#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on March 28, 2024; 14:46 GMT TreeBASE (cc) 1994-2008 Study reference: Guo L., Hyde K.D., & Liew E. 2001. Detection and taxonomic placement of endophytic fungi within frond tissues of Livistona chinensis based on rDNA sequences. Molecular Phylogenetics and Evolution, 20(1): 1-13. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S683] BEGIN TAXA; TITLE Taxa1; DIMENSIONS NTAX=21; TAXLABELS Botryosphaeria_dothidea Candida_glabrata Cladosporium_cladosporioides Cladosporium_fulvum Cladosporium_herbarum Cladosporium_oxysporum Cladosporium_sp. Cladosporium_sphaerospermum Cladosporium_tenuissimum Dothidea_hippophaeos Elsinoë_australis MS594 Mycosphaerella_graminicola Ophiosphaerella_herpotricha 'P4-5' 'P4-7' Phaeocryptopus_gaeumannii Phaeosphaeria_avenaria Pleospora_herbarum Saccharomyces_cerevisiae Torulaspora_delbrueckii ; END; BEGIN TAXA; TITLE Taxa2; DIMENSIONS NTAX=16; TAXLABELS 'Ceratobasidium oryzae-sativae' Cystofilobasidium_capitatum Gigaspora_albida Glomerella_graminicola Glomus_mosseae Hypocrea_rufa 'P1-9' Phaffia_rhodozyma Pleospora_herbarum Saccharomyces_cerevisiae Sorosporium_saponariae Sporisorium_sorghi Thanatephorus_cucumeris Ustilago_vaillantii Xanthophyllomyces_dendrorhous Xylaria_hypoxylon ; END; BEGIN TAXA; TITLE Taxa3; DIMENSIONS NTAX=14; TAXLABELS Amphisphaeria_umbrina Candida_glabrata Claviceps_purpurea Dothidea_hippophaeos Elsinoë_australis Gelasinospora_nigeriensis Glomerella_graminicola Hypocrea_rufa Ophiostoma_ulmi 'P2-6' Phaeocryptopus_gaeumannii Saccharomyces_cerevisiae Torulaspora_delbrueckii Xylaria_hypoxylon ; END; BEGIN TAXA; TITLE Taxa4; DIMENSIONS NTAX=20; TAXLABELS Candida_glabrata Capronia_coronata Capronia_pilosella Capronia_pulcherrima Coniosporium_perforans Dothidea_hippophaeos Elsinoe_australis Exophiala_jeanselmei Exophiala_spinifera Gelasinospora_nigeriensis Glomerella_graminicola Hypocrea_rufa 'P4-4' Phaeococcomyces_catenatus Phaeocryptopus_gaeumannii Rhinocladiella_atrovirens Saccharomyces_cerevisiae Torulaspora_delbrueckii Trimmatostroma_cordae Xylaria_hypoxylon ; END; BEGIN TAXA; TITLE Taxa5; DIMENSIONS NTAX=24; TAXLABELS Achlya_bisexualis Chlorella_ellipsoidea Cicer_reticulatum Eurotium_rubrum Gelasinospora_nigeriensis Ginkgo_biloba Glomerella_graminicola Glomus_mosseae Lentinula_edodes Lilium_parryi Morchella_crassipes Mycosphaerella_graminicola 'P1-9' 'P2-6' 'P3-2' 'P4-4' 'P4-5' 'P4-7' Phytophthora_ilicis Pleurotus_pulmonarius Pteridium_aquilinum Puccinia_caricina Tremella_foliacea Xylaria_hypoxylon ; END; BEGIN TAXA; TITLE Taxa6; DIMENSIONS NTAX=11; TAXLABELS Colletotrichum_acutatum Colletotrichum_coccodes Colletotrichum_fragariae Colletotrichum_musae Colletotrichum_orbiculare Elsinoë_australis Glomerella_cingulata Glomerella_graminicola Hypocrea_rufa 'P2-6' Saccharomyces_cerevisiae ; END; BEGIN TAXA; TITLE Taxa7; DIMENSIONS NTAX=21; TAXLABELS Colletotrichum_acutatum Colletotrichum_capsici Colletotrichum_coccodes Colletotrichum_dematium Colletotrichum_destructivum Colletotrichum_fragariae Colletotrichum_fuscum Colletotrichum_kahawae Colletotrichum_lindemuthianum Colletotrichum_linicola Colletotrichum_musae Colletotrichum_orbiculare Colletotrichum_sublineolum Colletotrichum_trichellum Colletotrichum_trifolii Elsinoë_australis Glomerella_cingulata Glomerella_graminicola Hypocrea_rufa 'P2-6' Saccharomyces_cerevisiae ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2265] TITLE 'ITS2 with P2-6'; LINK TAXA = Taxa6; DIMENSIONS NCHAR=171; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 ] [ . . . . . . . . . . . . . . . . . ] Colletotrichum_acutatum AACCCTCAAGCACCGCTTGGTTTTGGGG------CC-CCACGGCCGACGTGGGCCCTT---AAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAACTA--ACGTCTCGCACTGGG-ATCCGGAGGG-ACTCTTGCCGTTAAACCCCCAAATTTTTT----- Colletotrichum_coccodes AACCCTCAAGCTCTGCTTGGTGTTGGGG------CC-CTACGGTTGACGTAGGCCCTT---AAAGGTAGTGGCGGACCCTCTCGG-AGCCTCCTTTGCGTAGTAACTA--ACGTCTCGCACTGGG-ATTCGGAGGG-ACTCTTGCCGTAAAACCCCCAAATTTTTA----- Colletotrichum_fragariae AACCCTCAAGCTCTGCTTGGTGTTGGGG------CC-CTACAGCTGATGTAGGCCCTC---AAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAACTTT-ACGTCTCGCACTGGG-ATCCGGAGGG-ACTCTTGCCGTAAAACCCCCCAATTTTCC----- Colletotrichum_musae AACCCTCAAGCTCTGCTTGGTGTTGGGG------CC-CTACAGCACATGTAGGCCCTC---AAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAACTTT-ACGTCTCGCACTGGG-ATCCGGAGGG-ACTCTTGCCGTAAAACCCCCCAATTTTCC----- Colletotrichum_orbiculare AACCCTCAAGCACCGCTTGGCGTTGGGG------CTTCCACGGCTGACGTGGGCCCTC---AAAGACAGTGGCGGACCCTCGCGG-AGCCTCCTTTGCGTAGTAACATA-CAACCTCGCACCGGG-ACCCGCAGGGCACTCCTGCCGTAAAACCCCCCAATTTTTACAAGG Elsinoë_australis ACCAATCAAGCCCCGCTTGGTATTAGGCGCCTGGCCGCCCCCCCCGTGGCCGGCCCGCCCGAAATGCATCGGCGAGG---CACCG--ACCCCCGGCGTGTTAGAATTT---CGAAACGT-CAGGAGCACCGGTGTTAACCTCTGCCGTGAAACCTTTCAATTTTTCTAAG- Glomerella_cingulata AACCCTCAAGCTCTGCTTGGTGTTGGG-------CC-CTACAGCTGATGTAGGCCCTC---AAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAACTTT-TCGTCTCGCACTGGG-ATCCGGAGGG-ACTCTTGCCGTAAAACCCCCCAATTTTCCAAAGG Glomerella_graminicola AACCCTCAAGCTCTGCTTGGTGTTGGGG------CC-CTACGGTTGACGTAGGCCCTC---AAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAACT-A-ACGTCTCGCATCGGG-ATCCGGAGGG-ACTCTTGCCGTAAAACCCCCCAATTTTTCAATGG Hypocrea_rufa AACCCTCGAACCCCTCCGGGGGGTCGG-------CGTTGGGGACTTCGGGAACCCCTCCCGAAATACAGTGGCGGTC--TCGCCGCAGCCTCTCATGCGCAGTAGTTTGCACAACTCGCACCGGGAGCGCGGCGCGTCCACGT-CCGTAAAACACCCAACTTCTGAAATG- 