#NEXUS [written Mon Mar 13 13:00:39 EDT 2017 by Mesquite version 3.2 (build 801) at ag-plp-11ba0tj.ag.cornell.edu/132.236.30.46] BEGIN TAXA; TITLE Taxa; DIMENSIONS NTAX=16; TAXLABELS Puccinia_hordei_AY187089 Puccinia_graminis_f.sp._avenae_DQ460727 Puccinia_sp._Alder_Buckthorn_CT 'Puccinia hordei-secalini DQ460723' Puccinia_recondita_AY187088 Puccinia_striiformis_GQ457304 Puccinia_coronata_KC305496 Puccinia_coronata_DQ355443 Puccinia_coronata_DQ355449 Puccinia_brachypodii_GQ457303 Puccinia_triticina_DQ417418 Uromyces_scillarum_AY302495 Puccinia_bromina_DQ460719 'Puccinia cerinthes-agropyrina DQ460720' Uromyces_aemulus_AF511081 Puccinia_persistens_DQ460722 ; END; BEGIN CHARACTERS; TITLE 'ITS_Nearest matches in GenBank_alignment'; DIMENSIONS NCHAR=1263; FORMAT DATATYPE = DNA INTERLEAVE GAP = - MISSING = ?; MATRIX Puccinia_hordei_AY187089 TAAAAGAACTAGAGTGCACTTTATTGTGGCTCGACCCCTTTTTTAAAT-- Puccinia_graminis_f.sp._avenae_DQ460727 TAAAAGAATTAGAGTGCACTTTATTGTGGCTCAACTCTCTTAT-AAAC-- Puccinia_sp._Alder_Buckthorn_CT TAAAAGAA-TAGAGTGCACTTGATTGTGGCTCGACCCCT--TTTACCA-- 'Puccinia hordei-secalini DQ460723' TAAAAGAACTAGAGTGCACTTAATTGTGGCTCGACCCCTTTT--AAAT-- Puccinia_recondita_AY187088 TAAAAGAACTAGAGTGCACTTTATTGTGGCTCAACCCCTTTT--AAAT-- Puccinia_striiformis_GQ457304 TAAAAGAACTAGAGTGCACTTTATTGTGGCTCGACCCCTTT----TAT-- Puccinia_coronata_KC305496 TAAAAGAA-TAGAGTGCACTTTATTGTGGCTCGACCCCCCTTTTATAAAC Puccinia_coronata_DQ355443 TAAAAGAA-TAGAGTGCACTTGATTGTGGCTCGACCCCT--TTTATAA-- Puccinia_coronata_DQ355449 TAAAAGAA-TAGAGTGCACTTGATTGTGGCTTGACCCCC-TTTTATA--- Puccinia_brachypodii_GQ457303 TAAAAGAACTAGAGTGCACTTTATTGTGGCTCGACCCTTTTAA-ACAA-- Puccinia_triticina_DQ417418 TAAAAGAACTAGAGTGCACTTAATTGTGGCTCGACCCCTTTT--AAAT-- Uromyces_scillarum_AY302495 TAAAAGAATTAGAGTGCACTTTATTGTGGCTCGACCCCTTTTTTAAAC-- Puccinia_bromina_DQ460719 TAAAAGAACTAGAGTGCACTTCATTGTGGCTCGACCCCTTTT--AAAT-- 'Puccinia cerinthes-agropyrina DQ460720' TAAAAGAACTAGAGTGCACTTTATTGTGGCTCGACCCCTTTT--AAAT-- Uromyces_aemulus_AF511081 TAAAAGAAACAGAGTGCACTTTATTGTGGCTCAACCCCTTTT--AAAT-- Puccinia_persistens_DQ460722 TAAAAGAACTAGAGTGCACTTAATTGTGGCTCGACCCCTTTT--AAAT-- Puccinia_hordei_AY187089 -CTTACCCAAAT--TAACTAAGACTTTTTTGCATGATTTGAAAGAATCAT Puccinia_graminis_f.sp._avenae_DQ460727 -CAAACCCAAACACTTTTAAAAACTTGGTTGCATGACTGTCAAAGGTCAT Puccinia_sp._Alder_Buckthorn_CT -TTCACCCAACTT-AAA----GACTTGGTTGCATGATTTGAAAGAATCAT 'Puccinia hordei-secalini DQ460723' -CTTACCCAAA---CTTTTAACACTTCTTTGCATGATTTGAAAGAGTCAT Puccinia_recondita_AY187088 -CTTACCCAACT--TTACCAAGACTTCTTTGCATGATTTGAAAAGATCAT Puccinia_striiformis_GQ457304 -TCCACCCAAACT-T--TTAAGACTTGGTTGCATGATTTGAAAGAATCAT Puccinia_coronata_KC305496 CTTCACCCAAACC-CAAA---CACTTGTTTGCATGATTTGAAAGAGTCAT Puccinia_coronata_DQ355443 -TTCACCCAACTT-AAAAAAAGACTTGGTTGCATGATTTGAAAGAATCAT Puccinia_coronata_DQ355449 -TTCACCCAAACC-CAAA---CACTTGTTTGCATGATTTGAAAGGGTCAT Puccinia_brachypodii_GQ457303 -CTCACCCAAACA-CCATTAAGACTTGGTTGCATGATTTGAAAAAGTCAT Puccinia_triticina_DQ417418 -CTTACCCAAA---CTTTTAACACTTCTTTGCATGATTTGAAAGAATCAT Uromyces_scillarum_AY302495 -C--ACCC------TAACTAAGACTTTTTTGCATGATTTGAAAGAATCAT Puccinia_bromina_DQ460719 -CTTACCCAAAA--CTTTTAAAACTTCTTTGCATGATTTGAAAGAATCAT 'Puccinia cerinthes-agropyrina DQ460720' -CTTACCCAAAA--CTTTTAAAACTTCTTTGCATGATTTGAAAGAATCAT Uromyces_aemulus_AF511081 -CTTACCCAAA---CATTTAAAGCTTCTTTGCATGATTTGAAAGGATCAT Puccinia_persistens_DQ460722 -CTTACCCAAA---CTTTTAACACTTCTTTGCATGATTTGAAAGAATCAT Puccinia_hordei_AY187089 TGTGACTAAGTAGACGTAAC---TTCTTAATT-------GAATGTT-GCA Puccinia_graminis_f.sp._avenae_DQ460727 TGCAATTGAGTATACGTAAC--ATTCTTAATT-------GAATTGTTGCA Puccinia_sp._Alder_Buckthorn_CT TGCAATTGAGTATACGTAAC-GTCCTTTTATTA-----GGAGAGTT-ACA 'Puccinia hordei-secalini DQ460723' TGTGATTAAGTATACGTGGC--ATTCTTTATT-------GAATGTTCACA Puccinia_recondita_AY187088 TGTGATTAAGTATACGTAAT--ATTCTTTACT-------GAATGTT-ACA Puccinia_striiformis_GQ457304 TGCAATTGAGTAGACGTAAC---TTCTTTATT-------GAATGTT-GCA Puccinia_coronata_KC305496 TGCAATCAAGTATACGTAGCTGCCTTTT-ATTA-----GGAAAGTT-ACA Puccinia_coronata_DQ355443 TGCAATTGAGTATACGTAAC-GTCCTTTTATTA-----GGAGAGTT-ACA Puccinia_coronata_DQ355449 TGCAATCAAGTATACGTAGCTGCCTTTTTATTAA----GGAAAGTT-ACA Puccinia_brachypodii_GQ457303 TGCAATTGAGTAGACGTAAC---TTCTTGATT-------GAATGTT-GCA Puccinia_triticina_DQ417418 TGTGATTAAGTATACGTGGC--ATTCTTTATT-------GAATGTTCACA Uromyces_scillarum_AY302495 TGTGACTAAGCAGACGTAAC---TTCTTAATT-------GAATGTT-GCA Puccinia_bromina_DQ460719 TGTGATTAAGTATACGTGAC---TTTTT-ACATTTGTAAAAATGTT-GCA 'Puccinia cerinthes-agropyrina DQ460720' TGTGATTAAGTATACGTGAC---TTTTTTACATTTGTAAAAATGTT-GCA Uromyces_aemulus_AF511081 TGTGATTAAGTATACGTAAC---TTCTTTACT-------GAATGTT-ACA Puccinia_persistens_DQ460722 TGTGATTAAGTATACGTGGC--ATTCTTTATT-------GAATGTTCACA Puccinia_hordei_AY187089 TTACCCCCCCTCCTTTTTT------TTTTTTTATTATT---ATTAACACA Puccinia_graminis_f.sp._avenae_DQ460727 TTACCCCCCCTCCCTTTTATTTTTATTTTTTTTTT-------TAAACACA Puccinia_sp._Alder_Buckthorn_CT