#NEXUS [written Mon Feb 18 12:55:15 CST 2013 by Mesquite version 2.6 (build 486) at lenovo-PC/210.35.136.56] BEGIN TAXA; TITLE cpDNA_dataset_for_monophyly_assessment; DIMENSIONS NTAX=32; TAXLABELS Salweenia_wardii Thermopsis_alpina Piptanthus_nepalensis_ Sophora_flavescens Sophora_moorcroftiana_ Sophora_prazeri_ Sophora_tonkinensis_ Sophora_tomentosa Sophora_davidii_C2 Sophora_davidii_C5 Sophora_davidii_C6 Sophora_davidii_C4 Sophora_davidii_C1 Sophora_davidii_C3 Sophora_davidii_C20 Sophora_davidii_C17 Sophora_davidii_C9 Sophora_davidii_C16 Sophora_davidii_C11 Sophora_davidii_C15 Sophora_davidii_C14 Sophora_davidii_C22 Sophora_davidii_C19 Sophora_davidii_C21 Sophora_davidii_C8 Sophora_davidii_C13 Sophora_davidii_C12 Sophora_davidii_C18 Sophora_davidii_C10 Sophora_davidii_C7 Phaseolus_coccineus_ Trifolium_repens_ ; END; BEGIN CHARACTERS; TITLE 'Character Matrix (cpDNA dataset for monophyly assessment)'; DIMENSIONS NCHAR=1199; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX Salweenia_wardii TCGAAATCATAATAACGGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTTAAAAA------TGTAATATTTTTTAGT-----CA-------ACATTAA---AAT-----GATA-----AAT-----AAGAATT--CTA---------TTATAATTTA------------------------TATAAT------------------AGAATTCTTAT----------TTATTTT--------------------------TA--TTTA-------------------------TGAGAATAAA-------A-AATTTA-----------------------------------ATAATAAATA------------------ATTATAGACAATT-------CTA-TATGAA-----------ATATTCTATTGTATATT---------AGAAAATA-TTCTTTGAA----TCCAGTTAATTCAGATT-ATTCCAACTTT-CTCTATTTG----TTACACAAAAAAACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAAAGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAAGTTTTCCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTAC---ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TGACCTAGACTTCAA--TTTCAACCC---TTT---CGTTATCATTCTTTTTCTTCTAA-------------------------------------GATAAGATAAAATA-----AACAAAAAATGA----AATGGA----------AACAT---TCATTTTTTG------TTTATC----CTTTTTGGAATAC-ATATGACTTCGCAAGCAGCAATGTCA------------AAAATAAA---------------GACT--------TCTAAATAAA------------GAAGTAT----------A----CGAGTTTTTAAAG-------------------------GTAAAG----GAGCAATA---GAAACT----CTA-------CC---TTT--------AA--AAA-----------CTCGTATACTTTAACTTTAAGACCCAAACCA--AATATT--------ATCCATTT----ATAA Thermopsis_alpina TTGAAATCATAATAACCTATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTTAAAAA-----TTGTAATATTTTTTAGT-----CA-------ACGTTAA--------------------AAT-----AAGAATT--CTA---------TTATAATTTA------------------------TATAAT------------------AGAATTCTTAT----------TTATTTTT-----------------------ATTATATTTAAT-----------------------TTATTAGAAAT---------ATTTAT------T---------------------------AGAATAAATA------------------ATTATAGACAATT-------CTA-TATTAAATAAA------ATATTCTATTGTATATT---------AGAAAATA-TTCTTTGAA----TTCAGCTATTTCAGATT-ATTCCAACTTT-CTCTATTTG----TTACACAAAAAAACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAAAGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAAGTTTTCCGA---------------------------------CTTGGCTAC---ATCCGCCCCTAC----TACTAT---------GTAAAAA----TTACCTAGACTTCAA--TTTCAACCC---TTT---CGTTATCATTCTTTTTTCTT-----------------------------------------ATAAGATAAAATA-----AACCA-----GA----AATGGA----------AACAT---TCATTTTTTT-------CT-------CTTTTTGGAATAC-ATATGACTTCGCAAGC---AATATAA------------AAAATAAAGA-------------CTTCT-AAA---TATAAATAAA------------GAAGTAA------------------------AA---------------------------GTAAAG----GAGCAATA---GAAAAAACT-CTG--TTGCTCC---TTTACTTTT--TA--AAA-----------CTCGTATACTTTAA-----------GACCTA--AATATT--------ATCCATTT----AGAG Piptanthus_nepalensis_ TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTAAAAAA-----TTGTAATATTTTTTAGT-----CA-------ACGTTAA----AA--TAAGAATTCTATTAT-----ATAAATT--ATAATATA----TTATAATTTATATAATAGAATTCTTATTTA---TTATATTTAATATTTATTATATTTAATATTTATTATATTTAATAT-TTATTATATTTAATAT-------------TTATTATATTTAATA------------TTTATTATATTTAATATTTATTA-TATTTAATTTATTAGAAATATTT--AT------------------TAGAATAAATA------------------ATTATAGACAATTA-------TA-TATTAA-----------ATATTCTATTGTATATT---------AGAAAATA-TTCTTTGAA----TTCAGCTATTTCAGATT-ATTCCAACTTT-TTCTATTTG----TTACACAAAAAAACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAAAGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAAGTTTTCCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTAC---ATCCGCCCCTAC----TACTAT---------GTAAAAA----TTACCTAGACTTCAA--TTTCAACCC---TTT---CGTTATCATTCTTTTTTCTT-----------------------------------------ATAAGATAAAATA-----AACCA-----GA----AATGGA----------AACAT---TTA--------------------------------------------------------AATATAA-----------------------------------------------TATAAATAAA------------GAAGTAA------------------------AA---------------------------GTAAAG----GAGCAATA---GAAAAAACT-CTG--TTGCTCC---TTTACTTTT--AA--AAA-----------CTCGTATACTTTAA-----------GACCTA--AATATT--------ATCCATTT----AGAG Sophora_flavescens TCGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTAAAAAAA---AATGTAATATTTTTTAGTTA-GTCA-------ACATTAA----GA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAATTT------------------A--------TAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAATTTTATTTATTAG-----------TTTA------TTAGAATAAATTA-TAAA-AATTTAA-----ATAATT--AT------------------TAATATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGAATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAAAGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAAGTTTTCCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTAC---ATCCGCCCCTAT-----ACTATACT----ATGTAAAAA----TTACTTAGACTTCAA--TTTCAACCC---TTTTTTCGTTATCATTCTTTTTTATCT---------------------------------------TCTAAGATAAAATA-----AACAAAAAATGA----AATGGA----------AACATTCTTTTTTTTG-----T-TTATCC-----TTTTTTGGAATAC-ATATGACTTCGCAAGC---AATGTAA------------CAAAAAAAA--------------GACTT-CT-----AAAAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TCGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_moorcroftiana_ TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAA----AATGGAATATTTTTTAGTCAACATA-------AAAATAATAATAA-ATAAGAATT---CTAT----TATAAATT--ATATTA----TAATAGAATTCTTA--------------TTTA---TTTTATT------------------AAAATTCTTATTTAT------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAA-AAATTTA-----TATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATCTTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCCTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGGTAC---CTCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTTT-----------------------------------------------------------A-----AATAA-----------AATGGA----------AACAT---TTTTTTT---------TATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAA--------------A---A-AGAC-TTCTAAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATCCTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_prazeri_ TCGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATAAAAAAAA---AATGTAATATTTTTTAGTTAACTTTTAGTCA-ACATTAA----GA--TAATAATAA---AATT----AAGA-TA--ATAAA-------T---------------------------------------A-----------------AGAATTCTTAT----------TTATT-----------ATC------TTAATTTTTATTTA--TTAG-----------TTTATT---------ATAAAAAT-TAAAATA--TAA-AAA-TAAA-----------------------TAATTATAGATAATTA--------------ATTCTAT---ATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTCGAAAATA-TTCTTTGAA----TCCAGTTAATTCGAATT-ATTCCAACTTT-CTATATTTC----TTACACAAAAAGACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCTCTCTTTTTCCAAAAAGTTTTCCGAATTCTTTTTTTTGATATAAA-AGTACGTTTTTTCT-GGCTC-----TCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTAGACTTCAA--TTTCAACCC---CTTTTTCGTTATCATTCTTTTTTAT---------------------------------------------------------CT----------TCTAAGATA-GGA------------------------------------------------------------------T--AA------AATAAA------------CAAAAAAAA-----------------CTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTTTTTAAAA----------CTTGTATACTTTAA-----------AACCCC--GATATTATCTATTTATCCATTT----ATAG Sophora_tonkinensis_ TCGAAATCATAATAATCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTAAAAAA----AATGTAATATTTTTTAGT-----CA-------ACATTAA----GA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAATTTG--------------------------TAAT------------------AGAATTCTTAT----------TTATT------------------------AAATTTTATTTATTAG-----------TTTATT------AGAATAAATT-ATAAAAA-TTTAAATAA-TTATT-----AATATAAATAAAAAATTTAATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGAATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCCCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAAGTTTTCCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCT-----CTCCGCCC-TAT-----ACTAT---------GTAAAAA----TTACCTAGACTTCAA--TTTCAACCC---TTTTTTCGTTATCATTCTTTTTTAT-------------------CTTCTAAGATAGGATA-AA---ATAAACAAA----A-----AATGA-----------AATGGA----------AACATTCTTTTTTTT---------TATC-------TTTTTGGAATAC-ATATGACTTCGAAAGC---AATGTAACAAAAAA----AAAAAAAAAAA-----------AAGAATTTCT-------AAAAAAA------------GAAATAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TCGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_tomentosa TCGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAATTAAAAAAA--AAATGTAATATTTTTTAGT-TAGTCA-------ACATAA---------TAA-AATA----AAT-----AAGAAATTTCTA---------TTATAATTT------------------ATA-------AATA-----------------AGAATTCTTAT----------TTATTTTTTTTTTTTTTTTTTATTTA--------TTATTTATAAAAATTGAAATA-ATTATTAATATAAAAATAAATT---AAAAAATTTA------ATATT-----------------------AATAATAATAGACAATTA-----------ATTCTAT---ATTAAATATTCTACTGTATA-----------TTAGCTATTTGTATATTAGATA--TTAGAAAAGA-TTCTTTGAA----TCTAGTTAATTCGAATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCCTG--TAGAAATAGATTGTGCTAATGAAAAAGATTTCAATGCTGTCCAATATCCCCCCTTTTCC-AAAAAGTT--CCGA-CTCTTTTA------------------------CTTGGCTAC---ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATTTAGACTTCAA--TTTCAGCCC----TTTTTCGTTATCATTCGTTTTTAT------------------CT------TCTAAGATA-GG--------------ATAA----AATAAACAAAAAATGAAATGGA----------AACATTCTTTTTTTT---------TATCTT-----TTTTTGGAATAC-ATATGACTTCGCAAGC---AATGTAA-----------CAAAAAAAAAA-------------GAATT-CT-------AAAATAA-----------AGAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TCGCTCC---TTTACTTTTTTA---AAAA----------ATCGTATACTTTAA-----------AAACCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C2 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT------------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATTTTATT--------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C5 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT------------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATTTTATT--------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATATAAATA------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------GA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C6 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT------------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------GA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C4 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT-ATAT---------TATTATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATTTTATT--------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C1 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT------------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATTTTATT--------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTCGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C3 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATT------------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATTTTATT--------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTC-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTCA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTATCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AAAAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C20 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTG-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C17 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C9 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C16 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C11 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C15 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAATTATAAATTATAGTATAATAGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAATAAATAA----AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C14 