#NEXUS [written Tue Mar 03 12:56:35 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 Arabidopsis_thaliana__ANT Arabidopsis_thaliana_AIL5 Theobroma_cacao_AIL5_Putative Glycine_max_AIL5 Arabidopsis_thaliana_PLT2 Glycine_max_PLT2 Theobroma_cacao_PLT2_Putative Oryza_sativa_BBM1_Putative Arabidopsis_thaliana_BBM Brassica_napus_BBM1 Brassica_napus_BBM2 Zea_mays_BBM1_Putative Theobroma_cacao_BBM Vitis_vinifera_BBM_Lke Medicago_truncatula_BBM_Putative Glycine_max_BBM1 ; END; BEGIN CHARACTERS; TITLE 'TcBBM-AP2 Genes Alignment'; LINK TAXA = Taxa; DIMENSIONS NCHAR=938; FORMAT DATATYPE = Protein INTERLEAVE GAP = - MISSING = ?; MATRIX Arabidopsis_thaliana__ANT ------------MKSFCDNDDNNHSNTTNLLGFSLSSNMMKMGGRGGREAIYSSSTSSAATSSSSVPPQLVVGDNTSNFG Arabidopsis_thaliana_AIL5 MKNNNNKSSSSSSYDSSLSPSSSSSSHQNWLSFSLSNNNNNFNSSSNPN-----LTSSTSDHHHPHPSHLSLFQAFST-- Theobroma_cacao_AIL5_Putative -------------MDMSMG-NMDSSSTQNWLAFSLSNQQQQH------------LNLPTSSSSSHHSSHLCLFEAFTT-- Glycine_max_AIL5 -------------MDSSSS-SPPNSTNNNSLAFSLSNHFPNPS-----------SSPLSLFHSFTYPSLSLTGSNTVD-- Arabidopsis_thaliana_PLT2 ------------------------MNSNNWLAFPLSPTHSSLP----PH-----IHSSQNSHFNL----GLVNDNIDN-- Glycine_max_PLT2 -------------------------MNNNWLSFPLSPTHSSLP---AHD-----LQATQYHQFSL----GLVNENMEN-- Theobroma_cacao_PLT2_Putative ---------------------MGSMNSNNWLSFPLSPTNSSLP----TH-----LHPSQSHQFNL----GLVNDNMEN-- 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 Zea_mays_BBM1_Putative -----------------------MASANNWLGFSLSGQDNPQP-----------NQDSS----------PAAGIDISGAS Theobroma_cacao_BBM -----------------------MASMNNWLAFSLSPQELPSQTVDQDH-----HSQTAVSRLGFNSD-DISGADVSG-- Vitis_vinifera_BBM_Lke -LIKE-----------------------MASMNSWSSNMMKPRELPPQ---PEN-----HSQNSVSRLGFNSD-EISNTD Medicago_truncatula_BBM_Putative ---------------------------MNLLGFSLSPQEQHPS---TQD-------QTVASRFGFNPN-EISGSDVQG-D Glycine_max_BBM1 -----------------------MGSMN-LLGFSLSPHEEHPS---SQD-----HSQTTPSRFSFNPDGSISSTDVAG-G Arabidopsis_thaliana__ANT VCY----GSNPNGGIYSHMSVMPLRSDGSLCLMEALNR------------------------------------------ Arabidopsis_thaliana_AIL5 ------SPVERQDGSPGVSP------------------------------------------------------------ Theobroma_cacao_AIL5_Putative -------PNPTAPTSTINSSAREEDAAASGT------------------------------------------------- Glycine_max_AIL5 ------APPEPT-------------------------------------------------------------------- Arabidopsis_thaliana_PLT2 -------PFQNQG----------------------------------------------------WNMIN---------- Glycine_max_PLT2 -------PFQNH----------------------------------------------------DW-------------- Theobroma_cacao_PLT2_Putative -------PFQAQGTDHILSIFSLSIFVSLICLVCKFT---------------------------EW-------------- Oryza_sativa_BBM1_Putative -------PVLPHPPLQGKTS----------------------------------------HLMHQWGSAY---------- Arabidopsis_thaliana_BBM YCFDLAAPSDESSAVQTSFL------SPFGVTLEAFTRDNN-------------------SHSRDWDING---------- Brassica_napus_BBM1 YCYDPTAASDESSAIQTSFP------SPFGVVVDAFTRDNN-------------------SHSRDWDING---------- Brassica_napus_BBM2 YCYDPTAASDESSAIQTSFP------SPFGVVLDAFTRDNN-------------------SHSRDWDING---------- Zea_mays_BBM1_Putative DFYGL--PTQQGSDGHLGVPGLRDDHASYGI-MEAYNRVPQ--------------------ETQDWNMRGLDYNGGG--- Theobroma_cacao_BBM ECFDL--TSDSSAPS-LNLP------PPFGI-LEAFNRNNQSQGSVCFAPSKHTRTFSSFSHVKDWNMKGLGMNSDGNYK