TTACCCCC--TTATTTTTATTTTCACCCCCCCTTTATT---ATATACACA 'Puccinia hordei-secalini DQ460723' TTACCCCCCC-TCTTTTCTATTTTTTTTTTTTTTTTTTTAAAGTAACACA Puccinia_recondita_AY187088 TTACCCCCCC-TCTTTTC--------TTTATA-------AAAAAAACACA Puccinia_striiformis_GQ457304 TTACCCTCCCTTTTTTTTTTT----TTTTTTTTTATTCACCAAAAACACA Puccinia_coronata_KC305496 TTACCCTTCATTAATTT--TTATATCCCCCCCTTTATT---ATATACACA Puccinia_coronata_DQ355443 TTACCCCC--TTATTTTTATTTTCACCCCCCCTTTATT---ATATACACA Puccinia_coronata_DQ355449 TTACCCTTTATTAATTATATCCTTCCCCCCCCTTTATT---ATATACACA Puccinia_brachypodii_GQ457303 TTACCCCCCCCTTTAATTTTT----TTTATTTTTATA-AATATAAACACA Puccinia_triticina_DQ417418 TTACCCCCCC-TCTTTTCTATTTTTTTTTTTTTAA-------GTAACACA Uromyces_scillarum_AY302495 TTACCCCCCCTCCTTTTCT------TTTTTTGATTATT---ATTAACACA Puccinia_bromina_DQ460719 TTACCCCCCCCTCTTTTCTA------TTTTT---------AATAAACACA 'Puccinia cerinthes-agropyrina DQ460720' TTACCCCCCCCTCTTTTCTA------TTTTTTTTTTTA--AATAAACACA Uromyces_aemulus_AF511081 TTACCCCCCCCTCTGTTCAAATTTTTTTTTTTTTTTTT--AATAAACACA Puccinia_persistens_DQ460722 TTACCCCCCC-TCTTTTCTATTTTTTTTTTTTTAAT----AAGTAACACA Puccinia_hordei_AY187089 AGTTTAAATGAATGTAAAACAA-CCTTTAAATTATATA-TAACTTTTAAC Puccinia_graminis_f.sp._avenae_DQ460727 AGTTTAAATGAATGTAACCAAA-CCTTTAATTTATAAA-TAACTTTTAAC Puccinia_sp._Alder_Buckthorn_CT AGTTTAAATGAATGTAAAACCCCC-TTTAAATTAAA--ATAACTTTTAAC 'Puccinia hordei-secalini DQ460723' AGTTTAAATGAATGTAAAACAA-CCTTTAAATTATAAA-TAACTTTTAAC Puccinia_recondita_AY187088 AGTTTAAATGAATGTAAAACAAACCTTTAAATTATAAA-TAACTTTTAAC Puccinia_striiformis_GQ457304 AGTTTAAATGAATGTAACCAAA-CCTTTAA-TTATAAAATAACTTTTAAC Puccinia_coronata_KC305496 AGTTTAAATGAATGTAAAACCCCCCTTTAAATTAAA--ATAACTTTTAAC Puccinia_coronata_DQ355443 AGTTTAAATGAATGTAAAACCCCC-TTTAAATTAAA--ATAACTTTTAAC Puccinia_coronata_DQ355449 AGTTTAAATGAATGTAAAACCCCC-TTTAAATTAAAAAATAACTTTTAAC Puccinia_brachypodii_GQ457303 AGTTTAAATGAATGTAACCAAA-CCTTTAA-TTATAAA-TAACTTTTAAC Puccinia_triticina_DQ417418 AGTTTAAATGAATGTAAAACAA-CCTTTAAATTATAAA-TAACTTTTAAC Uromyces_scillarum_AY302495 AGTTTAAATGAATGTAAAACAA-CCTTTAAATTATATA-TAACTTTTAAC Puccinia_bromina_DQ460719 AGTTTAAATGAATGTAAAAAA--TCTTTAAATTATAAA-TAACTTTTAAC 'Puccinia cerinthes-agropyrina DQ460720' AGTTTAAATGAATGTAAAAAA--TCTTTAAATTATAAA-TAACTTTTAAC Uromyces_aemulus_AF511081 AGTTTAAATGAATGTAAAAAAAACCTTTAAATTATAAA-TAACTTTTAAC Puccinia_persistens_DQ460722 AGTTTAAATGAATGTAAAACAA-CCTTTAAATTATAAA-TAACTTTTAAC Puccinia_hordei_AY187089 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_graminis_f.sp._avenae_DQ460727 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_sp._Alder_Buckthorn_CT AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA 'Puccinia hordei-secalini DQ460723' AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_recondita_AY187088 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_striiformis_GQ457304 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_coronata_KC305496 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_coronata_DQ355443 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_coronata_DQ355449 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_brachypodii_GQ457303 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGCGAAATGTGATA Puccinia_triticina_DQ417418 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Uromyces_scillarum_AY302495 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_bromina_DQ460719 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA 'Puccinia cerinthes-agropyrina DQ460720' AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Uromyces_aemulus_AF511081 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_persistens_DQ460722 AATGGATCTCTAGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATA Puccinia_hordei_AY187089 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_graminis_f.sp._avenae_DQ460727 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_sp._Alder_Buckthorn_CT AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC 'Puccinia hordei-secalini DQ460723' AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_recondita_AY187088 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_striiformis_GQ457304 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC Puccinia_coronata_KC305496 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC Puccinia_coronata_DQ355443 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC Puccinia_coronata_DQ355449 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC Puccinia_brachypodii_GQ457303 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACC Puccinia_triticina_DQ417418 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Uromyces_scillarum_AY302495 AGTAATGTGAATTGCAGAATTCAGTGAATCATTGAATCTTTGAACGCATC Puccinia_bromina_DQ460719 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC 'Puccinia cerinthes-agropyrina DQ460720' AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Uromyces_aemulus_AF511081 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_persistens_DQ460722 AGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATC Puccinia_hordei_AY187089 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_graminis_f.sp._avenae_DQ460727 TTGCACCTTTTGGTATTCCAAAAGGTACACCTGTTTGAGTGTCATGAAAC Puccinia_sp._Alder_Buckthorn_CT TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC 'Puccinia hordei-secalini DQ460723' TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGCGTCATGAAAC Puccinia_recondita_AY187088 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_striiformis_GQ457304 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_coronata_KC305496 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_coronata_DQ355443 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_coronata_DQ355449 TTGCGCCTTTTGGTATTCCAAGAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_brachypodii_GQ457303 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_triticina_DQ417418 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Uromyces_scillarum_AY302495 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_bromina_DQ460719 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC 'Puccinia cerinthes-agropyrina DQ460720' TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Uromyces_aemulus_AF511081 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_persistens_DQ460722 TTGCGCCTTTTGGTATTCCAAAAGGCACACCTGTTTGAGTGTCATGAAAC Puccinia_hordei_AY187089 CCTCTCATTAAACCATTTTGTTCTTGAACAAGATAGTTTAGTGGATGTTG Puccinia_graminis_f.sp._avenae_DQ460727 CCTCTCATTAAACATTTTATTTTT------GATTTGTTTAGTGGATGTTG Puccinia_sp._Alder_Buckthorn_CT CCTCTCACAAAACAACTTTATTGT-------TGCTTTTTTGTGGATGTTG 'Puccinia hordei-secalini DQ460723' CCTCTCATTAAACATTTTTTAACTTGCTTAAACTTGTTTAGTGGATGTTG Puccinia_recondita_AY187088 CCTCTCATTAAACATTTTCTTTCTTTGAAAGATTTGTTTAGTGGATGTTG Puccinia_striiformis_GQ457304 CCTCTCATTAAATAATTTTGATT------AATTATTTTCAATGGATGTTG Puccinia_coronata_KC305496 CCCCTCACAAAACAACTTTATTGT-------TGCT---TTGTGGATGTTG Puccinia_coronata_DQ355443 CCTCTCACAAAACAACTTTATTGT-------TGCTTTTTTGTGGATGTTG Puccinia_coronata_DQ355449 CCTCTCACAAAATAACTTTATTGT-------TGCT---TTGTGGATGTTG Puccinia_brachypodii_GQ457303 CCTCTCATTAAATAATTTTGATT------AATTATTTTCAATGGATGTTG Puccinia_triticina_DQ417418 CCTCTCATTAAACATTTTTTAACTTGTTTAAACTTGTTTAGTGGATGTTG Uromyces_scillarum_AY302495 CCTCTCATTAAACCATTTTGTTCTTGAACAAGATAGTTTAGTGGATGTTG Puccinia_bromina_DQ460719 CCTCTCATTAAATATTTTT-------------CATATTTAATGGATGTTG 'Puccinia cerinthes-agropyrina DQ460720' CCTCTCATTAAAAATTTTTTTTTTTGTTAAATCATATTTAATGGATGTTG Uromyces_aemulus_AF511081 CCTCTCATTAAACAATTTTGT----AAAAGAAACTGTTTAGTGGATGTTG Puccinia_persistens_DQ460722 CCTCTCATTAAACATTTTTTAACTTGTTTAAACTTGTTTAGTGGATGTTG Puccinia_hordei_AY187089 AGTGTTGCTGTC----ATTA--GCTCACTTTAAATATATCAGTTACTT-- Puccinia_graminis_f.sp._avenae_DQ460727 AGTGTTGCTGTA----CCTATAGCTCACTTTAAATATATAAGTCACTT-- Puccinia_sp._Alder_Buckthorn_CT AGTGTTGCTATATTGTT--ATAGCTCACTTTAAATATATAAGTCACAC-- 'Puccinia hordei-secalini DQ460723' AGTGTTGCTGTC----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Puccinia_recondita_AY187088 AGTGTTGCTGTA----ATTA--GCTCACTTTAAATATATCAGTCACTT-- Puccinia_striiformis_GQ457304 AGTGCTGCTGTT----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Puccinia_coronata_KC305496 AGTGTTGCTATATAATATTATAGCTCACTTTAAATATATAAGTCACACAC Puccinia_coronata_DQ355443 AGTGTTGCTATATTTTTTTATAGCTCACTTTAAATATATAAGTCACAC-- Puccinia_coronata_DQ355449 AGTGTTGCTATATAAAATTATAGCTCACTTTAAATATATAAGTCACACAC Puccinia_brachypodii_GQ457303 AGTGTTGCTGTA----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Puccinia_triticina_DQ417418 AGTGTTGCTGTC----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Uromyces_scillarum_AY302495 AGTGTTGCTTTT----GTTA--GCTCGCTTTAAATATATCAGTTACTT-- Puccinia_bromina_DQ460719 AGTGTTGCTGTA----ATTA--GCTCACTTTAAATATATAAGTCACTT-- 'Puccinia cerinthes-agropyrina DQ460720' AGTGTTGCTGTA----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Uromyces_aemulus_AF511081 AGTGTTGCTGTA----ATTA--GCTCACTTTAAATAAATAAGTCACTT-- Puccinia_persistens_DQ460722 AGTGTTGCTGTC----ATTA--GCTCACTTTAAATATATAAGTCACTT-- Puccinia_hordei_AY187089 --T--TCAAATGAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_graminis_f.sp._avenae_DQ460727 --T--TCAAATAAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_sp._Alder_Buckthorn_CT --TTTTCAAGTAAGTTGGATTGACTTGGTGT-AATAAT-TTTCCATCATC 'Puccinia hordei-secalini DQ460723' --T--TCAAATAAGTTGGATTGACTTGGGGT-AATAAT-TTTAT--CATC Puccinia_recondita_AY187088 --T--TCAAATGAGTTGGATTGACTTGGTGTTAATAAT-TTTATATCATC Puccinia_striiformis_GQ457304 --T--TCAAATAAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_coronata_KC305496 ACTCTTCAAGTAAGTTGGATTGACTTGGTGT-AATAA---TTTAATCATC Puccinia_coronata_DQ355443 --TTTTCAAGTAAGTTGGATTGACTTGGTGT-AATAAT-TT--CATCATC Puccinia_coronata_DQ355449 --TCTTCAAGTAAGTTGGATTGACTTGGTGT-AATAATATTTTAATCATC Puccinia_brachypodii_GQ457303 --T--TCAA-TAAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_triticina_DQ417418 --T--TCAAATAAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Uromyces_scillarum_AY302495 --TTTTCAAATGAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_bromina_DQ460719 --T--TCTAATGAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC 'Puccinia cerinthes-agropyrina DQ460720' --T--TCTAATGAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Uromyces_aemulus_AF511081 --T--TCAAATGAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_persistens_DQ460722 --T--TCAAATAAGTTGGATTGACTTGGTGT-AATAAT-TTTAT--CATC Puccinia_hordei_AY187089 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTGTTTAAATAAA----- Puccinia_graminis_f.sp._avenae_DQ460727 ACATCAAGGAAAGTAGTAAAACACTTGCCATCTTGTTTGTTAATA----- Puccinia_sp._Alder_Buckthorn_CT ACATCAAGGAAAGTAGC--AATACTTGCCATCTT--TTGAAAGG------ 'Puccinia hordei-secalini DQ460723' ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTTAATATG----- Puccinia_recondita_AY187088 ACATTAAGGAAAGTAGCAA--TACTTGCCATCTTA-TTTAATGAA----- Puccinia_striiformis_GQ457304 ACATCAAGGATTGTAGCAA--TACT-GCCATCTTA-TT---GAAG----- Puccinia_coronata_KC305496 ACATCAAGGAAAGTAGTCAAATACTTGCCATCTT--TTGAAAGGGGAGAG Puccinia_coronata_DQ355443 ACATCAAGGAAAGTAGC--AATACTTGCCATCTT--TTGAAAGG------ Puccinia_coronata_DQ355449 ACATCAAGGAAAGTAGTCAAATACTTGCCATCTT--TTGAAAGGGGAGAG Puccinia_brachypodii_GQ457303 ACATCAAGGAAAGTAGTAA--TACT-GCCATCTTG-TTTCTGAAA----- Puccinia_triticina_DQ417418 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTGAATATA----- Uromyces_scillarum_AY302495 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTC--TAAAAAAAA----- Puccinia_bromina_DQ460719 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTAAAAG------- 'Puccinia cerinthes-agropyrina DQ460720' ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTAAAAG------- Uromyces_aemulus_AF511081 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTGAATG------- Puccinia_persistens_DQ460722 ACATCAAGGAAAGTAGCAA--TACTTGCCATCTTG-TTTAATATG----- Puccinia_hordei_AY187089 AGGGACTTCTAAAAA-CC--CAATTAATTATTTTT--TAAGACCTCAAAT Puccinia_graminis_f.sp._avenae_DQ460727 AGAGACTCCTAAAACCCAA-TATCTTATT------TTTAAGACCTCAAAT Puccinia_sp._Alder_Buckthorn_CT AGGGACTCCTAAAAAA---CCCCTCATAACACTTTTTTAAGACCTCAAAT 'Puccinia hordei-secalini DQ460723' AGG-ACTTCTAAAACCCC--CCTTTTTT---AAAATTTAAGACCTCAAAT Puccinia_recondita_AY187088 AGAGACTTCTAAAGAACCATACTTTTTTT-----ACTTAAGACCTCAAAT Puccinia_striiformis_GQ457304 GGAGACTCCTAAAAAACCCCCTTTTTTTT-----TT--AAGACCTCAAAT Puccinia_coronata_KC305496 AGGGACTTCTAAAAAAAA-CCCCATACATACAATATTTAAGACCTCAAAT Puccinia_coronata_DQ355443 AGGGACTCCTAAAAAAA--CCCCTCATAACACTTTTTTAAGACCTCAAAT Puccinia_coronata_DQ355449 AGGGACTTCTAAAA-----CCCCATTTTAAATAT-TTTAAGACCTCAAAT Puccinia_brachypodii_GQ457303 GGAGACTCCTAAAAAACCCTCTTTTTTTT-----TTTTAAGACCTCAAAT Puccinia_triticina_DQ417418 AGGGACTTCTAAAAACCC--CCCTTTTTTCCAAAATTTAAGACCTCAAAT Uromyces_scillarum_AY302495 AGGGACTTCTAAAAAACC--CAATTAATTATTATTATTAAGACCTCAAAT Puccinia_bromina_DQ460719 -G-GACTCCTAAAAAA----CCCCCTATT-TACATTTTAAGACCTCAAAT 'Puccinia cerinthes-agropyrina DQ460720' -G-GACTCCTAAAAAAAC--CCCCCTATT-TACATTTTAAGACCTCAAAT Uromyces_aemulus_AF511081 -GAGACTTCTAAAAAAAAAACCCCCCATGATACATTTTAAGACCTCAAAT Puccinia_persistens_DQ460722 AGGGACTTCTAAAAACCC--CCCCTTTTAT-AAAATTTAAGACCTCAAAT Puccinia_hordei_AY187089 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_graminis_f.sp._avenae_DQ460727 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_sp._Alder_Buckthorn_CT CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG 'Puccinia hordei-secalini DQ460723' CAGGTGG-ACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_recondita_AY187088 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_striiformis_GQ457304 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_coronata_KC305496 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_coronata_DQ355443 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_coronata_DQ355449 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_brachypodii_GQ457303 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_triticina_DQ417418 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Uromyces_scillarum_AY302495 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_bromina_DQ460719 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG 'Puccinia cerinthes-agropyrina DQ460720' CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Uromyces_aemulus_AF511081 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_persistens_DQ460722 CAGGTGGGACTACCCGCTGAACTTAAGCATATCAATAAGCGGAGGAAAAG Puccinia_hordei_AY187089 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_graminis_f.sp._avenae_DQ460727 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_sp._Alder_Buckthorn_CT AAACTAACAAGGATTCCCCCAGTAACGGCGAGTGAAGAGGGAAAAGCCCA 'Puccinia hordei-secalini DQ460723' AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_recondita_AY187088 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_striiformis_GQ457304 