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAATTATAAATTATAGTATAATAGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAATAAATAA----AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C22 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACT----------G-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGAAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C19 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---AATGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAATTCTATATTAAATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C21 TTGAAATCATAATAACCGATT-TTGAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTG----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C8 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C13 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATATAT----------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C12 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTTT---------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C18 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---AATGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAATTCTATATTAAATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCTTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTTT----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAG-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C10 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT-----------------GAAGTATAAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Sophora_davidii_C7 TTGAAATCATAATAACCGATT-TTTAGTCAATCGTCGAGATTGAAAGAATCAAT--AAAAAA---A-TGGAATATTTTTTAGT-----CA-------ACATAAA----AA--TAATAATA----AAT-----AAGAATT--CTA---------TTATAAATTT-----------------ATA---TTATAAT------------------AGAATTCTTAT----------TTATTTTATT-------------------AAACTTTATTTATTAG-----------TTTAAGTTTATTAGAATAAATTA-TAAA-AATTTAT-----ATAT------------------------AATAATAAATA------------------ATTATAGACAATTAA---TTCTA-TATTAA-----------ATATTCTATTGTATATTAGATA--TTAGAAAATA-TTCTTTGAA----TCCAGTTAATTCGGATT-ATTCCAACTTT-CTCTATTTC----TTACACAAAAAAACTTTTT--GAATTCCTCG--TAGAAATAGATTGCGCTAATGAAAAAGATTTCAATGCTGTCCAATACCCCCCCTTTTTCCAAAAATTTTTTCGAATTCTTTTTTTTGATATAGA-AGTACGTTTTTTCTTGGCTA----ATCCGCCCCTAT-----ACTAT---------GTAAAAA----TTACCTCGACTTCAA--TTTCAACCC---GTTTTTCGTTATCATTCTT-----------------------------------------------------------TA-----AATAA-----------AATGGA----------AACAT---TTTTTT-----------ATC-------TTTTTGGAATCC-ATATGACTTCGCAAGC---AATGTAA------------AAAAAAAAAA-------------GACTT-CT-------AAAAAAA------------GAAGTAT------------------------AAA--------------------------GTAAAG----GAGCAATA---GAA-------CTA--TTGCTCC---TTTACTTTTTTAA--AAA-----------CTCGTATACTTTAA-----------AACCCC--GATATT--------ATCCATTT----ATAG Phaseolus_coccineus_ TCGAAATCATAATAACCAATTCTTTAGTCAATCGTCGAGATTGAAAGAATCCATT--AAAG------TGCAATATTTATTTAGTACATT--------TCTTTGAC------TAAACATTTAG--TATAAATTCATAATT--ATAAGTAAAT--TTGAAATTTGGATTTATTCTAATATCAAAA----TATATT------------------AATATATATATAGAAAATAGAGAAATATATGATAGAT-------------AGAATATAGA-ATGTT-----------TTGA---TTTCTAGTGGAATGGA---ATGGGTTT---------------TT------------------CGTAGTTTACATGCAA-------------ATTAAAAAATAGCCC---TGTTGAAACTATAACTATGT-AGTT---CTGACTTCAATCCAGTA--ATGAAAAAGAACATTTTTAT----TGTAGTTGCTTATGACTCATTTTTTAGTTATTTCATTTTATGACTCTAAAGAAATACATTTC---TATTTTTGGAATGAAAGCAAATTATA--GTTAATTAATATAT--ATATC-TAAAATTTAACACTACATTCAAAAAAATG----AAAAAATGAGATTAGATATATA----ATCTAGT--CTTGGCTA---CATTCGCCCT------ATACT---------ATGTCTAAA----TGACATA-ACTT-----TTTAGACCT---TTT---CATTATCATTTTTTTTTTC-----------TTCATTTTACATTATGAAGTCATATGTA--TTACAAAAAGATCA----AAAAGATT---------GATGAG---------AAAAATGCATAAATGAAAG-------ATTAC----TAAATAAAAAAAAAGA--AAACTCAAAATTTACAAATTAATTTAGTTGACATGAAAGAAGGGTGCTCGATG-CTAAAGAA-TATGGAAGTTAATAAAAAATTGAT----TAATTTCTGTATA-------TGTATACAGAAAAAGACTA-----------CTAACAAAAAGTAAAGGGGAGAGTAATATC-AACGATA--TTATTCCCTTACCCCCTTTACTTT---CA--AAAA----------CTCGTATCCTTCTTT----------AAAACCAAAATATT--------ATCCATTT----ATAG Trifolium_repens_ TCGAAAGCATAATAACCAAAT-TGGAGTCAATTGTCGAGATTCAAAGAATCAATTCA--------AATACAATATTTGTTTACTAA-----------ACATTCA-------ATAA-AATAA---TTTT---AAAGAATT--CTA---------TTAGAATCTAT-------------TATA--------TAATG-----------------ATAATGTAAATTT--------CGAATCTCTT-------------------ATA-TATAT------------------------------AATGTAAATA--TCCTAAATTCA---------------T------------------AA--ATGAATATTCT--------------ATTAGATATCAA------TTTTA-TATGAA----------------TCTTTTTGTAT--------TTCAAAAAGA-TTCGTTGAA----TCAAGTTAATTGAAATT-ATTCTAACGTT--TGTATTTG----TTACAGAAAAAG-CTTTTA--GAATTCCCCG--TAAAAATAGATTGCGCTAATGAAAAAGCTTTTAATGCTGTAAAATATCCCTTCTTTTTCCATAAAGTGTTCCGAATAATTTTTTTTGAAATAGA-AGTACGTTTT--CTTGGCTAC---ATCCGCCCTTCT--TATACT---------ATCTAAAAAGGATCTATCTATATCTCAA--ATTCTACCC---TTT---CAATATCCTTTTTTTCTTTC------------------------------------GA----AAAAAGGAA--------AAAAA-----------GATAAG---------------------------------------------------GAATCATGAAAGAAATCAAAAAC------GT-A-----------TGTATAA------------------A----------TCTCAAAAAA------------AGATTACTAATC------------------CAAT--------------------------ATAAAG----GAGCAATATT-AACAAAGTTGATA--TTGCTCC---TTTATTTTCAAAC-AAAAA----------CTCGTCTACTTTTTTAAATT-----AAGATCAAAATTTT--------ATCCATTA----ACAG ; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1199; END; BEGIN TREES; Title 'Trees from "cpDNA dataset for monophyly assessment.tre"'; LINK Taxa = cpDNA_dataset_for_monophyly_assessment; TRANSLATE 1 Salweenia_wardii, 2 Thermopsis_alpina, 3 Piptanthus_nepalensis_, 4 Sophora_flavescens, 5 Sophora_moorcroftiana_, 6 Sophora_prazeri_, 7 Sophora_tonkinensis_, 8 Sophora_tomentosa, 9 Sophora_davidii_C2, 10 Sophora_davidii_C5, 11 Sophora_davidii_C6, 12 Sophora_davidii_C4, 13 Sophora_davidii_C1, 14 Sophora_davidii_C3, 15 Sophora_davidii_C20, 16 Sophora_davidii_C17, 17 Sophora_davidii_C9, 18 Sophora_davidii_C16, 19 Sophora_davidii_C11, 20 Sophora_davidii_C15, 21 Sophora_davidii_C14, 22 Sophora_davidii_C22, 23 Sophora_davidii_C19, 24 Sophora_davidii_C21, 25 Sophora_davidii_C8, 26 Sophora_davidii_C13, 27 Sophora_davidii_C12, 28 Sophora_davidii_C18, 29 Sophora_davidii_C10, 30 Sophora_davidii_C7, 31 Phaseolus_coccineus_, 32 Trifolium_repens_; TREE Strict = ((31,((((4,8),(6,7)),(5,((9,(10,11),12,13,14),((15,16,17,19,22,23,24),21,25,(26,27),29,30),18,20,28))),(1,(2,3)))),32); END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 1199; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1199; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 6604542561249866913; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 5938984532242150051; checksumv 0 2 3584985987 null; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1600 782; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #6604542561249866913 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #6604542561249866913; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.lists.TaxonList.TaxonListWindow.ibeam; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #6604542561249866913 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 935.1361160691342.6656104816253468530; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientRight; toggleCorners off; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setFontSize 12; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setFont DialogInput; setFontSize 10; setOffsetX 4; setOffsetY 4; setNote 100; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 97; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 91; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 100; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 85; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 87; setOffsetX 4; setOffsetY 4; endTell; endTell; newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker; tell It; getNote; tell It; setBounds 4 4 100 20; setOffsetX 4; setOffsetY 4; setNote 72; setOffsetX 4; setOffsetY 4; endTell; endTell; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #5938984532242150051 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -67; setLocation -8 -8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; getWindow; tell It; forceAutosize; endTell; hideWindow; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;