'P2-6' AACCCTCAAGCTCTGCTTGGTGTTGGGG------CC-CTACAGCTGATGTAGGCCCTC---AAAGGTAGTCGCGAACCCTCTCGGGAGCCTCCTTTGCGTAGTAACTTT-ACGTCTCGCACTGGGGATCCGGAGGG-ACTCTTGCCGTAAAACCCCC-AACTTTCCAAAGG Saccharomyces_cerevisiae AAATTGCTGGCCTTTCATTGGATGTTTTTTTTTTCCAAAGAGAGGTTTCTCTGCGTGCTTGAAATGCAAGTACGGTCGTTTTAGGTTACCAACTGCGGCTAATCTTTTTTACTGAGCGTATTGGAACGTTATCGATAAGAAGAGGCGTCTAGGCAACAATGTTCTTAAAGT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS2 with P2-6') = N: 1-171; CODONPOSSET CodonPositions (CHARACTERS = 'ITS2 with P2-6') = N: 1-171; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2262] TITLE 5.8_and_6_clones; LINK TAXA = Taxa5; DIMENSIONS NCHAR=160; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160] [ . . . . . . . . . . . . . . . .] Achlya_bisexualis CAACTTTCAACAGTGGATGTCTAGGCTCGCACATCGATGGAGGACGCTGCGGACTGCGATACGTAATGCGATTTGAAGAAT-CAGTGAGTCACCGAAATTTGGAACGCATATTGAACTTGCGGGTT-AGCCCTGGGAGTATGTTTGTTCCAGTGTCCGTA Chlorella_ellipsoidea CAACTCTCAACAACGGATATCTTGGCTCCCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAATTCCGTGAATCATCGAATCTTTGAACGCATATTGCGCTCGAGACCT--CGGTCAAGAGCATGTCTGGCTCAGCGTCGGCT Cicer_reticulatum TGACTCTCGGCAACGGATATCTAGGCTCTTGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGATGCCATTAGGTTGAGGGCACGTCTGCCTGGGTGTCACAT Eurotium_rubrum AAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAATTAATGTGAATTGCAGAATTCAGTGAATCATCGAGTCTTTGAACGCACATTGCGCCCCCTGGT--ATTCCGGGGGGCATGCCTGTCCGAGCGTCATTG Gelasinospora_nigeriensis AAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCTCGCCAGT--ATTCTGGCGAGCATGCCTGTTCGAGCGTCATTT Ginkgo_biloba CGACTCTCGGCAACGGATATCTTGGCTCTTACCACGATGAAGAACGTAACGAAATGCGATATTTAGTGTGAATTGTAGAATCCCATGAATCATCAAGTCTTTGAACGCAAGTTGTGGCCGAGGCT----GGT-GAGGGCACATCTACTTTGGCATTGCAT Glomerella_graminicola AAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGC--ATTCTGGCGGGCATGCCTGTTCGAGCGTCATTT Glomus_mosseae TCACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCATAATTTTGTGAATCATCGAATCTTTGAACGCAAATTGCACTCCCTGGT--ATTCCGGGGAGTATGCCTGTTTGAGGGTCGTTA Lentinula_edodes CAACTTTCAGCAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCTCTGGT--ATTCCG-GAGGCATGCCTGTTTGAGTGTCATTA Lilium_parryi CGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGCGATACTTGGTGTGAATTGCAGAATCCCGTGAACCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCCTTTCGGTTGAGGGCACGCCTGCCTGGGCGTCACGC Morchella_crassipes AAACTTTCAACAACGGATCTCTTGGTTCCCACATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTCTGGT--ATTCCGGAGGGCATGCCTGTTCGAGCGTCATAA Mycosphaerella_graminicola AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCCTGGT--ATTCCGGGGGGCATGCCCGTTCGAGCGTCATTA 'P1-9' TAACTTTTGACAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGT--ATTCCTTGGAGCATGCCTGTTTGAGTGTCATGA 'P2-6' AAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC-AAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGC--ATTCTGGCGGGCATGCCTGTTCGAGCGTCATTT 'P3-2' AAACCCCTAACAACGGATGTCTTGGCTCTCGCAACGAGGAAGAACGCAGCGAAGTGCGATATGTAGTGTGAATTGCAGAATTACGTGAATCATCGAATCTTTGAACGCATATGGCACCCGAGACCT--CGGTCGAGGGTATGTCTGCCTAAGAGTCGCCG 'P4-4' AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCCGTGAGTCATCGAATCTTTGAACGCACATTGCGGCCTTTGGC--ATTCCGAAGGGCATGCCTGTTCGAGCGTCATTA 'P4-5' AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCCGTGGT--ATTCCGCGGGGCATGCCTGTTCGAGCGTCATTT 'P4-7' AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGAACATTGCGCCCTTTGGC--ATTCCGAGGGGCATGCCCGTTCGAGCGTCATTA Phytophthora_ilicis CAACTTTCAGCAGTGGATGTCTAGGCTCGCACATCGATGAAGAACGCTGCGAACTGCGATACGTAATGCGAATTGCAGGATTCAGTGAGTCATCGAAATTTTGAACGCATATTGCACTTCCGGGTT-AGTCCTGGGAGTATGCCTGTATCAGTGTCCGTA Pleurotus_pulmonarius CAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCCCCTTGGT--ATTCCGAGGGGCATGCCTGTTTGAGTGTCATTA Pteridium_aquilinum TGACGCTCGGCAACGGATATCTTGGCTCTTGCAACGATGAAGAACGCAGCGAAATGCGATACGTGGTGTGAATTGCAGAATTCCGTGAATCATCGAGTCTTTGAACGCAAGTTGCGCCCGAGGCTT---GTCCGAGGGCACGCCTGCCTGAGCGTCTCAC Puccinia_caricina TAACTTTTAACAATGGATCTCTTGGCTCTCACATCGATGAAGAACACAGTGAAATGTGATAAGTAATGTGAATTGCAGAATCCAGTGAATCATTGAATCTTTGAACGCATCTTGCACCTTTTGGT--ATTCCAAAAGGTACACCTGTTTGAGTGTCATGA Tremella_foliacea AAACTTTTAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCCTTTGGT--ATTCCGAAGGGCATGCCTGTTTGAGTGTCATGA Xylaria_hypoxylon AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGT--ATTCTAGTGGGCATGCCTGTTCGAGCGTCATTT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 5.8_and_6_clones) = N: 1-160; CODONPOSSET CodonPositions (CHARACTERS = 5.8_and_6_clones) = N: 1-160; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2268] TITLE 'ITS1 5.8S ITS2 with P4-5 P4-7'; LINK TAXA = Taxa1; DIMENSIONS NCHAR=564; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Botryosphaeria_dothidea ---CCGAGTTGATTCGGG--C-T---CCGGCCCGATC-CTCCC-ACCCTTTGTGTACCTACCTC---TGTTGC----TTTGGCGGGCCGCGGTCCTCC--GCGGCCGCCCCCC-TCCCCGGGGGGTGACCAGCGCCCGCCAGAGGACCATCAAACTCCAGTCAGTA---AACGATG-CAGTCTGAAAAAC---ATT-TAATA-AACTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTACAA--CC-CTCAAGCTCTGCTTGGTATTGGGCACCGTCCTTTG--CGGG-------------CGCGCC-TCAAAGACCTCGGCGG--TGGCGTCTTGCCT-CAAGCGTAGTAGAACATACAT-CTCG-CTTCGGAGCGCAGGGCGTCGCCCGCCGGACGAACCTTCTGAA---CTTTTCTCAAGG---------- Candida_glabrata TGGATCTCTCTATTCCAAAGAGGTGTTTTATCACACGACTCGACACTTTCTAATTACTACACACAGTGGAGTTTACTTTACTACTATTCTTTTGTTCGTTGGGGGAACGCTCT-CTTTCGGGGGGGAGT--TCTCCCAGTGGATGCAAACACAAACAAATATTTTTTTAAACTAATTCAGTCAACA-CAAAGAAA---A-CAACTTCAAAACTTTCAACAATGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTCTGGTATTCCGGGGG-GCATGCCTGTTTGAGCGTCATTTCCTTCTCAAACACATTGTGTTTGGTAGTGAGTGATACTCGTTTTTGAGTTAACTTGAAATTGTAGGCCATATCAGTATGTGGGACACGAGCGCAAGCTTCTCTATTAATCTGCTGCTCGTTTGCGCGAGCGGCGGGGGTTAATACTGTATTAGGTTTTACCAACTCGGT-----GTTGATCTAGGGAGGGATAAG