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_coronata_KC305496 AAACTAACAAGGATTCCCCCAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_coronata_DQ355443 AAACTAACAAGGATTCCCCCAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_coronata_DQ355449 AAACTAACAAGGATTCCCCCAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_brachypodii_GQ457303 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_triticina_DQ417418 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Uromyces_scillarum_AY302495 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_bromina_DQ460719 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA 'Puccinia cerinthes-agropyrina DQ460720' AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Uromyces_aemulus_AF511081 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_persistens_DQ460722 AAACTAACAAGGATTCCCCTAGTAACGGCGAGTGAAGAGGGAAAAGCCCA Puccinia_hordei_AY187089 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_graminis_f.sp._avenae_DQ460727 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTAAGAACTGT Puccinia_sp._Alder_Buckthorn_CT AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT 'Puccinia hordei-secalini DQ460723' AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_recondita_AY187088 AATTTGTAATCTGGCTCTTTCAGGGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_striiformis_GQ457304 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_coronata_KC305496 AATTTGTAATCTGGCTCTTTTAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_coronata_DQ355443 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_coronata_DQ355449 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_brachypodii_GQ457303 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTAAGAACTGT Puccinia_triticina_DQ417418 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Uromyces_scillarum_AY302495 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_bromina_DQ460719 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT 'Puccinia cerinthes-agropyrina DQ460720' AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Uromyces_aemulus_AF511081 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_persistens_DQ460722 AATTTGTAATCTGGCTCTTTCAGAGTCCGAGTTGTAATTTTGAGAACTGT Puccinia_hordei_AY187089 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_graminis_f.sp._avenae_DQ460727 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_sp._Alder_Buckthorn_CT TTTCAGTGCTGGACCATATATAAGTCTGTTGAAAAGCAGCATCATTGAGG 'Puccinia hordei-secalini DQ460723' TTTCAGTGCTGGACCATGTACAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_recondita_AY187088 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_striiformis_GQ457304 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_coronata_KC305496 TTTCAGTGCTGGACCATATATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_coronata_DQ355443 TTTCAGTGCTGGACCATATATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_coronata_DQ355449 TTTCAGTGCTGGACCATATATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_brachypodii_GQ457303 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_triticina_DQ417418 TTTCAGTGCTGGACCATGTACAAGTCTGTTGAAAAGCAGCATCATTGAGG Uromyces_scillarum_AY302495 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_bromina_DQ460719 TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG 'Puccinia cerinthes-agropyrina DQ460720' TTTCAGTGCTGGACCATGTATAAGTCTGTTGAAAAGCAGCATCATTGAGG Uromyces_aemulus_AF511081 TTTCAGTGCTGGACCATGTACAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_persistens_DQ460722 TTTCAGTGCTGGACCATGTACAAGTCTGTTGAAAAGCAGCATCATTGAGG Puccinia_hordei_AY187089 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_graminis_f.sp._avenae_DQ460727 GTGATAATCCCGTTTATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_sp._Alder_Buckthorn_CT GTGATAATCCCGTTTATGATATGGACTCCCAGTGCAATATGATACAGTCT 'Puccinia hordei-secalini DQ460723' GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_recondita_AY187088 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_striiformis_GQ457304 GTGATAATCCCGTTTATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_coronata_KC305496 GTGATAATCCCGTTTATGATATGGACTCCCAGTGCAATATGATACAGTCT Puccinia_coronata_DQ355443 GTGATAATCCCGTTTATGATATGGACTCCCAGTGCAATATGATACAGTCT Puccinia_coronata_DQ355449 GTGATAATCCCGTTTATGATATGGACTCCCAGTGCAATATGATACAGTCT Puccinia_brachypodii_GQ457303 GTGATAATCCCGTTTATGATATGGACTACCAGTGCATTATGATACAGTTT Puccinia_triticina_DQ417418 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Uromyces_scillarum_AY302495 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_bromina_DQ460719 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT 'Puccinia cerinthes-agropyrina DQ460720' GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Uromyces_aemulus_AF511081 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_persistens_DQ460722 GTGATAATCCCGTTCATGATATGGACTACCAGTGCATTATGATACAGTCT Puccinia_hordei_AY187089 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_graminis_f.sp._avenae_DQ460727 