#NEXUS
[SS DNA, Triticeae, short locus, char=530 Diploids only - polymorphisms - edited MAR 95
hordeum vulgare exluded because probably not homologous; large unique duplications omitted]
begin data;
	dimensions ntax=14 nchar=1137;
	format datatype=dna interleave missing=- equate="1={A-} 2={C-} 3={G-} 4={T-}";
	matrix
Aeg_tau		4TTTTTAATT-TTTTTT--G2CGCCG-CGT3-CAAAA1CAAA--ACGCA2GTGCGCGA-CATAT----GTTTAGCACG444TATT-----------ATTTT-GCACGTTTAC-G
Aust_pect	-TTTTTAA--TTTTTTTT4G-TG-------------------------------------------------------------------------------------------
Bromus[in]	-TTTTTATTTATTTTTT--G-C--CT-CGTGGC---GTGGGAG--CGCGCGTGCGCGAT-GTAT---TTGTATGAAGTTT-CATTT----------ATTTT-CAGGATGTGT-G
Crith_del	--TTTTAAATATTTTTT--G-CGCCG-CGTG-CAAAA-CAGG--ACGCACGTGTGTGG-CATATA---TTTACCGCGTTTTRTT------------WTTT-CCCACGTTTGC-G
Hen_pers	-TTTTYAATTATWTTTT--G-CGYST-CGTGACAAA-YAT---SACGCWCGTGCAAGA-YATAYA---ATARCCACRTTCTCTC------------ATTTT-CCAYGTYTGC-G
Psa_jun		-4TTTTAAAWWWWWWTT---SCGTCT-CGTGGCAAG---TATAW-CGCACGAGCGCGA-TATAT----TTTAACCC-GTTTTT----------CTATTTTT-CCACGTGTGA-G
Pse_lib		-TTTTTAAWTTTTTT4-Y2G-CGCST-SGTGACAAA--CAWAA--CGCACGTGCGCGA-YATAT----ATTAACCCCGTTWT-CTT----------ATTTT-YSACRTYTGY-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
Tae_cm		TTTTTTAACATTTTTT---G-CGTAG-TGYG-CAAAA-CAAA--ACGCACGTGCGCGG-CATAT----ATTTACCATGTTTGATT-----------ATTTT-CCACGTTTGC-G
Thino_bes	-TTTTTAATT--TTTTT--G-YGCCG-CGTG-CAAAA-CAAA--ACGCACGCGCRCGG-CATAT----ATTTACCACGTTTCATTT----------ATTTT-CCACGTTTGC-G
Thino_elon	-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


Aeg_tau		GTAAGTTTT-AGCTCGCTGCTCATTATTCACGC-GTCTA3CGSSGSS--------------AA--GCGTGTT-CTGAAAGGGGTCGAAACCA-TGGTAAATA
Aust_pect	------------------------------------------------------------------------------------------------------
Bromus[in]	ATACATTTT-AACTCATTACTTGGTATTCACGC-ATTTAG-GGCGATGTTTGTGGAGCGGCA-TGCTCGTTT-TTGAAAGGG-TCGAAA-------TAATGG
Crith_del	TTAAGYTTA-AGYTCGTTGCTCATTATTCRCGT-GTCCAGCGGCGGHKKT4GYGGCGCGGCAA--G2G-TTM-V1GAAATGGGTTGAAACCG-TGGTAAATA
Hen_pers	RHGYGTTTT-AGCTCGSYACTWATWATTCMSRY-GTACATCGGCGRCSTT-GYGGMRCGGAAR--GC1YRWT-HCKRARRGGGTCKAAACCG-TGGTAMATA
Psa_jun		ATATGTTTT-AAATCGCAGCTAACTCTTCACGC-GTCCAAGCGACGGCGTCGTGGCGCGGCA--TGCGCGTT-CTGAGAG-GGTCGAAAGGG-TGGCACATT
Pse_lib		RTAYGYTTT-AGCTCGSTGCTCATTAYTCRCGC-GTCTAGSG3CGGCGTT-GTGGCGCGRMAA--GSKTBY--Y431AARGGGTCRAAACCG-TGGTWAATA
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
Tae_cm		GCAAGTTTTTAGCTCGCTGCTCATTATTCACGC-GTCTAGCGSYGGCGT3TGTGGCGCGAGRA--GCGTGCT-CTGAAAGGGATCGAAACCG-TGGTAAATA
Thino_bes	GTAAGTTTT-AGCTCGCTGCTCACTATTCACGC-GTCTAGCGGCGGCGTT-GTGGCGCGGCAG--GCGCGCT-CTGAAAGGGGTCGAAACCG-TGGTAAATA
Thino_elon	GTGCATTTT-AGCTCGCTGCTCATTATTCACGC-GTCTAGCCGCGGCATT-GTGGTGCGGCAA--GAGCGTT-CTAAAAGCGGTCGAAAAAA----TA----
Trit_mon	RTAAG4TTT-AGCTCGTTGCYCATKATTCACGC-GTGTA3CGRCGGG-------------------------------------------------------