Cladosporium_cladosporioides ----CAAGT-GACCCCGG--TCTAA-CCACCGGGATG-TTCATAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTTCGGGCG--GTG--GCTCCGGGT--GGATACTTCAAACTCTTGCGT------AACTTTG-CAGTCTGAGTAAACTTAAT-TAATA-AATTAAAACTTTTAACAACGTATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCAA-------CG--CGGTCC-------GCCGGTGGCC-TCAAATCGACCGGCTG--GGTCTTCTGTCCCCTAAGCGTTGTGGAAACTA-TT---CG-CTAAAGGGTGTT-CGGGAGGCTACGC-GT----AAAACAACC---CCATTTCTAAGG---------- Cladosporium_fulvum -------CTGAGTGAGGG--C-T---CACGCCCGACC-TCCA--ACCCTCTGT-GAACC--AAC---TCTG------T-TG------------CTTCG--GGGGCGACCC-GC--CGTTTCGGAACGGC--GCCCC--G---GAGATCATC-AA--ACACTGC------ATCTTT--GCGTCGGAGTCTT-AAAGT-AAATTTAAACAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCGTGGTATTCCGCGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTAGCTTGGTATTGGGCG-------TCG--CGGT----T-----CCGCGCGCC-TTGAAGTCTCCGGCTG--AGC-AGTTCGTCTCTAAGCGTTGTGGCATATA-TT--TCG-CTAAAGAGTTCG-GG---CGGCTTTTGG-----CCGTTAAAT---CTTT-TCAAAGG---------- Cladosporium_herbarum ----CAAGA-ACGCCCGG--GCTT--CGGCCTGGTTA-TTCATAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTTCGGGCG--GGG--GCTCCGGGT--GGACACTTCAAACTCTTGCGT------AACTTTG-CAGTCTGAGTAAACTTAAT-TAATA-AATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG--CATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCAAA------CG--CGGTCC-------GCCGCGTGCC-TCAAATCGTCCGGCTG--GGTCTTCTGTCCCCTAAGCGTTGTGGAAACTA-TT---CG-CTAAAGGGTGTT-CGGGGGGGTACCTG-T----AAAACAACC---CCATTTCTAAGG---------- Cladosporium_oxysporum ----CAAGA-ACGCCCGG--GCTT--CGGCCTGGTTA-TTCATAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTTCGGGCG--GGG--GCTCCGGGT--GGACACTTCAAACTCTTGCGT------AACTTTG-CAGTCTGAGTAAACTTAAT-TAATA-AATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCAA-------CT--CGGTCC-------GCCGGGTGCCCTCAAATCGTCCGGCTG--GGTTCTCTGTCCC-TAAGCGTTGTGGCAACTA-TT---CG-CTAAAGGGTGTT-CGGGAGGCTACGCGTT----AAAACAACC---CCATTTCTAAGG---------- Cladosporium_sp. ------AGT-GACCCCGG--TTTC--CCACCGGGATG-TTCATAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTTCGGGCG--GGG--GCTCCGGGT--GGGCACTTCAAACTCTTGCGT------AACTTTG-CAGTCTGAGTAAACTTAAT-TAATA-AATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCAA-------CG--CGGTCC-------GCCGCGTACC-TCAAATCGACCGGCTG--GGTCTTCTGTCCCCTAAGCGTTGTGGAAACTA-TT---CG-CTAAAGGGTGTT-CGGGAGGCTACGCCGT----AAAACAACC---CCATTTCTAAGG---------- Cladosporium_sphaerospermum ----CAAGTTGACACCCG--CCCTC-GGTCCGGGATG-TTCACAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTCCGGGCG--GGG--GCCCCGGGT--GGACATTTCAAACTCTTGCGT------AACTTTG-CAGTCTGAGTAAATTTAAT-TAATA-AATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCGA-------CG--CGGTCC-------GCCGGCG-CC-TCAAATCGACCGGCTG--GGTCTTTCGTCCCCTCAGCGTTGTGGAAACTA-TT---CG-CTAAAGGGTGCCGCGGGAGGCCACGCCGT----AAAACAACC---CCATTTCTAAGG---------- Cladosporium_tenuissimum ----CAAGT-GACCCCGG--TCTAA-CCACCGGGATG-TTCATAACCCTTTGTTGTCCGA---C---TCTG------T-TG------------CCTCC--GGGGCGACCCTGC--CTTCGGGCG--GGG--GCTCCGGGT--GGACACTTCAAACTCTTGCGT------AACTTTG-GAGTCTGAGTAAACTTAAT-TAATA-AATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGGAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTCGCTTGGTATTGGGCAA-------CG--CGGTCC-------GCCGGTG-CC-TCAAATCGACCGGCTG--GGTCTTCTGTCCCCTAAGCGTTGTGGAAACTA-TT---CG-CTAAAGGGTGTT-CGGGAGGCTACGCCGT----AAAACAACC---CCATTTCTAAGG---------- Dothidea_hippophaeos ---AAGATTGAGTGTCGCGACCTAAAAAATCGCGACCACTTCCAACCCTCTGTTGTTATAACTACCTTGTTGC----TTTGGCGGGACCGTTCGGTCCTCCGAGCGCA-CCAG-TCCTCG--GACAGGTGAGCGCCCGCCAGAGT-CCAACCAAACTCTTGTTTTT---AACCAG--TCGTCTGAGTATAAAATTT-TAATTAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTACA---CCACTCAAGCACTGCTTGGTATTGGGC-A------TCG--TCCGTC-GAAAGGCGGGCGTGCC-TCGAAGACCTCGGCGG--GGTTTCTCCAACTTCGGGCGTAGTAGAGTTAAATCGAACGTCTTATAAG--CTTGGTGGGACTCCATTG-----CCGTTAAAC---CTTT-----TATTTTTAT-AGG Elsinoë_australis ---ACGAGGAAGGGTT-T--CCGAAAGGAGCCCGAAC--TCCCCACCCTTTGCTGTTGCGAATC---TGTTGC----TTCGGCGGGCCCGCCCCCCCATCCCTGGGGGGCCGG-GCCTCACCGCCCGGACAGCGCCCGCCGGAGGACCGAATCAACTCTGTTTTTA---ACCATA--ATGTCGGAGTACTTTTGTA-CAATCAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCAATCAAGCCCCGCTTGGTATTAGGCGCCTG--GCCG--CCCCCC-CCGTGGCCGGCCCGCC-CGAAATGCATCGGCG---AGG--CACCGACCCCCGGCGTGTTAGAATTTC-GA-AACGTC--AGGAGCACCGGTGTTAA--CCTCTG-----CCGTGAAAC---CTTTCAAACTATTTTTCT-AAG MS594 ---CCGAGCGAAGGGGCG--CC-CG-C-GCCCCGACC-GCCC--ACCCTCTGT-GAACGAAACC---CGT---------TG------------CCTCG--GGGGCGACCCGGA--CGTCACGTC-CGGC--CGCCCCCG---GGGGTGACCCAA---CACTGC------ATCTGT--GCGTCGGAGTACT-TCAGT-AATG--AATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGCATTCCGGGGG-GCATGCCCGTTCGAGCGTCATTTCA---CCACTCCCGCCTGGCGGGGTATTGGGCG-------CCG--CGGCC-----TCGGCCGCGCGCC-TCGAAGTCTCCGGCCG--AGT-CGTTCGTCTCCCAGCGTTGTGGCACACA-AT-CTCG-CTG-CG-GTGGG-CG-GACGGC-GGCGG-----CCGTCGA-A---CTCC-TTACAGG---------- Mycosphaerella_graminicola -------CCGAGCGAGGG--CCTC--CGGGTCCGACC-TCCA--ACCCTTTGT-GAACACATCC---CGT---------TG------------CTTCG--GGGGC----------GACCCTGCC-GGGC--GCCCCCGG---AGGACCACCAAAAAACACTGC------ATCTCT--GCGTCGGAGTTTA-CGAGT-AAATCGAAACAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCCTGGTATTCCGGGGG-GCATGCCCGTTCGAGCGTCATTACA---CCACTCCAGCCTCGCTGGGTATTGGGCGTCTTTTCGCG--GGGGAT-CACTCCCCCGCGCGCC-TCAAAGTCTCCGGCTG--AGCGGTCTCGTCTCCCAGCGTTGTGGCATCAC-GT-CTCG-CCGCGGAGTTCA-CGAGCCCTC--ACGG-----CCGTTAAAT---CACA-CCTCAGG---------- Ophiosphaerella_herpotricha