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_sp._Alder_Buckthorn_CT CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC 'Puccinia hordei-secalini DQ460723' CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_recondita_AY187088 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_striiformis_GQ457304 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_coronata_KC305496 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_coronata_DQ355443 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_coronata_DQ355449 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_brachypodii_GQ457303 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_triticina_DQ417418 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Uromyces_scillarum_AY302495 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_bromina_DQ460719 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC 'Puccinia cerinthes-agropyrina DQ460720' CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Uromyces_aemulus_AF511081 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_persistens_DQ460722 CTAAGAGTCGAGTTGTTTGGGAATGCAGCTCAAAGTGGGTGGTAAATTCC Puccinia_hordei_AY187089 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_graminis_f.sp._avenae_DQ460727 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_sp._Alder_Buckthorn_CT ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG 'Puccinia hordei-secalini DQ460723' ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_recondita_AY187088 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_striiformis_GQ457304 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_coronata_KC305496 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_coronata_DQ355443 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_coronata_DQ355449 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_brachypodii_GQ457303 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_triticina_DQ417418 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Uromyces_scillarum_AY302495 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_bromina_DQ460719 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG 'Puccinia cerinthes-agropyrina DQ460720' ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Uromyces_aemulus_AF511081 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_persistens_DQ460722 ATCTAAGGCTAAATATAGGTGAGAGACCGATAGCAAACAAGTACCGTGAG Puccinia_hordei_AY187089 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_graminis_f.sp._avenae_DQ460727 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_sp._Alder_Buckthorn_CT GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT 'Puccinia hordei-secalini DQ460723' GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_recondita_AY187088 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_striiformis_GQ457304 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_coronata_KC305496 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_coronata_DQ355443 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_coronata_DQ355449 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_brachypodii_GQ457303 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_triticina_DQ417418 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Uromyces_scillarum_AY302495 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_bromina_DQ460719 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT 'Puccinia cerinthes-agropyrina DQ460720' GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Uromyces_aemulus_AF511081 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_persistens_DQ460722 GGAAAGATGAAAAGAACTTTGGAAAGAGAGTTAACAGTACGTGAAATTGT Puccinia_hordei_AY187089 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_graminis_f.sp._avenae_DQ460727 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_sp._Alder_Buckthorn_CT TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT 'Puccinia hordei-secalini DQ460723' TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_recondita_AY187088 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_striiformis_GQ457304 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_coronata_KC305496 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_coronata_DQ355443 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_coronata_DQ355449 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_brachypodii_GQ457303 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_triticina_DQ417418 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Uromyces_scillarum_AY302495 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_bromina_DQ460719 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT 'Puccinia cerinthes-agropyrina DQ460720' TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Uromyces_aemulus_AF511081 TAAAAGGGAAACAATTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_persistens_DQ460722 TAAAAGGGAAACACTTGAAGTTAGACTTGTTATTATTAGTTCAACCTTTT