#NEXUS [written Tue Mar 03 14:05:24 EST 2015 by Mesquite version 3.02 (build 681) at ww-235-iMac.local/130.203.235.238] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Theobroma_cacao_BBM Vitis_vinifera_BBM_Like Medicago_truncatula_BBM_Putative Glycine_max_BBM1 Zea_mays_BBM1_Putative Oryza_sativa_BBM1_Putative Arabidopsis_thaliana_BBM Brassica_napus_BBM1 Brassica_napus_BBM2 Arabidopsis_thaliana_ANT Theobroma_cacao_AIL5_Putative Glycine_max_AIL5 Arabidopsis_thaliana_AIL5 Arabidopsis_thaliana_PLT2 Glycine_max_PLT2 Theobroma_cacao_PLT2_Putative ; END; BEGIN CHARACTERS; TITLE Alignment; DIMENSIONS NCHAR=938; FORMAT DATATYPE = Protein INTERLEAVE GAP = - MISSING = ?; MATRIX Theobroma_cacao_BBM -----------------------MASMNNWLAFSLSPQELPSQTVDQDH-----HSQTAVSRLGFNSD-DISGADVSG-- Vitis_vinifera_BBM_Like -LIKE-----------------------MASMNSWSSNMMKPRELPPQ---PEN-----HSQNSVSRLGFNSD-EISNTD Medicago_truncatula_BBM_Putative ---------------------------MNLLGFSLSPQEQHPS---TQD-------QTVASRFGFNPN-EISGSDVQG-D Glycine_max_BBM1 -----------------------MGSMN-LLGFSLSPHEEHPS---SQD-----HSQTTPSRFSFNPDGSISSTDVAG-G Zea_mays_BBM1_Putative -----------------------MASANNWLGFSLSGQDNPQP-----------NQDSS----------PAAGIDISGAS Oryza_sativa_BBM1_Putative -----------------------MASITNWLGFSSSSF-------------------------------SGAGAD----- Arabidopsis_thaliana_BBM -----------------------MNSMNNWLGFSLSPHDQNHH---RTD-----VDSST----------TRTAVDVAG-G Brassica_napus_BBM1 -------------------------MNNNWLGFSLSPYEQNHH---RKD-----VYSST----------TTTVVDVAG-E Brassica_napus_BBM2 -------------------------MNNNWLGFSLSPYEQNHH---RKD-----VCSST----------TTTAVDVAG-E Arabidopsis_thaliana_ANT ------------MKSFCDNDDNNHSNTTNLLGFSLSSNMMKMGGRGGREAIYSSSTSSAATSSSSVPPQLVVGDNTSNFG Theobroma_cacao_AIL5_Putative -------------MDMSMG-NMDSSSTQNWLAFSLSNQQQQH------------LNLPTSSSSSHHSSHLCLFEAFTT-- Glycine_max_AIL5 -------------MDSSSS-SPPNSTNNNSLAFSLSNHFPNPS-----------SSPLSLFHSFTYPSLSLTGSNTVD-- Arabidopsis_thaliana_AIL5 MKNNNNKSSSSSSYDSSLSPSSSSSSHQNWLSFSLSNNNNNFNSSSNPN-----LTSSTSDHHHPHPSHLSLFQAFST-- Arabidopsis_thaliana_PLT2 ------------------------MNSNNWLAFPLSPTHSSLP----PH-----IHSSQNSHFNL----GLVNDNIDN-- Glycine_max_PLT2 -------------------------MNNNWLSFPLSPTHSSLP---AHD-----LQATQYHQFSL----GLVNENMEN-- Theobroma_cacao_PLT2_Putative ---------------------MGSMNSNNWLSFPLSPTNSSLP----TH-----LHPSQSHQFNL----GLVNDNMEN-- Theobroma_cacao_BBM ECFDL--TSDSSAPS-LNLP------PPFGI-LEAFNRNNQSQGSVCFAPSKHTRTFSSFSHVKDWNMKGLGMNSDGNYK Vitis_vinifera_BBM_Like V-G---LIKEENFDL--TMDSTAPS-LNLP------PPFGI-L--F--NNQ---------------------PQDWNMKG Medicago_truncatula_BBM_Putative HCYDL--SSHTTPHHSLNLS------HPFSI-YEAFHTNNN------------------IHTTQDWKENY---------- Glycine_max_BBM1 -CFDL--TSDSTPHL-LNLP-------SYGI-YEAFHRNNS------------------INTTQDWKENY---------- Zea_mays_BBM1_Putative