TCCGTAGGTGAACCTGCGGAAGGATCATTACACGATAGTACAGGCCCCAAGTGTAGAA-CAAACTACGCAGACGGGTTATGTCTATTA---CCCTTGTTTATTGAGTACCTAT-GTTTCCTTGGTGGGCTTGCCCGCCAAAAGGACACCCTATTAAACCTTTTTAT--TTTCAATCAGCGTCTGAATAAA---AA--TAAT--AATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCATGGG-GCATGCCTGTTCGAGCGTCATTTGTA--CC-TTCAAGCTCTGCTTGGTGTTGGGTGTTTG---TCT--ACTCCACTGCGTTTGGACTCGCC-TTAAAGTAATTGGCAGCCTATATTT-GGTTTTGA-GCGCAGCACATTTTGCG---TCTTACTGCCAG--TTATATAGGCACCCAAT------AAGCCT-------TTTTATCACGT---------- 'P4-5' ------CCTCGGGGAGAG--GG----CGGGCCGTATC-CCAC--ACCCTTTGT-GAACCACAAC---TCTG------T-TG------------CTTCG--GGGGCGACCCTGC--CGTCAGGCGGCGGT--GCCCCCGGTG-GCCTTCAACTAA--ACTCTGC------ATCTTTT-GCGTCGGAGTCTT-TTAAA-GAATT-AAACAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCGTGGTATTCCGCGGG-GCATGCCTGTTCGAGCGTCATTTCA---CCACTCAAGCCTAGCTTGGTATTGGGCG-------CCG--CGGCGAACTCATCGCTGCGCGCC-TTAAAGTCTCCGGCTG--AGC-AGCCTGTCTCCGAGCGTTGTGACACATG-T----CG-CTAGGGAGTGCA-GG---TCTGCCGCGG-----CCGTTAAAT---CTTTATCAAAGG---------- 'P4-7' -----AAGAGATGGCGGG--CCTCG-CTGCCCCCGTC-CCTC--ACCCTTTGTTGACCGAAAAA---CCTT------TTTG------------CCTCG--GGGGC---CGTGT--GGCCACGGC-CGCC--GCTCCCAG---AGGACCAACCAA---CGCTGT------CTCTGT--GTGTCGGAGTACA-TGATT-GAAT--AATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGAACATTGCGCCCTTTGGCATTCCGAGGG-GCATGCCCGTTCGAGCGTCATTAAAT--CCAATCCAGCCCGGCTGGGTGTTGGGCGAT-----CCG--GGGGCC-GTGTGGTCCCCGCGCC-TCAAAGTCCGTCGCTG--TTCGCACCCGAATCTCAGCGTCGTGGAATCCG-TT--TCG-CTGGCGAGAGGG-GG-GCCGTCCGGCCG-----TCGTCGAGA---CGAA-CGATGTTTTTTCTCAGG Phaeocryptopus_gaeumannii ---AAGAGTAAGGGTTATT-CGTAG-----CCCGACC---TCCAA{AC}CCTTTGTTGTTATAACTACCTCGTTGC----TTTGGCGGGACCGCTCGGTCT--CGAGCTG--CTGG-TCTTCG--GCCCGGCAAGTGCCCGCCAGAGT-CTACTCAAACTCTTGTTTT----AACCGG--TCGTCTGAGT-TAAACTTT-TAATTAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAAATCTTTGAAACGCACATTGCGCTCCCTGGTATTCCGGGGGAGCATGCCTGTTCGAGCGTCATTACA---CCACTCAAGCACTGCTTGGTATTAGGCCA------TCG--TCCCCC-GAAAGGTGGGCGTGCC-TCAAACACCTCGGCGG--AACCTCACCGGCTTTGGGCGTAATAAAATTTC-TC-AACGTCTTATAAGTACCGGTTCTGACTCCTTTG-----CCGTTAAAC---CCCA-----AACTTTTAA-AGG Phaeosphaeria_avenaria TCAGTAGTTTACTACTGTAAAGGAGGCTGTTAGTCT-GTATAG--CGCAAGCTGATGA-GCAGCTAGCCTC-----TTTTATCCA------CCCTTGTCTTTTGCGTACCCAC-GTTTCCTCGGCAGGCTTGCCTGCCGATTGGACAAACCTATAACCTTTTTAAT--TTTCAATCAGCGTCTGAA-AAA---CT--TAAT--AATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCATGGG-GCATGCCTGTTCGAGCGTCATTTGTA--CC-CTCAAGCTCTGCTTGGTGTTGGGTGTTTG---TCC--TCTCCCTAGTGTTTGGACTCGCC-TTAAAATAATTGGCAGCCAGTGTTTTGGTATTGAAGCGCAGCACAAGTCGCG---A-TTCTTATCAA--ATACTT--GCGTCCAC-------AAGCCC-------TTTTTTAACTT---------- Pleospora_herbarum -----------------CACAATATGAAAGCGGGTTGGGACCTCACCTCGGTGAGGGCTCCAGCTTGTCTGA-----ATTATTCA------CCCATGTCTTTTGCGCACTTCTTGTTTCCTGGGCGGGTTCGCCCGCCACCAGGACCAAACCATAAACCTTTTTGTAATTGCAATCAGCGTCAGTAAACA---ATG-TAAT--TATTACAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCAAAGG-GCATGCCTGTTCGAGCGTCATTTGTA--CC-CTCAAGCTTTGCTTGGTGTTGGGCGTCT----TTG--TCTCTCACGAG-----ACTCGCC-TTAAAATGATTGGCAGCCGACCTACTGGTTTCGGAGCGCAGCACAATTCTTGC--ACTTTGAATCAGCCTTGGTTGAGCATCCATC------AAGACCACA---TTTTTTTCAACT---------- Saccharomyces_cerevisiae ACGGTGAGAGATTTC---TGTGCTTTTGTTATAGGACAATTAAAACCGTTTCAATACAACACACTGTGGAGTTTTCATATCTTTG--CAACTTTTTCTTTGGG-----------CATTCGA--GCAATC--GGGGCCAGAGGTAACAAACACAAACAATTTTATTTATATTAAATTTTTGTCAAAAACAAGGAAATTTAAAATATTAAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTG-?CCCCTTGGTATTCCAGGGG-GCATGC-TGTTTGAGCGTCATTTCCTTCTCAAACA--TTCTGTTTGGTAGTGAGTGATACTCTTTG--GAGTTAACTTGAAATTGCTGGCCTTTTCATTGGATGTTTTTTTTTTCCAAAGA-------GAGGTTTCTCTGCGTGCTTGAGTATAATGCAAGT-ACGGTCGTTTTAGGTTTTACCAACTGCGGCTAACTTTTTTATACTGAGCG-TA-T Torulaspora_delbrueckii GGGGCTTCTGTATTC---ACTGTTTCTCTGTCTG--CGGTTCACTGCCTAAAAATTATACACACACTGGAGTTTTCTTTTAAAACA-CTTCTTCTTCTTTGGG-----------CTT------GCAA----GAGCCCGGAGTTGACAAACACAAACAATTTTGTT-ATATTATAATCAAGTCAAAACCAATGAAATACAAATAATTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCAGGGG-GCATGCCTGTTTGAGCGTCATTTCCTTCTCAAAGAACTCTTCTTTGGTAGTGAGTGACACTCTTTCTAGAGTTAACTTGAAATTGCTAGCCATATAATAGC-TGTTGATTGCTGACTTTG--------GACGGAGCGATTTGTCC---AGTCTGCTGATACCGATTGTCGTATTAGGTTTTACCAACTTCGACGGACGTAGTGTTAGTGGGCGTTACT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P4-5 P4-7') = N: 1-564; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P4-5 P4-7') = N: 1-564; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2264] TITLE 'ITS1 with P2-6'; LINK TAXA = Taxa7; DIMENSIONS NCHAR=211; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 ] [ . . . . . . . . . . . . . . . . . . . . . ] Colletotrichum_acutatum CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-GTACCT--AACCGTTGCTTCGGCGGGC-AGGGGA---AGCCTCTCGCGGGCCT------CCCCTCCCGGCGCCGGCCCCCACCAC-----GGGGACGGGGCGCCCGCCGGAGG-AAA--CCAAA----CTCT-ATTT---ACACGACGTCTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_capsici CTGAGTT-ACCGCTCATCAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGT-AGGCG-----TCCCCTAAAAAGGA-------CGTCTCCCGGCCCTCTCCCGTCC--------GCGGGTGGGGCGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGACACAAGCAAATAATCA Colletotrichum_coccodes CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGGGGT---GCCGCC--TGCGGAC-----CCCCCTCCCGGCCCTGCCCTC--AC---------GGGCGGAGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_dematium CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TA-CTGTTGCTTCGGCGGGC-AG-------AGTCCCC-TCGGGGA-------CCCCTCCCGGCCCGTCCCTC--GC---------GGACGGAGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_destructivum CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGC-AGGAGGACAACCCCCC-TCGGGGGG-CGGTCCCCCTCCCGGCCGCGCCCTC--AC---------GGGCGTGGCGCCCGCCGGAGG-ATA--CCAAAA---CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_fragariae CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTACAACTGTTGCTTCGGCGGGT-AGG-G-----TCCCCGT-----GA-------CC-CTCCCGGCCTCCCGCCCCCCC------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Colletotrichum_fuscum CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------CG-GGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Colletotrichum_kahawae CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGC-AGG-G-----TCTCCGT-----GA-------CC-CTCCCGGCCTCCCGCCCCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Colletotrichum_lindemuthianum CTGAGTTTA-CGCTCTATAACCCTTTGTGAAC-ATACCA--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CC-GGCCCCGCTCGC-----------------GGGGCGCCCGCCGGAGG-AAAA-CCCAA----CTCT-ATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAGTCA Colletotrichum_linicola CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT-TAACTGTTGCTTCGGCGGGC-AGGAGGACAACCCCCCCTCGGGGGGGCGGTCCCCCTCCCGGCCGCGCCCTC--AC---------GGGCGTGGCGCCCGCCGGAGG-ATA--CCAAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_musae CTGAGTT-TACGCTCTGCAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCCCCGT-----GA-------CC-CTCCCGGCCCCCCGCCCCCG-------GG-GCGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Colletotrichum_orbiculare CTGAGTTTAACGCTCTATAACCCTTTGTGAAC-ATACCT--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CCCGGCCCCGCTCGC-----------------GGGGAGCCCGCCGGAGG-AAAAACCCAA----CTCTTATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAATCA Colletotrichum_sublineolum CTGAGTT-ACCGCTCTATAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGTTAGGGGG----TCCCTC--CGGGGA------CGCCCTCCCGCCGGCGCCCTCCTCCTCCGGGAGGGGTCGCGGCGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Colletotrichum_trichellum CTGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGAGG----TCCCCC--CGGGGA------CCCCCTCCCGGCCCCGCCCTC--GC---------AGGCGGAGCGCCCGCCGGAGG-TCA--CCAAACTC-TTAT-TTTT---TAGCGACGTTTCTTCTGAGTGGCACAAGCAAATAATAA Colletotrichum_trifolii CTGAGTTTA-CGCTCCATAACCCTTTGTGAAC-ATACCT--AACCGTTGCTTCGGCGGGC-GGGAGG----TCCGCC-T-------------CCCC-CCCGGCCCCGCTCGC-----------------GGGGCGCCCGCCGGAGG-AAAACCCCAA----CTCTTATTT---TAACGACGTCTCTTCTGAGTGGCACAAGCAAATAATCA Elsinoë_australis CCGAAAGGA-GCCCGAACTCCCCACCCTTTGCTGTTGCG-AATCTGTTGCTTCGGCGGGCCCGC-------CCCCCCATCCCTGGG----GGGGCGGCCGGGCCTCACCGCCC-------------GGACAG-CGCCCGCCGGAGG----A-CCGAATCAACTCTGTTTTTAACCATAATGTCGGAGTACTTTTGTACAATCAAATTAAAA Glomerella_cingulata CTGAGTT-TACGCTCTATAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Glomerella_graminicola TCGAGTT-ACCGCTCTACAACCCTTTGTGAAC-ATACCT--AACTGTTGCTTCGGCGGGC-AGGGGG----TCCCCC--CGGGGA------CGCCCTCCCGGCCCCGCCCCCCTAC-C----AGGGGACGTGGCGCCCGCCGGAGG-ATA--CCCAA----CTCT-ATTT---TAACGACGTTTCTTCTGAGTGGCACAAGCAAATAATTA Hypocrea_rufa CCGAGTTTACAACTCCCAAACCCAATGTGAACCATACCA-AA-CTGTTGCCTCGGCGGG---G--------TCACGCC--------------CCGGGTGCGTCGCAGCCCCG-------------GAACCAGGCGCCCGCCGGAGGGACCAACCAAACTCTTTCTGTAGTCCCTCGCGGACGTTATTTTTACAGCTCTGAGCAAAAATTCA 'P2-6' CTGAGTT-TACGCTCTACAACCCTTTGTGAAC-ATACCTATAACTGTTGCTTCGGCGGGT-AGG-G-----TCTCCGC-----GA-------CC-CTCCCGGCCTCCCGCCTCCG-------GGCGGGTCGG-CGCCCGCCGGAGG-ATAA-CCAAA----CTCT-GATT---TAACGACGTTTCTTCTGAGTGGTACAAGCAAATAATCA Saccharomyces_cerevisiae TTTTGTTATAGGACTTAAAACCG-TT-T---CAATACAACACACTGTGGAGTTTTCATATCTTTGCAACTTTTTCTTT------------GGGCATTCGAGCAATCGGGGCCAGAG---------GTAACAAACACAAACAATTTTATTTATTCATTA--AATTT-TTGTCAAAAACAAGAATTTTCGTAACTGGAAATTTTAAAATATTA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 with P2-6') = N: 1-211; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1 with P2-6') = N: 1-211; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2267] TITLE 'ITS1 5.8s ITS2 with P4-4'; LINK TAXA = Taxa4; DIMENSIONS NCHAR=635; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 590 600 610 620 630 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Candida_glabrata GCCGACAAAGACCTGGGAGTGT----GCGTGGA---TCTCTCT---ATTCCAAAGGA----------GGTGTTTTA-TCACACGACTCGACACTTTCTAATTACTACACACAGTGGAGTTTACTTTACTACTATTCTTTTGTTCGTTGGGGCTCTTTCGGGGGGGAGTTCTCCCAGTGGATGCAAACACAAACAAATATTTTTTTAAACTAATTCA---------GTCAACA-CAAGA--TTTC-TTTTAGTAGAAAACAACTTCAAAACTTTCAACAATGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATT-CCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTCTGGTATTCCGGGGG-GCATGCCTGTTTGAGCGTCATTTCCTTCTCAAACACATTGTG-TTT------GGTAGTGAGTGATACTCGTTTTTGAGTTAACTTGAAATTGTAGGCCATATCAGTATGTGGGACACGAGCGCAAG---CTTCTCTATTAATCTGCTGCTC--GTTTGCGCGAG--CGGCGGGGGTTAATACTGTATT--AGGTTTTACCAACT--------CGG-T-GTTGATCTAGGG Capronia_coronata AAGAGTTAGGGTCTTCT-------CGGCCCGACC--TCCCAACCCCATGTTTATCAAACC----TGTGTTGCTTCGGCGCGCCCG--TCTTCGT---------------------GACC-GCCG--GAGGATCGTCGA------AAGGCGTCCT-CTGGCCCGCGC---CCGCCGATGGCCTACGCTT--AA-AATTCTG-AATCAACCG-TGTCTC------ATGTCTAAGTCC-----TTCAT-----------AAATAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCCAGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTATCACCCCTCAGGCCCCCGGGCTT------GGTGTTGGACGGCTTGGTCGAG---TC----CCCTCG---ACCCCTCCTAAAGACAATGACGGCGGCCTCGCGGGACCCCCGGTACACTGAGCTTC-TTAACTGAGCACGT-ACCGGACG---CATGGGTACCCAGGCTCCGGTCTTCTCCCTTCACAGGGAAACT--TTTTCAA-GG Capronia_pilosella