#NEXUS [written Wed Apr 11 21:29:39 EDT 2012 by Mesquite version 2.75 (build 566) at MLT/131.104.156.89] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=22; TAXLABELS Nicotiana_tabacum_TC80841 Nicotiana_tabacum_TC82241 Nicotiana_tabacum_FG638558 Nicotiana_tabacum_FG639711 Nicotiana_tabacum_TC92964 Nicotiana_tabacum_TC86004 Nicotiana_tabacum_TC79402 Nicotiana_tabacum_TC83180 Nicotiana_benthamiana_TC17973 Nicotiana_tabacum_TC98053 Nicotiana_tabacum_TC90991 Nicotiana_benthamiana_TC17637 Nicotiana_tabacum_TC79356 Nicotiana_tabacum_TC79198 Nicotiana_benthamiana_GU183155 Nicotiana_tabacum_TC92100 Nicotiana_tabacum_BP530541 Nicotiana_tabacum_TC80404 Nicotiana_tabacum_TC79226 Nicotiana_tabacum_TC78758 Nicotiana_tabacum_TC81122 Nicotiana_tabacum_TC81500 ; END; BEGIN CHARACTERS; TITLE Nicotiana_aligned_Mir_sequence_using_CLUSTALX_; DIMENSIONS NCHAR=318; FORMAT DATATYPE = Protein GAP = - MISSING = ?; MATRIX Nicotiana_tabacum_TC80841 -------------------------------MKSILLFLSLAFLPFSALATCTT-------------DTGHGNQVLRVVKDWKGHPLDKGARYFIVSAFNGAGGGGVRLANLGGQDENTCPT-SVVQSPRDKDDGIAVYFKPKEPK---H-QEIVESAPLNINFYLD-YYK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLG---SSYKLVFCP-------YGETFTCQNVGIVSESGYRRLVLTDNAKAFVFIKDDRIGKVEALSSITSAF------------------------------ Nicotiana_tabacum_TC82241 MTYMKRLIFNRLSMRVFISISSGARQVRNKKMKSILLFLSLAFLPFSALATCTT-------------DTGHGNQVLRVVKDWKGHPLDKGARYFIVSAFNGAGGGGVRLANLGGQDEDTCPT-SVVQSPRDKDDGIAVYFKPKEPK---H-QEIVESAPLNINFYLD-YYK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLG---SSYKLVFCP-------YGETFTCQNVGIVSESGYRRLVLTDNAKAFVFIKDDRIGKVEALSSITSAF------------------------------ Nicotiana_tabacum_FG638558 -------------------------------MKSILLFLSLAFLPFSALATCTT-------------DTGHGNQVLRVVKDWKGHPLDKGARYFIVSAFNGAGGGGVRLANLGGQDENTCPT-SVVQSPRDKDDGIAVYFKPKEPK---H-QEIVESAPLNINFYLD-YYK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLG---SSYKLVFCP-------YGETFTCQNVGIVSESGYRRLVLTDNAKAFVFIKDDRIGKIEALSSITSAF------------------------------ Nicotiana_tabacum_FG639711 -------------------------------MKSILLFLSLAFLPFSALATCTT-------------DTGHGNQVLRVVKDWKGHPLDKGARYFIVSAFNGAGGGGVRLANLGGQDENTCPT-SVVQSPRDKDDGIAVYFKPKEPK---H-QEIVESAPLNINFYLD-YYK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLE---SSYKLVFCP-------YGDVYLPK----CWHS?---------------------------------------------------------------- Nicotiana_tabacum_TC92964 -------------------------------MKTVLLFLSLAFLPFSALATCST-------------DIP--NQLLRVVKDLKGHPLDKNARYFIVSAFNGAGGGGVRLANLGGQEENTCLT-SVVQSPRDTDEGIAVYFKPKEPK---H-QQIVESASLNINFYLD-YIK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLG---SSYKLVFCP-------YGETFTCHNVGIVNESGYRRLVLTENAKAFVFIKDCRVGKAEA-------------------------------------- Nicotiana_tabacum_TC86004 -------------------------------MKTVLLFLSLAFFPFSALATCST-------------DIP--NQLLRVVKDLKGHPLDKNARYFIVSAFNGAGGGGVRLANLGGQEENTCLT-SVVQSPRDTDEGIAVYFKPKEPK---H-QQIVESASLNINFYLD-YIK-CANLTVWKVDHYPKPAEHY-TISTGAKLAN--PLDVNSWFQIKSLG---SSYKLVFCP-------YGETFTCHNVGIVNESGYRRLVLTENAKAFVFIKDCRVGKAEA-------------------------------------- Nicotiana_tabacum_TC79402 --------------------------MKSFIFSFLLLSTTLSLLPFVVFSSSFTSTNPIVLPTTTADGKGFPIPVLPEVLDIDGEPLQIGEKYHIISAIWGSGGGGVYLTNLG---NTKCPN-GVVQHGRDTRPGMPVKFFTTHPGPPPF-NVVRETNNINIMFSVP-TSRLCVNETVWKVGDPDLTARGVRFVVTGGTLGNPGPETINSWFKIEKVTNTAPFYKLRYCPDK-VLCPMCHPVDCLDVGVTDHFGYRRLALTNQPFMVFFRKFQKTDG----------------------------------------- Nicotiana_tabacum_TC83180 --------------------------MKSFIFGFLLLSTTLSLLPFVVFSSSFTSTNHIVLPTTTDDDKVFPIPGFSEVLDINGEPLHVGEEYHIISAIRGAGGGGVYLTYVG---NTKCPN-GVLQHGRDTRPGMPVKFVTTHSR--PF-NVVRENTDINIMFSVS-TSRLCVNETVWKVGDPDLTTRGTRFVVTGGTLGNSRPETTNNWFKIEKVTKQAPFYKLRYCPDK-FLCPECHPVDCLDVGVTDHFGYRRLALTKQPFMVFFRKFQKTDG----------------------------------------- Nicotiana_benthamiana_TC17973 ----------------------------------------MVPFLLVALSTSSF---------FLVKAQDVP----EPVLDVSGNPVRTGVNYFILPAGR-GNGGGLQVASIR---NRTNPL-VVSQHADESSIGGYLQFSPVNPNE----NIIRISTDLNVKFTS---IHISDSSTVWRINTEII-PQ-RYLVTVGGVEGNPGRETLSNWFSIDRYE---DAYKLVYCP---GVCETC-RPFCGDIGILVEGSKRVLFLRF--DKPLKVTFHKI------------------------------------------- Nicotiana_tabacum_TC98053 -----------------------------MEIINVTR--FMVPFLLVALSTSFS---------FLVKAQDVP----EPVLDVSGNAVRTGVNYYILPAGR-GNGGGLQVASIR---NRTNPL-VVSQHADESSIGGYLQFSPANPNE----NIIGISTDLNVKFTS---IHISDSSTVWRINTEII-PQ-RYLVTVGGVEGNPGRETLSNWFKIDKYE---DAYKLVYCP---GVCETC-RPFCGEIGILVEGSKRVLFVRS--DQ?LKVTFHKI------------------------------------------- Nicotiana_tabacum_TC90991 ----------------------------MKMEVNVRRRLFMVHLILVALSTSLF---------CLVKAQDV--------LDVSGKDVRKGGYYRIIPAGR-GNGGGITVASIR---NRTNPL-VVSQHADESIISISTQFSPANSNE----NTIKISTDLNIKFTSE--ITLSNSSNVWRINTELI-PQ-RYLVTVGGVEGNPGRETLSNWFKIDKYE---DAYKLVYCP---GVCETCSRPFCGDIGILVEGNERVLFVGS--DKPLKVTFDCIKYWDETINNYTPCPSASISNKLSALPFVKVVIWIVICYLIKLM Nicotiana_benthamiana_TC17637 ----------------------------------------MKIISRILLLSCLL---------FLTLFQVKA----EPVLDTNKQEIRPGYTYYILPATT-ANGGGLTLAKGE---NGSCPL-DVFQAKNVQSTGLPLKFLMVNSSAG---LVIDENEDINIKFAAPRYVSICNKSTVWKIED--------GFVSTGGIKGGSENGTATSLFTIQKYE---DVYALQYCPRATGCSFICPRLLCGYIGISPAANGSRRLAVN--RPVFKIVFKKV------------------------------------------- Nicotiana_tabacum_TC79356 ----------------------------------------MKIISRILLLSCLL---------FLTLFQVKA----EPVLDTNKQEVRPGYTYYILPATTAANGGGLTLAKGE---NGSCPL-DVFQAQNVQSTGLPLKFLMVNSSAG---LVIDENEDINIKFAAPRYVSICNKSTVWKID---------GFVTTGGIKGGTENGTATSLFTIQKYE---DAYALQYCPRATGCSFICPRLLCGYIGIAPAANGSRRLAVN--RPVFKIVFKKA------------------------------------------- Nicotiana_tabacum_TC79198 ----------------------------------------MKIISRILLLSCLL---------FFALFQVKA----EPVLDTNKQEVRPGYSYYILPATTGANGGGLTLAKGE---NGSCPL-DVFQAQNVQSKGLPLKFLMVNSSSG---LVIDENEDINIKFAAPRYVSICNKTTVWKIED--------GFVTTGGIKGGSENGTATSLFTIQKYE---DAYALQYCPRATGCSFICPRLLCGYIGIAPANNGSRRLAVN--RPVFKILFQKA------------------------------------------- Nicotiana_benthamiana_GU183155 -----------------------------------MKTKQLFLPFLIFT?SFNS---------FLSSAAEAP----PAVVDIAGKKLRTGIDYYILPVVR-GRGGGLTLDSTG---NESCPLDAVVQEQKEINNGFPLTFTPVNPKK----GVIRESTDLNIKFSA---ASICVQTTLWKLDDFDE-TTGKYFITIGGNEGNPGRETISNWFKIEKFE---RDYKLVYCP---TVCNFC-KVICKDIGIFIQDG-TRRLALS--DVPFKVMFKKA------------------------------------------- Nicotiana_tabacum_TC92100 -----------------------------------MKTNQLFLPFLIFTISFNS---------FLSSAAEAP----PAVVDIAGKKLRTGIDYYILPVVR-GRGGGLTLDSTG---NESCPLDAVVQEQQEIKNGLPLTFTPVNPKK----GVIRESTDLNIKFSA---ASICVQTTLWKLDDFDE-TTGKYFITIGGNEGNPGRETISNWFKIEKFE---RDYKLVYCP---TVCNFC-KVICKDVGIFIQDG-IRRLALS--DVPFKVMFKKAQVVKD-------------------------------------- Nicotiana_tabacum_BP530541 -------------------------------MNILLLSFIL-LQSFAFSLANPS---------ELLSAGPSP----SPVLDTNGDKIRTGSNYFVLPVIR-GRGGGLFPSNVKQ--NNTCPR-DIIQESLEVQQGLPAVFTPVDPKK----GVTRLSSDLNVRFFTP---TICARETIWKVGDFDE-KLKQYFVVTGGVEGNPGPQTVSNWFEIEKLG---TDYKFVFCP---SVCSFC-R-------LFERFG-IL------------------------------------------------------------- Nicotiana_tabacum_TC80404 -------------------------------MNILLLSFIL-LQSFAFSLANPS---------ELLSAGPSP----SPVLDTNGDKIRTGSNYFVLPVIR-GRGGGLFPSNVKQ--NNTCPR-DIIQESLEVQQGLPVVFTPVDPKK----GVIRLSSDLNVRFFTP---TICARETIWKVGDFDE-KLKQYFVVTGGVEGNPGPQTVSNWFKIEKLG---TDYKFVFCP---SVCSFC-KVICKDVGIFTKNG-VRFLALS--DTPFRVMFKKTF------------------------------------------ Nicotiana_tabacum_TC79226 -------------------------------MNILLLSFIL-LQYFAFSLANPS---------ELVSAGPSP----SPVLDTNGDKIRAGSNYFVLPVIR-GRGGGLLPSNVKQ--NNSCPR-DIIQNSNEVQEGLPVVFTPVDPKK----GVIRLSTDLNVRFFTP---TICARETIWKLGTYDE-KLKQYFIVTGGVEGNPGPLTVSNWFKIEKLG---TDYKFVFCP---SVCTFC-KVICKDVGIYNKDG-VRFLALS--DTPFRVMFKRTF------------------------------------------ Nicotiana_tabacum_TC78758 -------------------------------MNTLLLLLSLSVIPIALCVPNPS---------RFL-AGSSP----SPVLDINGDKVKVGLNYFVLPVIR-GRGGGLLPSNVKQ--NNTCPR-DIIQNSDEVQEGLPVVFTPFNTKK----GVVRLSIDLNVRFFTP---TICARETIWKLGTYDD-KLKQYFIVTGGVEGNPGPQTLSSWFKIEKLG---TDYKFVFCP---SVCKIC-KVICKDVGIYTKDG-VRFLALS--DTPLRVMFKKTF------------------------------------------ Nicotiana_tabacum_TC81122 -------------------------------MNTLLLLLSLSIIPLALCIPNPS---------RFL-AGSSP----SPVLDINGDKVRVGSNYFVLPVIR-GRGGGLLPSNVKQ--INTCPR-DIIQNSDEVQQGLPVVFTPFDAKK----GVVRLSTDLNVRFYTP---TICARETIWKLGTYDD-KLKQYFIVTGGVEGNPGPQTVSSWFKIEKLG---TDYKFLFCP---SVCKIC-KVICKDVGIYTKDG-VRFLALS--DTPFRVMFKKTF------------------------------------------ Nicotiana_tabacum_TC81500 ------------------------------MKNLILCLSIVLFLPLAFSSNFSS---------NLILPSEVSSALYPSVLDTDGNPLKVGLRYFVLPILR-GTGGGLILSRVVDKNVKNCPQ-DIVQDPNELHLGRPVEFFPAYPSKT--GELILKNNPINVKFYSPSATSRCANFTVWKMDKK------YKYVVGRGKVGILNN--IRNWFRIQPYG---KGYRFVYCPTLCVPCKIKCSDLVISYEQQGDNADIRRLAASGNELPFSVQFKKA------------------------------------------- ; END; BEGIN LABELS; TAXAGROUPLABEL Nicotiana_tabacum COLOR = (RGB 0.01568627 0.43529412 0.01568627) ; TAXAGROUPLABEL Nicotiana_benthamiana COLOR = (RGB 0.36470588 0.86666667 0.02745098) ; END; BEGIN SETS; TAXPARTITION * UNTITLED = Nicotiana_tabacum : 1 - 8 10 - 11 13 - 14 16 - 22, Nicotiana_benthamiana : 9 12 15; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 318; END; BEGIN TREES; Title 'Nicotiana Mir comparison - bootstrapped dendrogram'; LINK Taxa = Taxa; TRANSLATE 1 Nicotiana_tabacum_TC80841, 2 Nicotiana_tabacum_TC82241, 3 Nicotiana_tabacum_FG638558, 4 Nicotiana_tabacum_FG639711, 5 Nicotiana_tabacum_TC92964, 6 Nicotiana_tabacum_TC86004, 7 Nicotiana_tabacum_TC79402, 8 Nicotiana_tabacum_TC83180, 9 Nicotiana_benthamiana_TC17973, 10 Nicotiana_tabacum_TC98053, 11 Nicotiana_tabacum_TC90991, 12 Nicotiana_benthamiana_TC17637, 13 Nicotiana_tabacum_TC79356, 14 Nicotiana_tabacum_TC79198, 15 Nicotiana_benthamiana_GU183155, 16 Nicotiana_tabacum_TC92100, 17 Nicotiana_tabacum_BP530541, 18 Nicotiana_tabacum_TC80404, 19 Nicotiana_tabacum_TC79226, 20 Nicotiana_tabacum_TC78758, 21 Nicotiana_tabacum_TC81122, 22 Nicotiana_tabacum_TC81500; TREE 'PHYLIP 1+' = (22:0.36189,((((4:0.02836,(3:0.0025,(1:2.9E-4,2:0.00417)731:0.00197)1000:0.02878)851:0.02803,(5:0.0013,6:0.00338)1000:0.06222)1000:0.28337,(7:0.06794,8:0.07668)1000:0.22499)976:0.0571,((11:0.1174,(9:0.02441,10:0.04092)1000:0.05032)1000:0.22528,(14:0.03414,(12:0.022,13:0.018)853:0.01302)1000:0.27856)730:0.02856)273:0.00583,((15:0.01846,16:0.01568)1000:0.21173,((19:0.0525,(17:0.04107,18:0.01298)995:0.0362)973:0.03608,(20:0.03587,21:0.03112)1000:0.07044)1000:0.1602)836:0.03861)TRICHOTOMY[% ] [%unrooted = on ]; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 318; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 318; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1334194180284; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 9166065114063892241; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8060334191267439901; mqVersion 275; checksumv 0 3 3250750902 null getNumChars 318 numChars 318 getNumTaxa 22 numTaxa 22 short false bits 1048575 states 1048575 sumSquaresStatesOnly 5.5856940275893E13 sumSquares 5.5856940275893E13 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 700 464; setLocation 8 8; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; desuppress; endTell; endTell; end;