Vitis_vinifera_BBM_Lke 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---------- Arabidopsis_thaliana__ANT -----------SSHSNHHQDS------SPKVEDFFGTHHNNT------------------SHKEAM-------------D Arabidopsis_thaliana_AIL5 -----------SDATAVLSVYPG----GPKLENFLGGGASTT------------------TTR----------------P Theobroma_cacao_AIL5_Putative -----------TTAGATDLSMFR-G--GPKLEDFLGGSSTTT------------------GAG----------------D Glycine_max_AIL5 -----------AGAGPTNLSIFT-G--GPKFEDFLGGSAATA------------------TTVACAPP-----------Q Arabidopsis_thaliana_PLT2 -----------PHGGGGEGGE------VPKVADFLGVSKSGD------------------HHTDHNLV-----------P Glycine_max_PLT2 -----------SLINTHSSSE------VPKVADFLGVSKSEN------------------ESDLAA-------------S Theobroma_cacao_PLT2_Putative -----------NLINTHDTSE------VPKVADFLGVSKSES------------------PSLDLV-------------A 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 Zea_mays_BBM1_Putative ---SELSMLVGSSGGGGGNGKRAVEDSEPKLEDFLGGNSFVSDQD---------------QSGGYLFS-----------G Theobroma_cacao_BBM -TSSELSMLMGSSCNGQSLDQSN-Q--EPKLENFLGNHSFSNHQQNKLHGCNTMYNT---TTGEYMFPNCSLQLPSE--D Vitis_vinifera_BBM_Lke 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 Arabidopsis_thaliana__ANT LSLDSLFYNTTHEPNTT----------------TNFQEFFSFPQTRN------HEEETRNYGNDPSLTHGGSF------- Arabidopsis_thaliana_AIL5 MQQVQSLGG------------------------VVFSSDLQPPL---------HPPSAAEIYDSE--------------- Theobroma_cacao_AIL5_Putative APHPHFSAETP------------------------------------------VTVSDTEIYDSE--------------- Glycine_max_AIL5 LPQF-------------------------------------------------STDNNNHLYDSEL-------------- Arabidopsis_thaliana_PLT2 YNDIHQTNASD----------------------YYFQTNSLLPTVVT---CASNAPNNYELQESAHN------------- Glycine_max_PLT2 LNEIQSNDSD-----------------------YLFTNNSLVPMQNP---A--VDTPSNEYQENANSS------------ Theobroma_cacao_PLT2_Putative FNEIHQANDSD----------------------YSFQSNSIVPVQNA--VV--AANNNYEYQENANN------------- 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------------- Zea_mays_BBM1_Putative VPIASSANSNSGS--------------------NTMELSMIKTWLRNNQVAQPQPPAPHQPQPEEMSTDASGSSFGCSDS Theobroma_cacao_BBM TTNARTSNGGDDNDNNNNKNNNNNTNINTGNGSSSIGLSMIKTWLRN------QPAPPQPEAKNN------GG------- Vitis_vinifera_BBM_Lke -FPNCSLQLPSEPV--LIKETPTPRGGGGGSTTVNN-----------------SSIGLSMIKTWLSL------QPAP-HQ Medicago_truncatula_BBM_Putative QPEASCGGGDGSTSNN-----------------NSIGLSMIKTWLRN------QPPPPENNNNNNNESGAR--------- Glycine_max_BBM1 QPVSAGGGGSGGGSNNNNNS-------------NSIGLSMIKTWLRN------QPPNSENINNNNESGGNIRSSV----- Arabidopsis_thaliana__ANT ----NVGVYGEFQQSLSLSMSPGSQSSCITGSHHHQQNQNQNHQSQNHQQISEALVETSVGFETTTMAAAKKKRGQEDVV Arabidopsis_thaliana_AIL5 ------------LKSIAASFLGN-------------------YSGGHSSEVSSVHKQQPNPLAVSEA------------- Theobroma_cacao_AIL5_Putative ------------LKTIAASFLRG-------------------FSSERTDTHKQQQQQQQQLVPTA--------------- Glycine_max_AIL5 ------------KSTIAACFPRA-------------------LAAEQSTEPQ---------------------------- Arabidopsis_thaliana_PLT2 ------------LQSLTLSMGSTGAAAAEVATVKA-------SPAETSADNSSSTTNTSGGAIV---------------- Glycine_max_PLT2 ------------LQSLTLSMGSGKD-----------------STCETSGDNSTNTTTTTTV------------------- Theobroma_cacao_PLT2_Putative ------------LQSLTLSMGSGKG-----------------STCETSGENSTKTV------------------------ Oryza_sativa_BBM1_Putative ------------MMALAVSTSASPPVDATV------------PACISPDGMGSKAADGGGAAEAAAAAAA---------- Arabidopsis_thaliana_BBM ------------ARGLSLSMNSS-------------------TSDSNNYNNNDDVVQEKTIVDV-----V---------- Brassica_napus_BBM1 ------------AKGLSLSMNSS-------------------TSCDNNNDSNNNVVAQGKTIDDSV-------------- Brassica_napus_BBM2 ------------AKGLSLSMNSS-------------------TSCDNNNYSSNNLVAQGKTIDDSV-------------- Zea_mays_BBM1_Putative MGRNSMVAAGGSSQSLALSMSTGSHLPMVVPSGAASG-----AASESTSSENKR---ASGAMDS-PGSAV---------- Theobroma_cacao_BBM ----A-------SQSLSLSMSTGSQTGSPLPLLTSST--GGGSGGESSSSDNNKQQKTPTGMDS-ESGAI---------- Vitis_vinifera_BBM_Lke DN-KSTD-GPVGG--------LIKE----AAAGNLPNAQTQNHQSQTHQQISSPLPLLTASAGGGGGSGGESSSSDNKK- Medicago_truncatula_BBM_Putative ------------VQTLSLSMSTGSQSSSSVPLLNANV-----MSGEISSSENKQPPTTAVVLDSNQTSVV---------- Glycine_max_BBM1 ------------QQTLSLSMSTGSQSSTSLPLLTA-------SVDNGESPSDNKQPNTSAALDSTQTGAI---------- Arabidopsis_thaliana__ANT VVGQKQIVHRKSIDTFGQRTSQYRGVTRHRWTGRYEAHLWDNSFKKEGHSRKGRQVYLGGYDMEEKAARAYDLAALKYWG Arabidopsis_thaliana_AIL5 ----SPT-PKKNVESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Theobroma_cacao_AIL5_Putative ----EPA-PRRAVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQ---GGYDKEEKAARAYDLAALKYWG Glycine_max_AIL5 ----KPS-PKKTVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Arabidopsis_thaliana_PLT2 ----EAT-PRRTLETFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEEKAARAYDLAALKYWG Glycine_max_PLT2 ----EAA-PRRTLDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEEKAARSYDLAALKYWG Theobroma_cacao_PLT2_Putative ----EAP-PRRTLDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQ---GGYDKEEKAARAYDLAALKYWG Oryza_sativa_BBM1_Putative ----QRM--KAAMDTFGQRTSIYRGVTKHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWG Arabidopsis_thaliana_BBM ----ETT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Brassica_napus_BBM1 ----EAT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Brassica_napus_BBM2 ----EAT-PKKTIESFGQRTSIYRGVTRHRWTGRYEAHLWDNSCKREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Zea_mays_BBM1_Putative ----EAV-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQSRKGRQVYLGGYDKEDKAARAYDLAALKYWG Theobroma_cacao_BBM ----EAM-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQ---GGYDKEEKAARAYDLAALKYWG Vitis_vinifera_BBM_Lke ---ATPLDS-QTG-I-----------LIKE----ETV-PWDNSFKKEGHSRIGRQVYLGGYDMEEKAARAYDLCRRKYQT Medicago_truncatula_BBM_Putative ----ESAVPRKSVDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Glycine_max_BBM1 ----ETA-PRKSIDTFGQRTSIYRGVTRHRWTGRYEAHLWDNSCRREGQTRKGRQVYLGGYDKEEKAARAYDLAALKYWG Arabidopsis_thaliana__ANT PSTHTNFS------AENYQKEIEDMKNMTRQEYVAHLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_AIL5 PTTTTNFP------ISNYESELEEMKHMTRQEFVASLRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_AIL5_Putative PTTTTNFP------ISNYEKELGEMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_AIL5 PTTTTNFP------ISNYEKELEEMKNMTRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_PLT2 PSTTTNFP------ITNYEKEVEEMKNMTRQEFVASIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_PLT2 TSTTTNFP------ISNYEKELDEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_PLT2_Putative TSTTTNFPVYKFSTISNYEKELEEMKHMTRQEFVAAIRRKSSGFSRGASMYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Oryza_sativa_BBM1_Putative TTTTTNFP------VSNYEKELDEMKHMNRQEFVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana_BBM