AAGAGTTAGGGTCTTCT-------AGGCCCGACC--TCCCAACCCTGTGTTTAACAAACCA---TTTGTTGCTTCGGCGGGCCCG--TCTTTAT-T-------------------GACC-GCCG--GAGGACCGTCGA------GAGACGCCCT-CTGGCCAGCGC---CCGCCGATGGCCAACTATACCTA-AACTCT-GAAT-AAACA-TGCCT-------ATGTCTAAGTTA-----TTTGTT----------AAATAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCCAGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTATCACCCCTCAAGCCCCTGGGCTT------GGTGTTGGACGGTTTGGTGAAG-CCTC----CGGGCG-TCACCCCTCCTAAAGACAATGACGGCGGCCTGTTGGAACCCCCGGTACATTGAGCTTC-TTAACTGAGCACGT-ATCGGAT----CAAGGGAACCCAGGCCCCGGTCTTCTCCCTTTATTGGGAAACTCCTTTTTAA-GG Capronia_pulcherrima AAGAGTTAGGGTCTTCT-------AGGCCCGACC--TCCCAACCCTGTGTTTAACAAACCA---TTTGTTGCTTCGGCGAGCCCG--TCTTTAT-T-------------------GACC-GCCG--GAGGACCGTCGA------GAGACGCCCT-CTGGCCAGTGC---CCGCCGACGGCCAACTATACCTA-AACTCTTGAAT-AAACA-TGCCT-------ATGTCTAAGTAA-----TTTATT----------AAATAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCCAGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTATCACCCCTCAAGCCCCCGGGCTT------GGTGTTGGACGGTTTGGTGAAGGCCTC----CGGGCGGTCACCCCTCCTAAAGACAATGACGGCGGCCTGTTGGAACCCCCGGTACATTGAGCTTC-TTAACTGAGCACGT-ATCGGAT----CAAGGGAACCCAGGCCCCGGTCTTCTCCCTTCATTGGGAAAAT--TTATCAA-GG Coniosporium_perforans CCGAGTTAGGGTCTTCCCCTCCAGGAGCCCGACC--TCCCAACCCTGTGTCTAAACTACCTTGTCG--TTGCTTCGGCGGACCGG---TTGACCAACTGGTC----TT-------GACC-GCCG---GGGGGG-----------CCTCCCCCCCC-TGGAGAGCGT---CCGCCGACGGCCC-AACCACACA-AACTCTTGTACCAAACCATGT----------CGTCTGAAT--GTA--CTT--GAT-TAAGAATCAAAAAAACAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTTCCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCACTGGTATTCCGGTGG-GCATGCCTGTTCGAGCGTCATTATCCTCCCTC-AAACCCCGGGTTT------GGTGTTGGACCCAAGTTGTGCGT--------CTGAAC--AACTGGTCCCAAAGACAATGACGG-CGTCCGTGGG-ACCCTCGGTGCAACGAGCTTC----TAGGAGCACGC-GTCGAGT---TTCAAGGTCCTTCCGGGCCGGCCTCCTTTTT---------TTACTTTTACTAA-GG Dothidea_hippophaeos AAGATTGAGTGTCGCGACCTAAAAAATCGCGACCACTTCCAACCCTCTGTTGTTATAACTAC--CTTGTTGCTTTGGCGGGACCGTTCGGTCCT----------------------CCGAGCGC-A----CCAGT----------CCTCG--GA-CAGGTGAGCGC---CCGCCAGAGT-CC-----AACCA-AACTCTTGTTTTTAACC-AGT----------CGTCTGAGTATAAA--ATTTT-----------AATTAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTA-CACCACTC--AAGCACTG-CTT------GGTATTGGGC-----ATCGTCCGTCGA----AAGGCG--GGCGTGCCTCGAAGACCTCGGCGG-GGTTTCTCCA-ACTTCGGGCGTAGTAGAGTTAAA--TCGAACGTCTT-ATAAGCT---TGGTGGGACTCCATTGCCGTTAAACCTTT--------------TATTTTTATA-GG Elsinoe_australis ACGAGGAAGGGTT-T--CCGAAAGGAGCCCGAAC--TCCCCACCCTTTGCTGTTGCGAAT-C---T-GTTGCTTCGGCGGGCCCGCCCCCCCAT----------------------CCCTGGGGGGGCGGCCGGG----------CCTCACCGC-CCGGACAGCGC---CCGCCGGAGGACC-----GAATC-AACTCTGTTTTTAACCA-TAA----------TGTCGGAGTACTTT--TGTAC-----------AATCAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTT-CACCAATC--AAGCCCCG-CTT------GGTATTAGGCGCCTGGCCGCCCCCCCC----GTGGCC--GGCCCGCCCGAAATGCATCGGCG--AGG--CACCG-ACCCCCGGCGTGTTAGAATTTC----GAAACGTC---AGGAGCACC-GGTGTTAA--CCTCTGCCGTGAAACCTTTCA---------AACTATTTTTCTA-AG Exophiala_jeanselmei CCGAGTTAGGGTCCTCA-CA----GGGCCCGACC--TCCCAACCCTTTGTTTATGATACCT---AGTGTTGCTTCGGTAGGCCTGG-TCTCC-----------------------GACCTGCCG--GGGGGCCGT---------GAAACGCCCCGCCGGAGAGCGC---CTGCCGACAGCCCCAACCTTTAA-AATTCTT-AACCAAACG-TGTCT--------TGTCTGAGTAAACG--TCTTTT---------AAATAAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCTCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTTTCACCCCTCAAGCCCCCGG-CTT------GGTGTTGGACGGTTTGGTCTCGGGTCCG--ACCCCCCTTGACCCCTCCCAAAGACAATGACGGCGGGCTGTTCG-ACCCCCGGTACACTGAGCATC-TTAACGGAGCACGT-ACCGGTCCT-TTGAGGGTCGACGGCACCCGGTCT-ACACCTT--------ATATCTTTTACAA-GG Exophiala_spinifera CCGAGTTAGGGTCCTCA-C-----AGGCCCGACC--TCCCAACCCATTGTTTATGATACTC---AGTGTTGCTTCGGCAGGCCTGG-TCTTT-----------------------GACCTGCCG--GAGGGCCGT---------AACACGCCCC-CCGGAGAGCGC---CTGCCGACGGCCCCAAC-TTCAA-AATTCTT-AACTAAACA-TGTCT-------TTGTCTAAGTAAA-G--TCTTTA---------ATAA--AAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCTCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTTTCACCCCTCAAGCCCCCGG-CTT------GGTGTTGGACGGTTTGGTCCCGGGACC------CCCCTGGACCCCTCCCAAAGACAATGACGGCGGGCTGTCGC-ACCCCCGGTACACTGAGCATC-TTCACGGAGCACGT-ACCGGTC---TTCAGGGACGACGGCACCCGGTCTCACACCT---------ATATCTTT--CAA-GG Gelasinospora_nigeriensis ------CAGAGTTGC--------------AAAACTCCCACAAACCATCGCGAATCTTACCCGT-ACGGTTGCCTCGGCGCT--GGCGGTCCGGAAGGCC----------------CTCGGGCCCCCGGATCCTCGGGT-------CTCCCGCTCGCGGGAGGCTGG--CCCGCCGGAGTGCCGAAAC------CAAACTCTTGATATTTTATGTCTC---------TCTGAGTAA-AC--TTTT-----------AAA-TAAGTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCTCGCCAGTATTCTGGCGA-GCATGCCTGTTCGAGCGTCATTT-CAACCATC--AAGCTCTGCTTG--------CGTTGGGGATCCGCGGCTGCCCG---------------CGGTCCCTCAAAAACAGTGGCGG-GCTCGCT-AGTCACACCGA-GCGTAGTAACTCT-----ACA--TCGT-TCTGGTCGTGCGGCGGGTTCTTG---CCGTAAAACCCCCC-------------AATTTCT-AA-GG Glomerella_graminicola ------TCGAGTT----------------ACCGCTCT-ACAACCCTTTGTGAA-CATACCTA--ACTGTTGCTTCGGCGGGCAGGGGGTCCCCCCGGG-----------------GACGCCCTCCCGG--CCCCGC---------CCCCCTACCAGGGGACGTGGC--GCCCGCCG-GAGGATACCC------AACTCTATTTTAACGACGTTTCT----------TCTGAGTGGCAC--AAGC-----------AAA-T-AATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGCATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTT-CAACCCTC--AAGCTCTGCTTG-------GTGTTGGGGCCCTACGGTTGACGT-A---------------GGCCCTCAAAGGTAGTGGCGG-ACCCTCCCGGAGCCTCCTTTGCGTAGTAACTA------ACGTCTCGC-ATCGGGATC-CGGAGGGACTCTTG--CCGTAAAACCCCCC-------------AATTTTTCAATGG Hypocrea_rufa ------CCGAGTTT---------------ACAACTCCCA-AACCCAATGTGAACCATACCAA--ACTGTTGCCTCGGCGGG--GTCACGCCCCGGGTGC----------------GTCGCAGCCCCGGAACCAGG----------CGCCCGCCGGAGGGACCAACC--AAACTCTTTCTGTAGTCCC------CTCGCGGACGTTATTTT-TACAGC---------TCTGAGCAA-AA--ATTC-----------AAAATGAATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGTATTCTGGCGG-GCATGCCTGTCCGAGCGTCATTT-CAACCCTCG-AACCCCTCCGGGGG-GTCGGCGTTGGGGACTTCGGGAACCCCTAAG---ACGGGA-TCCCGGCCCCGAAATACAGTGGCGG-TCTCGCC-GCAGCCTCTCATGCGCAGTAGTTTG----CACAACTCGC-ACCGGGAGCGCGGCGCGTCCACGT--CCGTAAAACACCC--------------AACTTCTGAAATG 'P4-4' CCGAGTTAGGGTCCCTCCCAC--GGGGCCCGACC--TCCCAACCCCGTGTCTAATAAACCTGTACGTGTTGCTTCGGCGGACCGG---TTCGCTGCGTGGTCTCACGACCACAACGCCT-GCCGCCGGGGGAAAAGGAGTTTACCCTCCGCCCCC-TGGAGAGCGT---CCGTCGATGGCCC-AACCAAACA-AACTCCCAAACCAAAATGTATGTGAAACACAATTCTGAATCAGAC--CTTTTGATATACCAATCAAAAA--CAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTTCCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGGCCTTTGGCATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTATCCTCCCTCCAAAACCCTGCTTTACCGCGGGTGTTGGACCGCGTTGGACCGTT--C----GCGGCC--AACTGGTCTCAAAGACAATGACGGGCGTCCATGGGGACCCTCTTCGCACTGAGCTTT----CCGGAGCACGC-GTCGAGT---TGCAAGGTCTTGTGGGCCCGGCCACCTCTAA---------ATCTATTTTTTCA-GG Phaeococcomyces_catenatus CCGAGTTAGGGCCTCGT--T-----GGCCCGACC--TCCCAACCCCTTGTTTAATTATACCATTTG--TTGCTTCGGCGGGCCGG--TCTACCCA--------------------GACC-GCCGGAGGGTGCA------------CACCGCCCCTCTGGAGAGTTTTGCCCGCCGATGGCCC---CCTTCAA-AAATCTTGAACCCAACCGTGA----------CGCCTAAATT-GAT--TTATTG-TATAATGTACAAAAAA-CAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTTCCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTATCCCCCCTC-AAACCTCGGGTTT------GGTGTTGGACCGACGTTGGTCGTTACC----CCGACC--AACTGGTCTCAAAGACAATGACGG-CGTCCGTGGG-ACCCTCGATACACCGAGCTTTCTTTTCGAAGCACGT-ACCGAGT---TGCAAGGACCCACG--CCCGCCGGTCGCTCT---------C-CCCTTCTCGGA-GA Phaeocryptopus_gaeumannii AAGAGTAAGGGTTATT-CGTA-----GCCCGACC--T-CCAA-CCTTTGTTGTTATAACTAC--CTCGTTGCTTTGGCGGGACCGCTCGGTC-T-----------------------CGAGCTG------CTGGT----------CTTCG--GC-CCGGCAAGTGC---CCGCCAGAGT-CT-----ACTCA-AACTCTTGTTTT-AACC-GGT----------CGTCTGAGT-TAAA--CTTTT-----------AATTAAATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAAATCTTTGAAACGCACATTGCGCTCCCTGGTATTCCGGGGGAGCATGCCTGTTCGAGCGTCATTA-CACCACTC--AAGCACTG-CTT------GGTATTAGGCC----ATCGTCCCCCGA----AAGGTG--GGCGTGCCTCAAACACCTCGGCGG-AACCTCACCG-GCTTTGGGCGTAATAAAATTTC---TC-AACGTCTT-ATAAGTACC-GGTTCTGACTCCTTTGCCGTTAAACCCCA--------------AACTTTTAAA-GG Rhinocladiella_atrovirens CCGAGTTAGGGTCCTCATC-----GGGCCCGACC--TCCCAACCCATTGTTTATGATACCT---AGTGTTGCTTCGGTAGGCCTGG-TCTATCTGTTATA---------------GACCTGCCG--GGGGGCCGT---------AAGACGCCGG-CCGGAGAGTGC---CTACCGACAGCCTCAAC-TCCAA-AATTCTTTAACCAAACG-TGTCT-------TTGTCTGAGTAAC-G--TCTTTT---------AAAATAAAGCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTCTCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGTATTCCGAAGG-GCATGCCTGTTCGAGCGTCATTTTCACCCCTCAAGCCCCCGG-CTT------GGTGTTGGACGGTCTGGTCCGGGGACCTCAAACCCCCTGGACCCCTCCCAAAGACAATGACGGCGGGCTGTTGA-ACCCCCGGTACACTGAGCATC-TTCACGGAGCACGT-ACCGGTC---TCAAGGGTCGACGGCACCCGGTCT-ATACCT---------ATATTTTT--CAA-GG Saccharomyces_cerevisiae GCGCTTAAGTGCGCGGTCTTGCT-AGGCTTGTAA-GTTTCTTTCCTATTCCAACGGTGAGAGATTTCTGTGCTTTTGTTATAGGACTTAAAACCGTTTCAATACAACACACTGTGGAGTTTTCATA--TCTTTG-CAACTTTTTCTTTGGGCATTCGAGCAATCGGG----GCCAGAGGTAACAAACACAAACAATTTTATTTATATTAAATTTTT---------GTCAAAAACAAGAATTTTCGTAATGAAATTTAAAATATTAAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATT-CCGTGAATCATCGAA-TCTTTGAA-CGCACATTG--CCCCTTGGTATTCCAGGGG-GCATGC-TGTTTGAGCGTCATTTCCTTCTCAAACA--TTCTG-TTT------GGTAGTGAGTGATACTCTTTG--GAGTTAACTTGAAATTGCTGGCCTTTTCA-----TTG--GATGTTTTTTT-----TT-TCCAAAGAGAGGTTTCTCT-GCGTGCTTGAGGTATAATGCAAGTACGGTCGTTTT--AGGTTTTACCAACTGC----GGCTAATCTTTTTTATACTG Torulaspora_delbrueckii GCGCTTAATTGCGCGGTTCTCC----GCCGGG---GCTTCTGT---ATTC--ACTGT-------TTCTCTGTCTGCGGTTCACTGCCTAAAA--------ATTATACACACACTGGAGTTTTCTTT--TAAAACACTTCTTCTTCTTTGGGCT-T---GCAA--GAG----CCCGGAGTTGACAAACACAAACAATTTTGTT-ATATTATAATCAA---------GTCAAAACCAA----TTTCGTTATGAAATACAAATAATTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATT-CCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCAGGGG-GCATGCCTGTTTGAGCGTCATTTCCTTCTCAAAGAACTCTTC-TTT------GGTAGTGAGTGACACTCTTTCTAGAGTTAACTTGAAATTGCTAGCCATATAA-----TAGCTGTTGATTGCTGA---CTT-TGGACGGAGCGATTTGTCCAGTCTGCTG-----ATACCG-----ATTGTCGTATT--AGGTTTTACCAACTTC----GACGGA-CGTAGTGTTAGTG Trimmatostroma_cordae CCGAGTTAGGGTCTCCTCCGT--GAGGCCCGACC--TCCCAACCCTGTGTCTAACAAACCTGTTTGTGTTGCTTCGGCGGAACGGCAGTGACCTATTAGCCCCCCCTTCACCGGCGTCC-GTCGCCGGGGGACTTACGGTCTCACGACCGCCCC--TGGAGAGCGT---CCGCCGATGGCCCCAACCAAAAC-AACTACCAAACCCAAAT-TGTGAACAAAAAACTTCTGAATCAGAT--CTTT-GATATACCAATCAAAAA--CAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGCGAATTGCAGAATTTCCGTGAGTCATCGAA-TCTTTGAA-CGCACATTGCGCCCTTTGGCATTCCGAAGG-GCATGCCTGTCCGAGCGTCATTATCCTCCCTCAAACCCCCGGGTTT------GGTGTTGGACCGCGTTGGCCC-TTA-A----CCGGCC--AACTGGTCTCAAAGACAATGACGG-CGTCCCCGGG-ACCCTCTTTGCACTGAGCTTT----TCGGAGCACGC-AGGGAGT---TTCAAGGGCCCAGGGACCCGGTCGCCTCTAA---------A-CTATTTTTC-A-GG Xylaria_hypoxylon ------AAGAGTTTTGA------------TAAACTCCCA-AACCCA-TGTGAA-CTTACCTT---CTGTTGCCTCGGCAGGTCGCGTCTACCCTGTGG-----------------G-CACCTACCCTGTA---GG----------ACCCGACCTGGTGGTCGCGGT--CATGCCTGCCGGTGGCCCTTT--A-AACTTTCTGTGTATTCTATGTTAT---------TCTGAGTTGGCA--ACTA-----------AAA-TAAGTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATT-CAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCATTAGTATTCTAGTGG-GCATGCCTGTTCGAGCGTCATTT-CAACCCTTA-AGCCCCTGTCGC----TTAGTGTTGGGAGCCTACAGTCTTCTGTA---------------GCTCCCTAAAGTTAGTGGCGG-AGTCGGT-TTGTACTCTAG-ACGTAGTAGATT-------CTA-TCTC-GTCTATAGTTAAGCCGGTCTCTTG--CCGTAAAACCCCCT-------------AATTTCTCAA-GG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 