Puccinia_hordei_AY187089 ----GGGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_graminis_f.sp._avenae_DQ460727 TATTAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_sp._Alder_Buckthorn_CT C-TTAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG 'Puccinia hordei-secalini DQ460723' T--AAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Puccinia_recondita_AY187088 TTCAAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Puccinia_striiformis_GQ457304 T-CTAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Puccinia_coronata_KC305496 C-TAAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTA Puccinia_coronata_DQ355443 C-TTAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_coronata_DQ355449 C-TGAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_brachypodii_GQ457303 C-TTAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Puccinia_triticina_DQ417418 T--AAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Uromyces_scillarum_AY302495 ----GGGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_bromina_DQ460719 T--AAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG 'Puccinia cerinthes-agropyrina DQ460720' T--AAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Uromyces_aemulus_AF511081 ----AAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGAGTG Puccinia_persistens_DQ460722 T--AAAGGGAGTATTCTAATGATTAACAGACCAACATCAATTTTTGGGTG Puccinia_hordei_AY187089 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_graminis_f.sp._avenae_DQ460727 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_sp._Alder_Buckthorn_CT TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTCTGGCTGTGTTATAGTCC 'Puccinia hordei-secalini DQ460723' TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTCTGGCTGTGTTATAGTCC Puccinia_recondita_AY187088 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_striiformis_GQ457304 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTCTGACTGTGTTATAGTCC Puccinia_coronata_KC305496 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_coronata_DQ355443 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTCTGGCTGTGTTATAGTCC Puccinia_coronata_DQ355449 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_brachypodii_GQ457303 TTGGAGAAGGGTTTAAGGAAATGTAGCAGTCTCTGACTGTGTTATAGTCC Puccinia_triticina_DQ417418 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTCTGGCTGTGTTATAGTCC Uromyces_scillarum_AY302495 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_bromina_DQ460719 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTCTGACTGTGTTATAGTCC 'Puccinia cerinthes-agropyrina DQ460720' TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTCTGACTGTGTTATAGTCC Uromyces_aemulus_AF511081 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTTTGGCTGTGTTATAGTCC Puccinia_persistens_DQ460722 TTGGATAAGGGTTTAAGGAAATGTAGCAGTCTCTGGCTGTGTTATAGTCC Puccinia_hordei_AY187089 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_graminis_f.sp._avenae_DQ460727 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_sp._Alder_Buckthorn_CT TGAACTTTGATACAATGCTTAA---------------------------- 'Puccinia hordei-secalini DQ460723' TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_recondita_AY187088 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_striiformis_GQ457304 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_coronata_KC305496 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_coronata_DQ355443 TGAACTTTGATACAATGCTTAA---------------------------- Puccinia_coronata_DQ355449 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_brachypodii_GQ457303 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_triticina_DQ417418 TGAGCTTTGATACAATGCTTAA---------------------------- Uromyces_scillarum_AY302495 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_bromina_DQ460719 TGAGCTTTGATACAATGCTTAA---------------------------- 'Puccinia cerinthes-agropyrina DQ460720' TGAGCTTTGATACAATGCTTAA---------------------------- Uromyces_aemulus_AF511081 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_persistens_DQ460722 TGAGCTTTGATACAATGCTTAA---------------------------- Puccinia_hordei_AY187089 ------------- Puccinia_graminis_f.sp._avenae_DQ460727 ------------- Puccinia_sp._Alder_Buckthorn_CT ------------- 'Puccinia hordei-secalini DQ460723' ------------- Puccinia_recondita_AY187088 ------------- Puccinia_striiformis_GQ457304 ------------- Puccinia_coronata_KC305496 ------------- Puccinia_coronata_DQ355443 ------------- Puccinia_coronata_DQ355449 ------------- Puccinia_brachypodii_GQ457303 ------------- Puccinia_triticina_DQ417418 ------------- Uromyces_scillarum_AY302495 ------------- Puccinia_bromina_DQ460719 ------------- 'Puccinia cerinthes-agropyrina DQ460720' ------------- Uromyces_aemulus_AF511081 ------------- Puccinia_persistens_DQ460722 ------------- ; END; BEGIN PAUP; factory; set criterion = parsimony; END; BEGIN PAUP; outgroup DQ460723.1 / only; set root = outgroup outroot = paraphyl; set maxtrees = 10000 