TTTTTNFP------LSEYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Brassica_napus_BBM1 TTTTTNFP------MSEYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Brassica_napus_BBM2 TTTTTNFP------MSEYEKEIEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Zea_mays_BBM1_Putative TTTTTNFP------ISNYEKELEEMKHMTRQEYIAYLRRNSSGFSRGASKYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Theobroma_cacao_BBM TTTTTNFP------ISNYEKELEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Vitis_vinifera_BBM_Lke ------------K------------------LIKETTRTKSSP------ISRGETRHHEHGHWQARIGRVSGNKDLYLGT Medicago_truncatula_BBM_Putative TTTTTNFP------ISHYEKEVEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Glycine_max_BBM1 TTTTTNFP------ISHYEKELEEMKHMTRQEYVASLRRKSSGFSRGASIYRGVTRHHQHGRWQARIGRVAGNKDLYLGT Arabidopsis_thaliana__ANT FGTQEEAAEAYDVAAIKFRGTNAVTNFDITRYDVDRIMSSNTLLSG-ELARRNNN------------------------S Arabidopsis_thaliana_AIL5 FSTQEEAAEAYDIAAIKFRGLNAVTNFDISRYDVKSI-ASCNLPVG-GLMPKPSPATAAADK---TVDLSPSDSP----S Theobroma_cacao_AIL5_Putative FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSI-ANSNLPIG-GLSNKSKNCSDSASD------------------ Glycine_max_AIL5 FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSI-ANSTLPIG-GLSGKNKNSTDSASE------------------ Arabidopsis_thaliana_PLT2 FSTEEEAAEAYDIAAIKFRGLNAVTNFEINRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Glycine_max_PLT2 FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Theobroma_cacao_PLT2_Putative FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKAILESNTLPIGGGAAKRLKE-AQALES-------SRKREE----M Oryza_sativa_BBM1_Putative FGTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSIIESSNLPIGTGTTRRLKDSSDHTDN---VMDINVNTEP----N Arabidopsis_thaliana_BBM FGTQEEAAEAYDIAAIKFRGLSAVTNFDMNRYNVKAILESPSLPIG-SSAKRLKDVNNPVPA------------------ Brassica_napus_BBM1 FGTQEEAAEAYDIAAIKFRGLTAVTNFDMNRYNVKAILESPSLPIG-SAAKRLKEANRPVPS-----------------M Brassica_napus_BBM2 FGTQEEAAEAYDIAAIKFRGLTAVTNFDMNRYNVKAILESPSLPIG-SAAKRLKEANRPVPS-----------------M Zea_mays_BBM1_Putative FSTEEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSILESSTLPVG-GAARRLKDAVDHVEA---GATIWRADMD----- Theobroma_cacao_BBM FSTQEEAAEAYDIAAIKFRGLNAVTNFDMSRYDVKSILESSTLPIG-GAAKRLKD-VEQAEM---ALDVQRVDDD----- Vitis_vinifera_BBM_Lke ------------------------------------LIKENSLLSG-ELARRINN-----L-------MS----NS-LES Medicago_truncatula_BBM_Putative FSTQEEAAEAYDVAAIKFRGLSAVTNFDMSRYDVKTILESSTLPIG-GAAKRLKD-MEQVELNHVNVDISHRTEQ-DHSI Glycine_max_BBM1 FSTQEEAAEAYDVAAIKFRGLSAVTNFDMSRYDVKSILESTTLPIG-GAAKRLKD-MEQVEL---SVDNGHRADQVDHSI Arabidopsis_thaliana__ANT IVVRNTEDQ------------------------TALNAVVEG-------------------------------------- Arabidopsis_thaliana_AIL5 LTTPSLTFN----------VATPVNDHGGTFYHTGIPIKPDP-------------------ADHYWSN------------ Theobroma_cacao_AIL5_Putative ---GKSTDD-----------DRDHSSASSA---VTFASQPAP------SSALSFAVPIKQDPSDYWSNI-----FGYNNT Glycine_max_AIL5 ----SKSHE-----------PSQSDGDPSSASSVTFASQQQP-----SSSNLSFAIPIKQDPSDYWSILG----YHNTPL Arabidopsis_thaliana_PLT2 IALGSNFHQ-----------YGAASGSSSVASSSRLQLQPYP---------LSIQQPFEHLHHHQPLL------TLQNNN Glycine_max_PLT2 IALGSSTFQ-----YGTTSSNSRLHAYPLMQHHHQFE-QPQP-LLTLQNHDISSHFSHQQDPLHQGYIQTQLQLHQQQSG Theobroma_cacao_PLT2_Putative IALGSSFQY-------GSSTSSRLQAYPLMQ--TPFE-QPQP-LLTLQNQDMSQYAQDTSSFHQNYIQT-----QLQLHQ 