DFYGL--PTQQGSDGHLGVPGLRDDHASYGI-MEAYNRVPQ--------------------ETQDWNMRGLDYNGGG--- Oryza_sativa_BBM1_Putative -------PVLPHPPLQGKTS----------------------------------------HLMHQWGSAY---------- Arabidopsis_thaliana_BBM YCFDLAAPSDESSAVQTSFL------SPFGVTLEAFTRDNN-------------------SHSRDWDING---------- Brassica_napus_BBM1 YCYDPTAASDESSAIQTSFP------SPFGVVVDAFTRDNN-------------------SHSRDWDING---------- Brassica_napus_BBM2 YCYDPTAASDESSAIQTSFP------SPFGVVLDAFTRDNN-------------------SHSRDWDING---------- Arabidopsis_thaliana_ANT VCY----GSNPNGGIYSHMSVMPLRSDGSLCLMEALNR------------------------------------------ Theobroma_cacao_AIL5_Putative -------PNPTAPTSTINSSAREEDAAASGT------------------------------------------------- Glycine_max_AIL5 ------APPEPT-------------------------------------------------------------------- Arabidopsis_thaliana_AIL5 ------SPVERQDGSPGVSP------------------------------------------------------------ Arabidopsis_thaliana_PLT2 -------PFQNQG----------------------------------------------------WNMIN---------- Glycine_max_PLT2 -------PFQNH----------------------------------------------------DW-------------- Theobroma_cacao_PLT2_Putative -------PFQAQGTDHILSIFSLSIFVSLICLVCKFT---------------------------EW-------------- Theobroma_cacao_BBM -TSSELSMLMGSSCNGQSLDQSN-Q--EPKLENFLGNHSFSNHQQNKLHGCNTMYNT---TTGEYMFPNCSLQLPSE--D Vitis_vinifera_BBM_Like LGMNSDTNYK-LIKETTTSELSMLMG-SCKSEDNLENQ----E--L-N-L-CRSFADHEQ-KLQGCNSIAAAAYD-SADY Medicago_truncatula_BBM_Putative ---NNQNLLLGTSCMNQNVNNNN-QQAQPKLENFLGGHSFTDHQEYGGSNS---------YSSLHLPP-----------H Glycine_max_BBM1 ---NSQNLLLGTSCNKQNMNQNQ-QQ-QPKLENFLGGHSFGEHEQTYGGNS---------ASTDYMFP-----------A Zea_mays_BBM1_Putative ---SELSMLVGSSGGGGGNGKRAVEDSEPKLEDFLGGNSFVSDQD---------------QSGGYLFS-----------G Oryza_sativa_BBM1_Putative ---EG------GGTVAAAGGEET-A--APKLEDFLGMQVQQE------------------TA-----------------A Arabidopsis_thaliana_BBM -----------GACNNINNNEQN----GPKLENFLGRTTTIY------------------NTNETV-------------V Brassica_napus_BBM1 -----------CACNNIHNDEQD----GPKLENFLGRTTTIY------------------NTNENVG------------D Brassica_napus_BBM2 -----------SACNNIHNDEQD----GPKLENFLGRTTTIY------------------NTNENVG------------D Arabidopsis_thaliana_ANT -----------SSHSNHHQDS------SPKVEDFFGTHHNNT------------------SHKEAM-------------D Theobroma_cacao_AIL5_Putative -----------TTAGATDLSMFR-G--GPKLEDFLGGSSTTT------------------GAG----------------D Glycine_max_AIL5 -----------AGAGPTNLSIFT-G--GPKFEDFLGGSAATA------------------TTVACAPP-----------Q Arabidopsis_thaliana_AIL5 -----------SDATAVLSVYPG----GPKLENFLGGGASTT------------------TTR----------------P Arabidopsis_thaliana_PLT2 -----------PHGGGGEGGE------VPKVADFLGVSKSGD------------------HHTDHNLV-----------P Glycine_max_PLT2 -----------SLINTHSSSE------VPKVADFLGVSKSEN------------------ESDLAA-------------S Theobroma_cacao_PLT2_Putative -----------NLINTHDTSE------VPKVADFLGVSKSES------------------PSLDLV-------------A Theobroma_cacao_BBM TTNARTSNGGDDNDNNNNKNNNNNTNINTGNGSSSIGLSMIKTWLRN------QPAPPQPEAKNN------GG------- Vitis_vinifera_BBM_Like -FPNCSLQLPSEPV--LIKETPTPRGGGGGSTTVNN-----------------SSIGLSMIKTWLSL------QPAP-HQ Medicago_truncatula_BBM_Putative QPEASCGGGDGSTSNN-----------------NSIGLSMIKTWLRN------QPPPPENNNNNNNESGAR--------- Glycine_max_BBM1 QPVSAGGGGSGGGSNNNNNS-------------NSIGLSMIKTWLRN------QPPNSENINNNNESGGNIRSSV----- Zea_mays_BBM1_Putative VPIASSANSNSGS--------------------NTMELSMIKTWLRNNQVAQPQPPAPHQPQPEEMSTDASGSSFGCSDS Oryza_sativa_BBM1_Putative AAAGHGRGGSS----------------------SVVGLSMIKNWLRS------QPPPAVVGGEDA--------------- Arabidopsis_thaliana_BBM DGNGDCGGGDGGGG-------------------GSLGLSMIKTWLSN------HSVANANHQDNGNG------------- Brassica_napus_BBM1 GSGSGCYGGGDGGG-------------------GSLGLSMIKTWLRN------QPVDNVDNQENGNA------------- Brassica_napus_BBM2 IDGSGCYGGGDGGG-------------------GSLGLSMIKTWLRN------QPVDNVDNQENGNG------------- Arabidopsis_thaliana_ANT LSLDSLFYNTTHEPNTT----------------TNFQEFFSFPQTRN------HEEETRNYGNDPSLTHGGSF------- Theobroma_cacao_AIL5_Putative APHPHFSAETP------------------------------------------VTVSDTEIYDSE--------------- Glycine_max_AIL5 LPQF-------------------------------------------------STDNNNHLYDSEL-------------- Arabidopsis_thaliana_AIL5 MQQVQSLGG------------------------VVFSSDLQPPL---------HPPSAAEIYDSE--------------- Arabidopsis_thaliana_PLT2 YNDIHQTNASD----------------------YYFQTNSLLPTVVT---CASNAPNNYELQESAHN------------- Glycine_max_PLT2 LNEIQSNDSD-----------------------YLFTNNSLVPMQNP---A--VDTPSNEYQENANSS------------ Theobroma_cacao_PLT2_Putative FNEIHQANDSD----------------------YSFQSNSIVPVQNA--VV--AANNNYEYQENANN------------- Theobroma_cacao_BBM ----A-------SQSLSLSMSTGSQTGSPLPLLTSST--GGGSGGESSSSDNNKQQKTPTGMDS-ESGAI---------- Vitis_vinifera_BBM_Like DN-KSTD-GPVGG--------LIKE----AAAGNLPNAQTQNHQSQTHQQISSPLPLLTASAGGGGGSGGESSSSDNKK- Medicago_truncatula_BBM_Putative ------------VQTLSLSMSTGSQSSSSVPLLNANV-----MSGEISSSENKQPPTTAVVLDSNQTSVV---------- Glycine_max_BBM1 ------------QQTLSLSMSTGSQSSTSLPLLTA-------SVDNGESPSDNKQPNTSAALDSTQTGAI---------- Zea_mays_BBM1_Putative MGRNSMVAAGGSSQSLALSMSTGSHLPMVVPSGAASG-----AASESTSSENKR---ASGAMDS-PGSAV---------- Oryza_sativa_BBM1_Putative ------------MMALAVSTSASPPVDATV------------PACISPDGMGSKAADGGGAAEAAAAAAA---------- Arabidopsis_thaliana_BBM ------------ARGLSLSMNSS-------------------TSDSNNYNNNDDVVQEKTIVDV-----V---------- Brassica_napus_BBM1 ------------AKGLSLSMNSS-------------------TSCDNNNDSNNNVVAQGKTIDDSV-------------- Brassica_napus_BBM2 ------------AKGLSLSMNSS-------------------TSCDNNNYSSNNLVAQGKTIDDSV-------------- Arabidopsis_thaliana_ANT ----NVGVYGEFQQSLSLSMSPGSQSSCITGSHHHQQNQNQNHQSQNHQQISEALVETSVGFETTTMAAAKKKRGQEDVV Theobroma_cacao_AIL5_Putative ------------LKTIAASFLRG-------------------FSSERTDTHKQQQQQQQQLVPTA--------------- Glycine_max_AIL5 ------------KSTIAACFPRA-------------------LAAEQSTEPQ---------------------------- Arabidopsis_thaliana_AIL5 ------------LKSIAASFLGN-------------------YSGGHSSEVSSVHKQQPNPLAVSEA------------- Arabidopsis_thaliana_PLT2 ------------LQSLTLSMGSTGAAAAEVATVKA-------SPAETSADNSSSTTNTSGGAIV---------------- Glycine_max_PLT2 ------------LQSLTLSMGSGKD-----------------STCETSGDNSTNTTTTTTV------------------- Theobroma_cacao_PLT2_Putative ------------LQSLTLSMGSGKG-----------------STCETSGENSTKTV------------------------ Theobroma_cacao_BBM ----EAM-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWG Vitis_vinifera_BBM_Like ---ATPLDS-QTG-I-----------LIKE----ETV-PWDNSFKKEGHSRIGRQVYLGGYDMEEKAARAYDLCRRKYQT Medicago_truncatula_BBM_Putative ----ESAVPRKSVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Glycine_max_BBM1 ----ETA-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Zea_mays_BBM1_Putative ----EAV-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Oryza_sativa_BBM1_Putative ----QRM--KAAMDTFGQRTSIYRGVTKHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWG Arabidopsis_thaliana_BBM ----ETT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Brassica_napus_BBM1 ----EAT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Brassica_napus_BBM2 ----EAT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Arabidopsis_thaliana_ANT VVGQKQIVHRKSIDTFGQRTSQYRGVTRHRWTGRYEAHLWDNSFKKEGHSRKGRQVYLGGYDMEEKAARAYDLAALKYWG Theobroma_cacao_AIL5_Putative ----EPA-PRRAVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQ---GGYDKEEKAARAYDLAALKYWG Glycine_max_AIL5 ----KPS-PKKTVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Arabidopsis_thaliana_AIL5 ----SPT-PKKNVESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Arabidopsis_thaliana_PLT2 ----EAT-PRRTLETFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEEKAARAYDLAALKYWG Glycine_max_PLT2 ----EAA-PRRTLDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEEKAARSYDLAALKYWG Theobroma_cacao_PLT2_Putative ----EAP-PRRTLDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQ---GGYDKEEKAARAYDLAALKYWG Theobroma_cacao_BBM TTTTTNFP------ISNYEKELEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Vitis_vinifera_BBM_Like ------------K------------------LIKETTRTKSSP------ISRGETRHHEHGHWQARIGRVSGNKDLYLGT Medicago_truncatula_BBM_Putative TTTTTNFP------ISHYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_BBM1 TTTTTNFP------ISHYEKELEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Zea_mays_BBM1_Putative