#1]
[TAAGTAGTATAGGACATTAT, TTATT, GGTTGTAGTGGTAGTAAGAA inserts in thsc5]
;
end;
begin PAUP;                                  
set root=outgroup;
end;