                                                    
Aeg_tau		GGCACTGGTGCGG--TT-G--------------------AACC-GTGGTAAAACTCG42TCTGTAG4TTGAGCGGGA3CGG-----CCAAAGGAATGTG-CAA-TCGT
Aust_pect	---CWT-GTGCRGTTTT-G------AGGGAG3GGTG-GMAACC-GTGGT-AAACTCGYCTCCGTAK-TTSASCGGGAGTR-----AMCRAAAGAATGTC-CAA-TYGT
Bromus[in]	CAATTACCGTGTATGTG-GCAGAGGGGGGAAAGGTG--AAAACAACGGTGAA-TTCGTTT-----GAGCGCAAGGGGA-------GCC-----------------CGT
Crith_del	GGCGCTGG4KCGG--TT4G-AGA--GGGAGG34T4G-3AAACC-GTGGT-AAACTCGTCTCBKTGG-TTGAGYGGGGAGCG----SCCAAAGCA1TGYAS-AV-YCGT
Hen_pers	CGYGTTRCRGCGG--TT-K-WGG--GGSAG-TGGTS-SAAACC-RHGGT-AAAGYCGTCTCCKTAG-TYGRRCGGGAGTGG-----GKMAAATAATGTAG-AA-TCRT
Psa_jun		TGCGTTGCTGCGG--TT-G--GGA-GGGAGG-GGTA-GAAACCA-TGGT-AAATTCGTCTCCRTAG-TTGAGCGGGAGGGGT----CYAG-ATAACGTAG-AA-TCGT
Pse_lib		CGTGKYGRTGCGG--CT-K-AGA--GGGAGGG-GTG-3AAACC-GTGGT-AAACTCGTCTCCGYAG-TTGAGYGG3AGYGG-----CCA1AAGRATGYRC-AA-TCRT
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
Tae_cm		GGCGCTGGTGCGG--T4-G-AGAGGG--AGG-SGTG-GAAAMC-GTGGT-AAA2TRGTCTTCGTAG-TTGAGCGGGAGY33-----CCAAAGCAATGTA-CAA-TAGT
Thino_bes	GGCGCTGGTGCGG--TT-G---AGGGGGAGG-GGTG-GAAACC-GTGGT-AAAGTCGTCTCCGTAG-TTGAGCGGGAGYGG-----CCAAAGCAATGTA-CAA-TCGT
Thino_elon	CGGCTTGCTGCGG--TT-G-AGAGAGGGAGG-GGTG-GAAACC-GTGGT-AAACTCGTCTCGGTAG-TTGAGCGGGAGCGG-----CCAAAGCAATGTA-CAA-TCGT
Trit_mon	---------------------------------------------------------------------------------------CAAAGCAAAGTG-CAA-CCGT
											