TTTTTNFP------ISNYEKELEEMKHMTRQEYIAYLRRNSSGFSRGASKYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Oryza_sativa_BBM1_Putative TTTTTNFP------VSNYEKELDEMKHMNRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_BBM TTTTTNFP------LSEYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Brassica_napus_BBM1 TTTTTNFP------MSEYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Brassica_napus_BBM2 TTTTTNFP------MSEYEKEIEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_ANT PSTHTNFS------AENYQKEIEDMKNMTRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_AIL5_Putative PTTTTNFP------ISNYEKELGEMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_AIL5 PTTTTNFP------ISNYEKELEEMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_AIL5 PTTTTNFP------ISNYESELEEMKHMTRQEFVASLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_PLT2 PSTTTNFP------ITNYEKEVEEMKNMTRQEFVASIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_PLT2 TSTTTNFP------ISNYEKELDEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_PLT2_Putative TSTTTNFPVYKFSTISNYEKELEEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_BBM FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSILESSTLPIG-GAAKRLKD-VEQAEM---ALDVQRVDDD----- Vitis_vinifera_BBM_Like ------------------------------------LIKENSLLSG-ELARRINN-----L-------MS----NS-LES Medicago_truncatula_BBM_Putative FSTQEEAAEAYDVAAIKFRGLSAVTNFDMSRYDVKTILESSTLPIG-GAAKRLKD-MEQVELNHVNVDISHRTEQ-DHSI Glycine_max_BBM1 FSTQEEAAEAYDVAAIKFRGLSAVTNFDMSRYDVKSILESTTLPIG-GAAKRLKD-MEQVEL---SVDNGHRADQVDHSI Zea_mays_BBM1_Putative FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSILESSTLPVG-GAARRLKDAVDHVEA---GATIWRADMD----- Oryza_sativa_BBM1_Putative FGTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSIIESSNLPIGTGTTRRLKDSSDHTDN---VMDINVNTEP----N Arabidopsis_thaliana_BBM FGTQEEAAEAYDIAAIKFRGLSAVTNFDMNRYNVKAILESPSLPIG-SSAKRLKDVNNPVPA------------------ Brassica_napus_BBM1 FGTQEEAAEAYDIAAIKFRGLTAVTNFDMNRYNVKAILESPSLPIG-SAAKRLKEANRPVPS-----------------M Brassica_napus_BBM2 FGTQEEAAEAYDIAAIKFRGLTAVTNFDMNRYNVKAILESPSLPIG-SAAKRLKEANRPVPS-----------------M Arabidopsis_thaliana_ANT FGTQEEAAEAYDVAAIKFRGTNAVTNFDITRYDVDRIMSSNTLLSG-ELARRNNN------------------------S Theobroma_cacao_AIL5_Putative FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSI-ANSNLPIG-GLSNKSKNCSDSASD------------------ Glycine_max_AIL5 FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSI-ANSTLPIG-GLSGKNKNSTDSASE------------------ Arabidopsis_thaliana_AIL5 FSTQEEAAEAYDIAAIKFRGLNAVTNFDISRYDVKSI-ASCNLPVG-GLMPKPSPATAAADK---TVDLSPSDSP----S Arabidopsis_thaliana_PLT2 FSTEEEAAEAYDIAAIKFRGLNAVTNFEINRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Glycine_max_PLT2 FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Theobroma_cacao_PLT2_Putative FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Theobroma_cacao_BBM -NMSSQLTD-GINNY-----GAAHHGWP-T---IAFQ-QAQP---------FSMHYPYGQR---VWCK------QEQDSD Vitis_vinifera_BBM_Like S--PI--GA-K-LKD-AEQAEM---TIDGQRTDDE------LIKE--MSSQLTD-GINNY-----GAHHHGWP-T---V- Medicago_truncatula_BBM_Putative INNTSHLTE---QAIYAATNAS---NWH-A---LSFQ-HQQPHHHYNANNMQLQNYPYGTQTQKLWCK------QEQDSD Glycine_max_BBM1 I-MSSHLTQ-GINNNYAGGGTATHHNWHNA---HAFH-QPQP--------CTTMHYPYGQRIN--WCK------QEQQDN Zea_mays_BBM1_Putative GAVISQLAEAGMGGY----ASYGHHGWP-T---IAFQ-QPSP---------LSVHYPYGQPSRG-WCK------PEQDAA Oryza_sativa_BBM1_Putative NVVSSHFTN-GVGNY--GSQHYGYNGWS-P---ISMQ-PIPS------------QYANGQPRA--WLK------QEQDSS Arabidopsis_thaliana_BBM MMISNNVSE----------SANNVSGWQ-N---TAFQ-HHQG-------MDLSLLQQQQERYVGYYN-------GGNLST Brassica_napus_BBM1 MMISNNVSE----------SENSASGWQ-N---AAVQ-HHQG-------VDLSLLHQHQERYNGYYYN------GGNLSS Brassica_napus_BBM2 MMISNNVSE----------SENNASGWQ-N---AAVQ-HHQG-------VDLSLLQQHQERYNGYYYN------GGNLSS Arabidopsis_thaliana_ANT IVVRNTEDQ------------------------TALNAVVEG-------------------------------------- Theobroma_cacao_AIL5_Putative ---GKSTDD-----------DRDHSSASSA---VTFASQPAP------SSALSFAVPIKQDPSDYWSNI-----FGYNNT Glycine_max_AIL5 ----SKSHE-----------PSQSDGDPSSASSVTFASQQQP-----SSSNLSFAIPIKQDPSDYWSILG----YHNTPL Arabidopsis_thaliana_AIL5 LTTPSLTFN----------VATPVNDHGGTFYHTGIPIKPDP-------------------ADHYWSN------------ Arabidopsis_thaliana_PLT2 IALGSNFHQ-----------YGAASGSSSVASSSRLQLQPYP---------LSIQQPFEHLHHHQPLL------TLQNNN Glycine_max_PLT2 IALGSSTFQ-----YGTTSSNSRLHAYPLMQHHHQFE-QPQP-LLTLQNHDISSHFSHQQDPLHQGYIQTQLQLHQQQSG Theobroma_cacao_PLT2_Putative IALGSSFQY-------GSSTSSRLQAYPLMQ--TPFE-QPQP-LLTLQNQDMSQYAQDTSSFHQNYIQT-----QLQLHQ Theobroma_cacao_BBM ANHTF----QDLHQLQLG----STHNFFQPS-VLHNLMA--MD-SSSMEHSSGSNSVIYCNGGGGDAAGSNG--ASGSYQ Vitis_vinifera_BBM_Like FQ-QAQP---------FSMHYPYGHQQRAVWCK------QEQDPD-LIKEGTHNF----QDLHQLQLG----NTHNFFQP Medicago_truncatula_BBM_Putative DHSTYTTA-TDIHQLQLGNNNNNTHNFF----GLQNIMS--MD-SASMDNSSGSNSVVYGGGDHG--------------- Glycine_max_BBM1 SDAPHSLSYSDIHQLQLG--NNGTHNFFHTNSGLHPMLS--MD-SASIDNSSSSNSVVY-----D--------------- Zea_mays_BBM1_Putative AAAAHSL--QDLQQLHLG---SAAHNFFQAS----------------------SSSTVYNGGAGA----------SGGYQ Oryza_sativa_BBM1_Putative VVTAA----QNLHNLHHFSSLGYTHNFFQQSDVPDVTGF--VD-APS--RSSDSYSFRYNGTNGFH-------------- Arabidopsis_thaliana_BBM ESTRVCFKQEE-----------EQQHFLRNSP-----SH--MT-NVDHHSSTSDDSVTVCGNVV---------------- Brassica_napus_BBM1 ESARACFKQED-----------DQHHFLSNTQSL-------MT-NIDHQSSVSDDSVTVCGNVV---------------- Brassica_napus_BBM2 ESARACFKQED-----------DQHHFLSNTQSL-------MT-NIDHQSSVSDDSVTVCGNVV---------------- Arabidopsis_thaliana_ANT --------------------------------------------GSNKEVSTPERLLSF--------------------- Theobroma_cacao_AIL5_Putative