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 Zea_mays_BBM1_Putative GAVISQLAEAGMGGY----ASYGHHGWP-T---IAFQ-QPSP---------LSVHYPYGQPSRG-WCK------PEQDAA Theobroma_cacao_BBM -NMSSQLTD-GINNY-----GAAHHGWP-T---IAFQ-QAQP---------FSMHYPYGQR---VWCK------QEQDSD Vitis_vinifera_BBM_Lke 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 Arabidopsis_thaliana__ANT --------------------------------------------GSNKEVSTPERLLSF--------------------- Arabidopsis_thaliana_AIL5 -----IFGFQANPKAEMRPLANFGSDLHNPSP------------GYAIMPVMQEGENNFGG------------------- Theobroma_cacao_AIL5_Putative AASLSSAKNPSVAPTLFHQSSNNGSAFQDPSA---------FSMAFGVNSLVNESSN----------------------- Glycine_max_AIL5 DNSGIRNTTSTVTTTTFPSSNNGTASSLTP-------FN--MEFSSAPSSTGSDNNAAF--------------------- Arabidopsis_thaliana_PLT2 DISQYHDSFSYI-QTQLHLHQQQTNNYLQSSSHTSQLYNAYLQSNPGLLHGFVSDNNNTS-------------------- Glycine_max_PLT2 GSSSYSFQNNNINNAQFY----NGYNLQNHPALLQGMIN--MG-SSSSSSVLENNNSNNNNVG----------------- Theobroma_cacao_PLT2_Putative QSGSYLHQPSQNSQF-------YNSHIQNNPALLHGLMS--MGCSSTVVDNNGSSSGSYSG------------------- 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---------------- Zea_mays_BBM1_Putative AAAAHSL--QDLQQLHLG---SAAHNFFQAS----------------------SSSTVYNGGAGA----------SGGYQ Theobroma_cacao_BBM ANHTF----QDLHQLQLG----STHNFFQPS-VLHNLMA--MD-SSSMEHSSGSNSVIYCNGGGGDAAGSNG--ASGSYQ Vitis_vinifera_BBM_Lke FQ-QAQP---------FSMHYPYGHQQRAVWCK------QEQDPD-LIKEGTHNF----QDLHQLQLG----NTHNFFQP Medicago_truncatula_BBM_Putative DHSTYTTA-TDIHQLQLGNNNNNTHNFF----GLQNIMS--MD-SASMDNSSGSNSVVYGGGDHG--------------- Glycine_max_BBM1 SDAPHSLSYSDIHQLQLG--NNGTHNFFHTNSGLHPMLS--MD-SASIDNSSSSNSVVY-----D--------------- Arabidopsis_thaliana__ANT -----------------------------------------------------------------------PAIFALPQV Arabidopsis_thaliana_AIL5 --SFVGSDGY-------------------------------NNHSAA-----------------------SNPVSAIPLS Theobroma_cacao_AIL5_Putative --GLFNGGGY---------------------------------VQQQSGVSTST----------------SSLPLATPTA Glycine_max_AIL5 ---FSGGGIF-----------VQQQTSHG----------HGNASSGSSSSSLSCSIPF------------ATPIFSLNSN Arabidopsis_thaliana_PLT2 --GFLGNNGI------------------------------GIGSSSTVGSSAEEEFPA------------VKVDYDMPPS Glycine_max_PLT2 --GFVGSGFG-----------------------------MASNATSGNTVGTAEELGL------------VKVDYDMPT- Theobroma_cacao_PLT2_Putative --GYLGNGIG-----------------------------MASNSTAGNAVGSTEELAL------------VKVDYDMPS- 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 Zea_mays_BBM1_Putative --GLGGGSSF-LMPSS--TVVAAADQGHSSTANQGSTCSYGDDHQEGKLIGYDAAMVATAAGGDPYAA--ARNGYQFSQG Theobroma_cacao_BBM AVGYGGNGGY-VIPMG---TVVASDSNQN-QGN-G----FGDN--EVKTLGYETMYGS-A---DPYH---PRNLYYLSQQ Vitis_vinifera_BBM_Lke 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 Arabidopsis_thaliana__ANT NQK-------MFGSNMGGNMSPWTSNPNAELKTVALTLPQM--------PVFAAWADS Arabidopsis_thaliana_AIL5 STT-----TMSNGNEGYGGNINWI---NNNISSSYQTAKSNLSVLHT--PVFGLE--- Theobroma_cacao_AIL5_Putative LNN-----SGNNNYESSSGYGSWI---AQSLHSYQTA-KPSLSVFQT--PIFGME--- Glycine_max_AIL5 TS-----------YESSAGYGNWI---GPTLHTFQSHAKPSLFQT----PIFGME--- Arabidopsis_thaliana_PLT2 GGA--------------TGYGGWN--SGESAQGSNPG------------GVFTMWNE- Glycine_max_PLT2 -----------------GGYGGWSAAAAESMQTSNS-------------GVFTMWND- Theobroma_cacao_PLT2_Putative -----------------GGYGGWS---GDSVQGTNA-------------GVFSMWND- 