Aeg_tau		GTGTGTAGTGGAGCT--GGGA-GGGGCAAGCAT--AA-GGG-ASSAA-GACGGGGG-TAACA-TGTCGGATG-CGAT-CATACC-AGC-ACTAAA3GCACCG-GAT-CC-CAT-CAGAA-
Aust_pect	CTTTGTAGTGGGGCT--GGGA-GGGGYAAGCATM--A-GGG-ACGRAKG-CGGGAG-TAAC--TGTMGGATG-CRAT-CATACC-AGC-ACTAAA-GCAYCG-GAT-CC-CAT-CAGAA-
Bromus[in]	CTCCGTAGTGCATCT--GGGA-GTGAGAGGCAT--AA-GGG-GCGAAGG-TTGGGG-AAAC-TTGACGGATG-CG-ATCATACC-AGC-ACTAAA-GCACCG-GATCCC-CAT-CAAAAA 
Crith_del	CTTTGTAGTGRAGCC--GGKA-GRGGCAAGCAT--AA-GGD-RYGAAGR-MGGGGSRAAACA-TGTYGRATG-CGAT-CATACC-AGC-ACTAAA-GCAMCG-GAT-CC-CAT-YAGAA- 
Hen_pers	C21CGTAG43GAT2T43GG-A-GGG3CAAGCAT--RA-GGR-MCKAAGGCDGGG3A-TAASA-TGTYGGATG-CGAT-YATACC-AGC-AYTAAA1GCAY2G-GAT-CC-CA42-ARAA-
Psa_jun		CTCCGTAGTGGAACT--GGGA-GGGGCAWGCAT--AA-GGG-AYRAAGAA-GTAGR--AACA-TGTCGGATG-CAAT-CATASS-AGC-ACTAAA-KCACCG-GAT-CC-CAT-CAGAA-
Pse_lib		CTWTGTASYGGAG2T--GGGA-GGGGCA1GCAT--AA-GGG-AMGAAGRM-GGGG-341ACA-TGTCGGATG-CGAT-CATACC-AGS-ASTAAA-GCACCG-GAT-CC-CAT-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-
Tae_cm		CTTTGTAGTKGAG24--3331-3GGGCAAGCAT--AA-GGG-AMGAA-RASGGGGK-TA1CA-TGTYGGATG-CGAT-CATACC2AGM-ACTAAA-GCAMYG-GAT-CC-CAT-CAGAA-
Thino_bes	CTTTGTAGTGGAGCT--GGGA-GGGGCAAGCAT--AA-GGG-ACGAA-GACGGGGG-TAACA-TGTCGGATG-CRAT-CATACC-AGC-ACTAAA-GCACCG-GAT-CC-CAT-CAGAA-
Thino_elon	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-


Aeg_tau		CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCYTGGGAA-G2TCC-TCGTGTTGCATTCC2
Aust_pect	CTCCGAAGTT-RAGCRTGC--TTKGGCGAGAGTA-GTAC-TAGGATRGGT-GACCTCCTRGGAA-G-TCC-TCGTGTTGCATTCCC
Bromus[in]	CTCCGAAGTTAAACCGTGC--TTGG-CGAGAGTAAGTACCTAGGATGGGT-GACCCCCTGGGAA-G-TCCCTCGTGTTGCA-TCCC
Crith_del	CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCS
Hen_pers	YTCCRAAGTT-AAGCRTGC-WTG2GGYGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGKAA-G-TCC-TYGWKTTGCATTCCC
Psa_jun		CTCCGAAGTT-AAGCGTGC--TTGGGCKAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Pse_lib		CTCCGAAGTT-AAGCRTGS--TTGGGCGAKAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
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
Tae_cm		CTCCGAAGTT-AAGCGTGC--TTGGGCGAKAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCC-
Thino_bes	CYCCGAAGTT-AAGCGTGM--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Thino_elon	CTCCGAAGTT-AAGCGTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
Trit_mon	CTYCGAAGTT-AAGCRTGC--TTGGGCGAGAGTA-GTAC-TAGGATGGGT-GACCTCCTGGGAA-G-TCC-TCGTGTTGCATTCCC
[-CGAGAGTAGTAC-TAGGACAGG insert into gene in psli#1]
[TAAGTAGTATAGGACATTAT, TTATT, GGTTGTAGTGGTAGTAAGAA inserts in thsc5]