AASLSSAKNPSVAPTLFHQSSNNGSAFQDPSA---------FSMAFGVNSLVNESSN----------------------- Glycine_max_AIL5 DNSGIRNTTSTVTTTTFPSSNNGTASSLTP-------FN--MEFSSAPSSTGSDNNAAF--------------------- Arabidopsis_thaliana_AIL5 -----IFGFQANPKAEMRPLANFGSDLHNPSP------------GYAIMPVMQEGENNFGG------------------- Arabidopsis_thaliana_PLT2 DISQYHDSFSYI-QTQLHLHQQQTNNYLQSSSHTSQLYNAYLQSNPGLLHGFVSDNNNTS-------------------- Glycine_max_PLT2 GSSSYSFQNNNINNAQFY----NGYNLQNHPALLQGMIN--MG-SSSSSSVLENNNSNNNNVG----------------- Theobroma_cacao_PLT2_Putative QSGSYLHQPSQNSQF-------YNSHIQNNPALLHGLMS--MGCSSTVVDNNGSSSGSYSG------------------- Theobroma_cacao_BBM AVGYGGNGGY-VIPMG---TVVASDSNQN-QGN-G----FGDN--EVKTLGYETMYGS-A---DPYH---PRNLYYLSQQ Vitis_vinifera_BBM_Like N-VLHNLMS--MD-S-SMDH-SGSNSVIYSGGGAADGSAATGGSGSGSFQ-LIKEGVGYGNNIGF-VMPIS---TVIAHE Medicago_truncatula_BBM_Putative --GYGGNGGY-MIPMA-----IANDGNQNPRSNNN----FGES--EIKGFGYENVFGTTT---DPYHAQAARNLYYQPQQ Glycine_max_BBM1 --GYGGGGGYNVMPMGTTTAVVASDGDQNPRSNHG----FGDN--EIKALGYESVYGSAT---DSYHAH-ARNLYYLTQQ Zea_mays_BBM1_Putative --GLGGGSSF-LMPSS--TVVAAADQGHSSTANQGSTCSYGDDHQEGKLIGYDAAMVATAAGGDPYAA--ARNGYQFSQG Oryza_sativa_BBM1_Putative --GLPGGISY-AMPVA-----TAVDQGQGIHG-------YGED--GVAGIDTTH---------DLYG---SRNVYYLSEG Arabidopsis_thaliana_BBM --SYGGYQGF-AIPVGTS---------------------VNYDPFTAAEIAYN-----------------ARNHYYYAQH Brassica_napus_BBM1 --GYGGYQGF-AAPVN-------------------------CDAYAASEFDYN-----------------ARNHYYFAQQ Brassica_napus_BBM2 --GYGGYQGF-AAPVN-------------------------CDAYAASEFDYN-----------------ARNHYYFAQQ Arabidopsis_thaliana_ANT -----------------------------------------------------------------------PAIFALPQV Theobroma_cacao_AIL5_Putative --GLFNGGGY---------------------------------VQQQSGVSTST----------------SSLPLATPTA Glycine_max_AIL5 ---FSGGGIF-----------VQQQTSHG----------HGNASSGSSSSSLSCSIPF------------ATPIFSLNSN Arabidopsis_thaliana_AIL5 --SFVGSDGY-------------------------------NNHSAA-----------------------SNPVSAIPLS Arabidopsis_thaliana_PLT2 --GFLGNNGI------------------------------GIGSSSTVGSSAEEEFPA------------VKVDYDMPPS Glycine_max_PLT2 --GFVGSGFG-----------------------------MASNATSGNTVGTAEELGL------------VKVDYDMPT- Theobroma_cacao_PLT2_Putative --GYLGNGIG-----------------------------MASNSTAGNAVGSTEELAL------------VKVDYDMPS- Theobroma_cacao_BBM SST--GGVKASS-YDQASACNNWV---PTAVPTIAQR-SSNMAVCHGA-PTFTVWNDT Vitis_vinifera_BBM_Like GGHG-QGNGG----FGDS--EVKAIGYDNMFGS-T---DPYH---ARSLYY-S-Q-LI Medicago_truncatula_BBM_Putative SSA--GMVKGSSAYDQGSGCNNWV---PTAVPTLAPR-TNSLAVCHGT-PTFTVWNDT Glycine_max_BBM1 LSV-----------DQGS---NWV---PTAIPTLAPR-TTNVSLC----PPFTLLHE- Zea_mays_BBM1_Putative SGSTVSIARANG------YANNWS-------------------------SPFNNGMG- Oryza_sativa_BBM1_Putative SLL--ADVEKEGDYGQSVGGNSWV------LPT----------------P-------- Arabidopsis_thaliana_BBM