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 Zea_mays_BBM1_Putative SGSTVSIARANG------YANNWS-------------------------SPFNNGMG- Theobroma_cacao_BBM SST--GGVKASS-YDQASACNNWV---PTAVPTIAQR-SSNMAVCHGA-PTFTVWNDT Vitis_vinifera_BBM_Lke 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- ; Gm_BBM1 QSSSVDTVKASA - YDQ.SACNT.V - - - PTAIP.H.PRSTTSMALCHGATTP.SLLHE -; END; BEGIN TAXA; TITLE Taxa2; 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 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 TREES; Title 'TcBBM-AP2 Tree'; LINK Taxa = Taxa2; TRANSLATE [0] 1 Theobroma_cacao_BBM, [1] 2 Vitis_vinifera_BBM_Like, [2] 3 Medicago_truncatula_BBM_Putative, [3] 4 Glycine_max_BBM1, [4] 5 Zea_mays_BBM1_Putative, [5] 6 Oryza_sativa_BBM1_Putative, [6] 7 Arabidopsis_thaliana_BBM, [7] 8 Brassica_napus_BBM1, [8] 9 Brassica_napus_BBM2, [9] 10 Arabidopsis_thaliana_ANT, [10] 11 Theobroma_cacao_AIL5_Putative, [11] 12 Glycine_max_AIL5, [12] 13 Arabidopsis_thaliana_AIL5, [13] 14 Arabidopsis_thaliana_PLT2, [14] 15 Glycine_max_PLT2, [15] 16 Theobroma_cacao_PLT2_Putative; TREE Imported_tree_1 = ((((((1:0.10502274,2:0.11208493)1.0000:0.07122961,(3:0.14303813,4:0.15485854)1.0000:0.06885147)1.0000:0.08255121,5:0.26477327)0.6760:0.03269806,6:0.32422432)0.5450:0.02460104,(7:0.11059359,(8:0.01343341,9:0.01104334)1.0000:0.08534604)1.0000:0.27395058)0.9240:0.03154872,(10:0.39948031,(((11:0.26449663,12:0.23556897)0.8440:0.03459397,13:0.31865079)1.0000:0.07891397,(14:0.23677592,(15:0.14291277,16:0.1585973)0.9860:0.05338538)1.0000:0.14862029)0.4360:0.01179143)0.9240:0.00673672); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1425405395544; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5068573239888186931; setID 1 8221699885227347105; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 3437201136756279089; mqVersion 302; checksumv 0 3 810094599 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 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1441 639; setLocation 36 104; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #8221699885227347105 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTaxa #8221699885227347105; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 974.1425405343968.6085067098674845605; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1341 567; setLocation 36 104; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareLineTree.SquareLineTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle off; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; setFixedTaxonDistance 0; endTell; setEdgeWidth 4; showEdgeLines on; orientUp; 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; setColor Black; toggleColorPartition off; toggleColorAssigned on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; 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 off; toggleHorizontal on; toggleWhiteEdges on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocStrings.DrawTreeAssocStrings; tell It; setOn on; 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 #3437201136756279089 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1341 567; setLocation 36 104; 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; showWindow; getWindow; tell It; forceAutosize; endTell; 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;