[ITS for 5S Short char=607]

Aeg_tau		TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGTGACGG-CACT
Aust_pect	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGCCGGCGATGA-CATC
Bromus[tec]	TCGTGACCCTGACCAAAACAAACCGCGCACGCGTTATCCAATCCGTCGACGATGGGCATC
Crith_del	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGACGACGG-TTTA
Hen_pers	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGTGACGG-CATC
Psa_junc	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGCCGGTGACGG-CACC
Pse_lib		TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGCGACGG-CACC
Pse_spic	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGCGACGG-CACC
Sec_cer		TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGTGACGG-CACC
Sec_mon		TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGTGACGG-CACC
Tae_cm		TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCAAATCCGTCGGCGACGG-CACC
Thino_bes	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGCGACGG-CACC
Thino_elon	TCGTGACCCTGACCAAAACAGACCGCGCACGCGTCATCCAATCCGTCGGCGACGG-CATC
Trit_mon	TCGTGACCCTGACCAAAACAGACCGTGCACGCGTCATCCAATCCGTCGGCGATGG-CATT


Aeg_tau		GTCCGTCGCTCGGCCAAT--GCCTCGACCACCTCCCCTCCTCGGAGCGGGTGGTGGCTCG
Aust_pect	GTTCGTCGCTCGGCCAAG--TCCTCGACCACCTCCCCTCCTCGGAGCGGG----GGCTCG
Bromus[tec]	GTCCATTGCTCGGCCA----TCCTCGGTCACCTACACTTCTCGGAGTGGG---GTGCTCG
Crith_del	CACCGTCGCTCGGCCAA--TGCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Hen_pers	GTCCGTCGCTCGGCCAAT--GCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Psa_junc	GTCCGTCGCTCGGCCAAG--TCCTCGACCGCCTCCCCTCCTCGGAGTGGG----GGCTCG
Pse_lib		GTCCGTCGCTCGGCCAAG--TCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Pse_spic	GTCCGTCGCTCGGCCAAG--TCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Sec_cer		GTCCGTCGCTCGGCC--TATGCCTCGACCACCTCCCCTCCACGGAGTGGGTGGGGGCTCG
Sec_mon		GTCCGTCGCTCGGCC--TATGCCTCGACCACCTCCCCTCCACGGAGTGGGTGGGGGCTCG
Tae_cm		GACCGTCGCTCGGCCAAT--GCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Thino_bes	GTCCGTCGCTTGACCAAT--GCCTCGACCACCTCCCCTCCTCGGAGTGGGTGGGGGCTCG
Thino_elon	GTCTGTCGCTCGACCAAT--GCCCCGACCACCTCCCCTCCTTGGAGTGGGTGGGGGCTCG
Trit_mon	GTCCGTCGCTCGGCCAATATGCCTCGACCACCTCCCCTCCTTGGAGTGGGTGGGGGCTCG


Aeg_tau		GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Aust_pect	GGGTAAAAGAACC-ACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACTCGGGGGCAT
Bromus[tec]	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGTCTAACCCGAGGGCAT
Crith_del	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Hen_pers	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Psa_junc	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Pse_lib		GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Pse_spic	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Sec_cer		AGGCAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACACGGGGCCAT
Sec_mon		AGGCAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACACGGGGCCAT
Tae_cm		AGGCAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGTGGGCAT
Thino_bes	GGGCAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACTCGGGGGCAT
Thino_elon	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT
Trit_mon	GGGTAAAAGAACCCACGGCGCCGAAGGCGTCAAGGAACACTGTGCCTAACCCGGGGGCAT