increase = auto autoclose = no torder = right tcompress = yes taxlabels = full storebrlens = yes storetreewts = yes; END; BEGIN PAUP; log file = Pc_alder_MP_ITS_Full_Nov9.log; set autoclose = yes; hsearch start = stepwise addseq = random nreps = 10000 savereps = yes randomize = addseq rstatus = yes hold = 1 swap = tbr multrees = yes; savetrees file = Pc_alder_MP_ITS_Full_Nov.all.tre brlen = yes; filter best = yes permdel = yes; savetrees file = Pc_alder_MP_ITS_Full_Nov.best.tre brlen = yes; log stop; END; begin paup; set storetreewts = yes; bootstrap nreps = 1000 treefile = Pc_alder_MP_ITS_Full_Nov.tre replace = no brlen = yes / start = stepwise addseq = random nreps = 100 savereps = no randomize = addseq hold = 1 swap = tbr multrees = yes; END; begin paup; gettrees allblocks = yes duptrees = keep storetreewts = yes storebrlens = yes mode = 7 file = Pc_alder_MP_ITS_Full_Nov.tre end; begin paup; log file = Pc_alder_MP_ITS_Full_Nov.log; contree / majrule = yes strict = no le50 = yes usetreewts = yes showtree = yes treefile = Pc_alder_MP_ITS_Full_Nov.bootstrap.tre grpfreq = yes; log stop; END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED = unord: 1 - 1263; END; BEGIN CODONS; CODESET * UNTITLED = universal: 1 - 1263; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1263; END; BEGIN TREES; Title 'ITS_GenBank_MJ consensus tree_MP analysis'; ID 015ac84fe8d123; LINK Taxa = Taxa; TRANSLATE [0] 1 Puccinia_hordei_AY187089, [1] 2 Puccinia_graminis_f.sp._avenae_DQ460727, [2] 3 Puccinia_sp._Alder_Buckthorn_CT, [3] 4 'Puccinia hordei-secalini DQ460723', [4] 5 Puccinia_recondita_AY187088, [5] 6 Puccinia_striiformis_GQ457304, [6] 7 Puccinia_coronata_KC305496, [7] 8 Puccinia_coronata_DQ355443, [8] 9 Puccinia_coronata_DQ355449, [9] 10 Puccinia_brachypodii_GQ457303, [10] 11 Puccinia_triticina_DQ417418, [11] 12 Uromyces_scillarum_AY302495, [12] 13 Puccinia_bromina_DQ460719, [13] 14 'Puccinia cerinthes-agropyrina DQ460720', [14] 15 Uromyces_aemulus_AF511081, [15] 16 Puccinia_persistens_DQ460722; TREE MajRule = ((((((1,12),((13,14),15)),((2,((3,8),(7,9))),(6,10))),5),(11,16)),4); END; BEGIN TREES; Title 'ITS_GenBank_MJ consensus tree_ML analaysis'; ID 015ac8576c1b24; LINK Taxa = Taxa; TRANSLATE [0] 1 Puccinia_hordei_AY187089, [1] 2 Puccinia_graminis_f.sp._avenae_DQ460727, [2] 3 Puccinia_sp._Alder_Buckthorn_CT, [3] 4 'Puccinia hordei-secalini DQ460723', [4] 5 Puccinia_recondita_AY187088, [5] 6 Puccinia_striiformis_GQ457304, [6] 7 Puccinia_coronata_KC305496, [7] 8 Puccinia_coronata_DQ355443, [8] 9 Puccinia_coronata_DQ355449, [9] 10 Puccinia_brachypodii_GQ457303, [10] 11 Puccinia_triticina_DQ417418, [11] 12 Uromyces_scillarum_AY302495, [12] 13 Puccinia_bromina_DQ460719, [13] 14 'Puccinia cerinthes-agropyrina DQ460720', [14] 15 Uromyces_aemulus_AF511081, [15] 16 Puccinia_persistens_DQ460722; TREE MajRule = (((((1,12),(((2,(6,10)),((3,8),(7,9))),(5,((13,14),15)))),16),11),4); END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1489424440262; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 7970756475599757860; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 4657631983459816777; mqVersion 320; checksumv 0 3 1303087691 null getNumChars 1263 numChars 1263 getNumTaxa 16 numTaxa 16 short true bits 15 states 15 sumSquaresStatesOnly 451597.0 sumSquares 451597.0 longCompressibleToShort false usingShortMatrix true NumFiles 1 NumMatrices 1; mqVersion; endTell; getWindow; tell It; suppress; setResourcesState false false 582; setPopoutState 300; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 1687 842; setLocation 116 281; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #7970756475599757860 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; setTreeBlockID 015ac84fe8d123; toggleUseWeights off; endTell; setAssignedID 2542.1489420085816.2115226042065683076; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1105 770; setLocation 116 281; setFont SanSerif; setFontSize 10; getToolPalette; tell It; 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 off; toggleEven off; setFixedTaxonDistance 0; endTell; setEdgeWidth 6; orientRight; setCornerMode Right_Angle 50; 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; togglePrintName on; 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; toggleShowOnTerminals 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; toggleShowOnTerminals on; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #4657631983459816777 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; getTable; tell It; rowNamesWidth 279; endTell; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 1105 770; setLocation 116 281; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam; endTell; setActive; 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.AlterData.AlterData; tell It; toggleBySubmenus off; 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 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;