QQQ--QQIQQSPGGDFPVAISNNH---SSNMYFHGEGGGEGA-------PTFSVWNDT Brassica_napus_BBM1 QQT-----QQSPGGDFPAAMTNNV---GSNMYYHGEGGGEVA-------PTFTVWNDN Brassica_napus_BBM2 QQT-----QHSPGGDFPAAMTNNV---GSNMYYHGEGGGEVA-------PTFTVWNDN Arabidopsis_thaliana_ANT NQK-------MFGSNMGGNMSPWTSNPNAELKTVALTLPQM--------PVFAAWADS Theobroma_cacao_AIL5_Putative LNN-----SGNNNYESSSGYGSWI---AQSLHSYQTA-KPSLSVFQT--PIFGME--- Glycine_max_AIL5 TS-----------YESSAGYGNWI---GPTLHTFQSHAKPSLFQT----PIFGME--- Arabidopsis_thaliana_AIL5 STT-----TMSNGNEGYGGNINWI---NNNISSSYQTAKSNLSVLHT--PVFGLE--- Arabidopsis_thaliana_PLT2 GGA--------------TGYGGWN--SGESAQGSNPG------------GVFTMWNE- Glycine_max_PLT2 -----------------GGYGGWSAAAAESMQTSNS-------------GVFTMWND- Theobroma_cacao_PLT2_Putative -----------------GGYGGWS---GDSVQGTNA-------------GVFSMWND- ; Gm_BBM1 QSSSVDTVKASA - YDQ.SACNT.V - - - PTAIP.H.PRSTTSMALCHGATTP.SLLHE -; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 938; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 938; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 938; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1425409524354; linkFile ExportedTREE1.nwk.nex; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5068573239888186931; tell It; setDefaultOrder 12 13 14 15 11 7 8 9 10 0 2 3 1 4 5 6; attachments ; endTell; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3437201136756279089; mqVersion 302; checksumv 0 3 1056282245 null getNumChars 938 numChars 938 getNumTaxa 16 numTaxa 16 short false bits 1048575 states 1048575 sumSquaresStatesOnly 1.26529776555494E14 sumSquares 1.26529776555494E14 longCompressibleToShort false usingShortMatrix false NumFiles 2 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState true false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1441 639; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #5068573239888186931 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #5068573239888186931; getWindow; tell It; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #3437201136756279089 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 0 -72; setLocation 8 23; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; colorCells #mesquite.charMatrices.ColorByState.ColorByState; tell It; setStateLimit 9; toggleUniformMaximum on; endTell; 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; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleShowPaleGrid off; toggleShowPaleCellColors off; toggleShowPaleExcluded off; togglePaleInapplicable on; toggleShowBoldCellText 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.charMatrices.SelSummaryStrip.SelSummaryStrip; tell It; showStrip off; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5 5; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; endTell; endTell; end;