Aeg_tau		GGCTA-GCTTGCTAGCCGTCCCTTGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Aust_pect	GGCTA-GCTTGCTAGCCGTCCCCCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Bromus[tec]	GGCTA-GCTTGCTGGTCATCTCTTGGGTTGCAATCGTATTTAATCCACACGACTCTCGGC
Crith_del	GCCTA-GCTTGCTAGGCGTCCCTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Hen_pers	GGCTA-GCTTGCTAGCCGTCCCTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Psa_junc	GGCTA-GCTTGCTAGCCGTCCCCCGTGTTGCGAAGCTATTTAATCCACACGACTCTCGGC
Pse_lib		GGCTA-GCTTGCTAGCCGTCCCCCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Pse_spic	GGCTA-GCTTGCTAGCCGTCCCCCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Sec_cer		GGCTA-GCTTGCTAGCTGTGACTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Sec_mon		GGCTA-GCTTGCTAGCTGTGACTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Tae_cm		GGCTA-GCTTGCTAGCCGTCCCATGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Thino_bes	GGCTA-GCTTGCTAGCCGTCCCTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Thino_elon	GGCTA-GCTTGCTAGCCGTCCCTCGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC
Trit_mon	GGCTA-GCTTGCTAGCCATCCCTTGTGTTGCAAAGCTATTTAATCCACACGACTCTCGGC


Aeg_tau		AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Aust_pect	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Bromus[tec]	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Crith_del	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Hen_pers	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Psa_junc	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Pse_lib		AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Pse_spic	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Sec_cer		AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Sec_mon		AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Tae_cm		AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Thino_bes	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Thino_elon	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA
Trit_mon	AACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACCTGGTGTGA


Aeg_tau		ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Aust_pect	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Bromus[tec]	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Crith_del	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Hen_pers	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Psa_junc	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Pse_lib		ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Pse_spic	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Sec_cer		ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Sec_mon		ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Tae_cm		ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Thino_bes	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Thino_elon	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG
Trit_mon	ATTGCAGAATCCCGCGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCACTCGG


Aeg_tau		CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACCACCCTCATCGGGA
Aust_pect	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACCCCC-TCATCGGGA
Bromus[tec]	TCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTTCCAACC-CTCTCATCGGGG
Crith_del	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACCCCACTCATTGGAT
Hen_pers	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACA-CCCTCATCGGGA
Psa_junc	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACCCCCTTCATCGGGA
Pse_lib		CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAATC-CCCTCATCGGGA
Pse_spic	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAATC-CCCTCATCGGGA
Sec_cer		CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCA-CACCCCTCATTGGGA
Sec_mon		CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCA-CACCCCTCATTGGGA
Tae_cm		CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACCCCCCTCATCGGGA
Thino_bes	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAAAC-CCCTCATCGGGA
Thino_elon	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAAAC-CCCTCATCGGGA
Trit_mon	CCGAGGGCACGCCTGCCTGGGCGTCACGCCAAAACACGCTCCCAACC-CCCTCATCGGGA


Aeg_tau		ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Aust_pect	ATTGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Bromus[tec]	ATCGGGATGCGGCATATGGCCCCTCGTCTCGCAAGGGACGGTGAGCCGAAGATTGGGCTG
Crith_del	TTTGGGATGCGGCCTCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Hen_pers	ATTGGGATGCGGCATCTGGTCCCTCGTCTCTCAAGGGACGGTGGACCGAAGATCGGGCTG
Psa_junc	ATAGGGATGCGGCATATGGTCCCTCGTCTCGCAAGAGGCGGTGGGCCGAAGATCGGGCTG
Pse_lib		ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Pse_spic	ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Sec_cer		ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGTTCGGGCTG
Sec_mon		ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGTTCGGGCTG
Tae_cm		ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Thino_bes	ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Thino_elon	ATCGGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG
Trit_mon	ATCAGGATGCGGCATCTGGTCCCTCGTCTCGCAAGGGGCGGTGGACCGAAGATCGGGCTG


Aeg_tau		CCGGTGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Aust_pect	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTAGCTTTA-TCAACGCAGTGC
Bromus[tec]	CCGACGTATCGTGTCGGACACAGCGCATGGTGGGCGTCTTTGCTTTA-TCTGCGCAGTGC
Crith_del	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Hen_pers	CCGGTGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Psa_junc	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTTGCTTTA-TCAACGCAGTGC
Pse_lib		CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Pse_spic	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Sec_cer		CCGGCGTACCGTGTCAAACACAGCGCGTGGTGGGCGTCTTTGCTTTA-TCAACGCAGTGC
Sec_mon		CCGGCGTACCGTGTCAAACACAGCGCGTGGTGGGCGTCTTTGCTTTA-TCAACGCAGTGC
Tae_cm		CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Thino_bes	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Thino_elon	CCGGCGTACCGCGTCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC
Trit_mon	CCGGCGTACCGCGCCGGACACAGCGCATGGTGGGCGTCCTCGCTTTA-TCAACGCAGTGC


Aeg_tau		ATCCGACGCGCAGCCGACATTATGGCCTCAGAACGACCCAGCAAACGAAGCGCACGTCGC
Aust_pect	ATCCGACGCGCAGCCGGCATGATGGCCTCAAAACGACCCAGCGAACGAAGCGCACGTCGC
Bromus[tec]	ATTCGATGCGTAGCCG-CATGATGGCCTAAAAAAGACCCAACTAACCGAGCGCGTGTCGC
Crith_del	ATCCGACGCGCAGCCGACATGATGGCCTCAAAACGACCCAGCAAACGAAGCGCACGTCGC
Hen_pers	ATCCGACGCGTAGCCGACATGATGGCCTCAAAACGACCCAGTAAACGAAGCGCACGTCGC
Psa_junc	ATCCGACGCGTAGCCGGCGTGATGGCCTCAAAACGACCCAGGAAACGAAGCGCACGTCGC
Pse_lib		ATCCGACGCGTAGCCGGCATGATGGCCTCAAAACGACCCAGCAAACGAAGCGCACGTCGC
Pse_spic	ATCCGACGCGTAGCCGGCATGATGGCCTCAAAACGACCCAGCAAACGAAGCGCACGTCGC
Sec_cer		ATACGACGCGTAGCCGGCATGATGGCCTCAAAACGACCCAACAAACGTAGCGCACGTCGC
Sec_mon		ATACGACGCGTAGCCGGCATGATGGCCTCAAAACGACCCAACAAACGTAGCGCACGTCGC
Tae_cm		ATCCGACGCGCAGCCGGCATGATGGCCTCAAAACGACCCAGCAAACGAAGCGCACGTCGC
Thino_bes	ATCCGACGCGCAGCCGGCATGCTGGCCTCAAAATGACCCAGCAAACGAAGCGCACGTCGC
Thino_elon	ATCCGACGCGCAGCCGGCATGATGGCCTCAAAACGACCCAGCAAACGAAGCGCACGTCGC
Trit_mon	ATCCGACGCGCAGCCGGCATGACGGCCTCAAAATGACCCAGCAAACGAAGCGCACGTCGC



Aeg_tau		TTCGACC
Aust_pect	TTCGACC
Bromus[tec]	TTCGATC
Crith_del	TTCGACC
Hen_pers	TTCGACC
Psa_junc	TTCGACC
Pse_lib		TTCGACC
Pse_spic	TTCGACC
Sec_cer		TTCGACC
Sec_mon		TTCGACC
Tae_cm		TTCGACC
Thino_bes	TTCGACC
Thino_elon	TTCGACC
Trit_mon	TTCGACC

;

endblock;

begin assumptions;
charset 5sshort=1-530;
charset ITS=531-1137;
	usertype nucleotide stepmatrix = 4 ACGT
		0 3 1 3
		3 0 3 1
		1 3 0 3
		3 1 3 0
		;
		
	endblock;
	



begin PAUP;                                  
set root=outgroup;
end;