5.8s ITS2 with P4-4') = N: 1-635; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1 5.8s ITS2 with P4-4') = N: 1-635; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2263] TITLE 'ITS1 5.8S ITS2 with P2-6'; LINK TAXA = Taxa3; DIMENSIONS NCHAR=580; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 460 470 480 490 500 510 520 530 540 550 560 570 580 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Amphisphaeria_umbrina AAGAGTTT---ACA-AAACTCCCA-AACCCATGTGAAT---TTACCC----CTG-TTGCCTCGGCGGA-A---GT-TACCCTGTAG-CAC-CTACCCTACAG-------CGGTTCGAGCCTACCCTGTAA----CCCGCCGGTGGATTTTGAAACTCT-TGT-TATTACAG---TGTCATCTGAGCG--TCTTATTCTAAATAA-GTCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGA-TTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCATTAGTATTCTATTGG-GCATGCCTGTTCGAGCGTCATTTCGACCATT--AAGCC--------TAGCTTAGCGTTGGGAATCTACTGTCCGGGCGGAGCTACCTGTAGCTTACCCTGTAGTTCCTGAAAATGAACGGCGGATTCG--TGGTGTCCTCTGA-GCGTAGTAAT---------ATTTCTCGCT---TCTGTTAGGTGCTACGATCT--GGCAGTTAA---------CCC-AATCT-T------ Candida_glabrata AGGTGTTTTATCACACGACTCGAC--A-CTTTCTAATTACTACACACAGTGGAGTTTACTTTACTACTATCTTTTGTTCGTTGGGGGAACGCTCTCTTTCGGGG----GGGAGTTCTCCCAGTGGATGCAAACACAAACAAATATTTTTTT--AAACTAATTCAGTCAACA-CAAGA--TTTCTTTT-----AGTAGAAAACAACTTCAAAACTTTCAACAATGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCTCTGGTATTCCGGGGG-GCATGCCTGTTTGAGCGTCATTTC-CTTCTCA-AACACATTGT--G---TTTGGTAGTGAGTGATACTCGTTTT--------TGAGTTAACTTGAAATTGTAGGCCATATCAGTATGTGGGACACGAGCGCAAGCTTCTCTATTAATCTGCTGCTC-------GTTTGCGCGA-G--CGGCGGGGGTTAATACTGTATTAGGTTTTACCAACTCGGTGTTGATCTAGGGAGGG Claviceps_purpurea CCGAGTT-----TA-CAACTCCCA-AACCCATTGTGAACTTATACCC-AAAACG-TTGCCTCGGCGGACACA-GCGGTACCCGA-GCCCC-CGCAAGGGAGCAAA--GGCGCCC-----CGTCCGCCAGGGGACCAAAACTCTT-CTGTAT-ACCCATAGCGGCATGTCTG---AGTGGATTTA--A--AAAC-----AAATGA-ATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGACTTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGTATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCCCTGCTTGG--TGTTGGGGACCGGCTCAGCGGGTGCGGG-----CTTC--GGCCCGCCCCGTGCCGCCCCCGAAATGGATCGGCGGT--CTCGTCGCAGCCTTCTTTGCGTAGTAAC---------ATAC-CACCTCGCAACAGGAGCGCGGCGCGGCCACTGCCGTAAA------ACGCCC-AACTTTTTAGA-G Dothidea_hippophaeos CGACCTAA---AAAATCGCGACCACTTCCAACCCTCTGTTGTTATAACTACCTTGTTGCTTTGGCGGGACC--GTTCGGTCCTCC-------GAGCGCACCAG-------TCCT-----CGGACAGGTGA----GCGCCCGCCAGAGT-CCAACCAAACTCTTGTTTTTAA-CCAGTCGTCTGAGTA--TAAAATTTTAATTAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTACACCACTC--AAGCACT-----G---CTTGGTATTGGGC-----ATCGTCCGTC----GAAAGGCG----------GGCGTGCCTCGAAGACCTCGGCGGGGTTT---CTCCAACTTCGG-GCGTAGTAGAGTTAAA---TCGAACGTCT-TATAAG--CTTGGTGGGACTCCATTGCCGTTAAACCTTT-------TATTTTTATA-GG Elsinoë_australis AAGGGTTTCCGAAAGGAGCCCGAACTCCCCACCCTTTGCTGTTGCGAAT--CT-GTTGCTTCGGCGGGCCC--GCCCCCCCATCCCTGGG-GGGGCGGCCGGG-------CCTCA----CCGCCCGGACA----GCGCCCGCCGGAGGACCGAATCAACTCTGTTTTT-AACCATAATGTCGGAGTA--CTTTTGTACAATCAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCGAGGG-GCATGCCTGTTCGAGCGTCATTTCACCAATC--AAGCCCC-----G---CTTGGTATTAGGCGCCTGGCCGCCCCCC----CCGTGGCC----------GGCCCGCCCGAAATGCATCGGCGAGG------CACCGACCCCCG-GCGTGTTAGAATTTC-----GAAACGTC---AGGAGCACCGGTGTTAAC--CTCTGCCGTGAAACCTTT-CAAAC-TATTTTTCTAA-G Gelasinospora_nigeriensis CAGAGTTG---CAA--AACTCCCACAAACCATCGCGAATC-TTACCC-GTAC-GGTTGCCTC-GGCGCTGGCGGTCCGGAAGGCCCTCGG-GCCCCCGGATCCTCGGGTCTCCC-GCTCG--CGGGAGGCTGGCCCGCCGGAGTGCCGAA--ACCAAACTCTTGATATTTTATGTCTC-TCTGAGTA--AACTT-TT-AAATAA-GTCAAAACTTTCAACAACGGATCTCTTGGTTCCGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCTCGCCAGTATTCTGGCGA-GCATGCCTGTTCGAGCGTCATTTCAACCATC--AAGCTCT---------GCTTGCGTTGGGGATCCGCGG--CTGC-----CCGC----------------GGTCCCTCAAAAACAGTGGCGGGCTCG-CTAGTCA-CACCGA-GCGTAGTAAC----------TCTACATC--GTTCTGGTCGTGCGGCGGGT-TCTTGCCGTAAA------ACCCCCCAATTTCT-AA-GG Glomerella_graminicola TCGAGTT-----AC-CG-CTCTAC-AACCCTTTGTGAAC--ATACCT--AACTG-TTGCTTCGGCGGGCAGGGGGTCCCCCCGGGGACGC-CCTCCCGGCCCC-----GCCCCC-----CTACCAGGGGACGTGGCGCCCGCCGGAGGATA--CCCAACTCTATTTTAACGACGTTTCTTCTGAGTG--GCACAAGC-AAAT-A-ATTAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGCATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCTCTGCTTGG--TGTTGG-----GGCCCTACGGTTGACG-------TA------------------GGCCCTCAAAGGTAGTGGCGGACCCTCCCGG-AGCCTCCTTTGCGTAGTAAC---------TA--ACGTCTCGCA-TCGGGATCCGGAGGGACTCTTGCCGTAAA------ACCCCCCAATTTTTCAATGG Hypocrea_rufa CCGAGTT-----TA-CAACTCCCA-AACCCAATGTGAACC-ATACC--AAACTG-TTGCCTCGGCGGGGTCACGCCCCGGGTGC-GTCGC-AGCCCCGGAACCA---GGCGCCC------GCCGGAGGGACCAACCAAACTCTTTCTGTAG-TCCCCTCGCGGACGTTATTTTTACAGCTCTGAGCA--AAAATTCA-AAATGA-ATCAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGTATTCTGGCGG-GCATGCCTGTCCGAGCGTCATTTCAACCCTCG-AACCCCTCCGGGG--GGTCGGCGTTGGGGACTTCGGGAACCC------CTAA--GACGGGATCC----CGGCCCCGAAATACAGTGGCGGT--CTCGCCGCAGCCTCTCATGCGCAGTAGT---------TTGCACAACTCGCACCGGGAGCGCGGCGCGTCCACGTCCGTAAA------ACACCC-AACTTCTGAAATG Ophiostoma_ulmi CAGAGTTT---TTT-CAACTCCCA-ACCCTTGCGAA--CC-GTACCCCGTTCTGTTTGCTTCTGGCGGGAGGGGAGGGGCGCGTCTTCGG-GGCGCTGCCTC-TC---TCTCCCAGGTCCTTCGGGCGCCCGCCACGGCCGCGAGCCGCCTGAACCTTTTCTAAACCAGTAACGAAACGTCTGAGAA--ACAAA-CA-AAAACA-GCCAAAACTTTCAACAACGGATCTCTTGGCTCTGGCATCGATGAAGAACGCAGCAAAATGCGATACGTAATGCGAATTGCAGAATTCAG-GAGTCATCGAA-TCTTTGAA-CGCACATTGGGCCCGCCAGTATTCTGGCGG-GCATGCCTGTCCGAGCGTCATTTCCCCCCTCAGATGCCCTTTTGGGAGGGCTGGTGTTGGGCTCCTGCCCT-CTGC-----GTGC--G-A-----------GGGCCCTCAAAACCAGTGGCGGGCCCGTCTGGTTGGCTCCGA-GCGCAGTACCGAACGCAAGTTCTCTCTCTCGCTCTGCAGCCCCGGTCGGTGCCCAGCCGTCAACGGCGCTCGGCCCTGCTTGC--A-GG 'P2-6' CTGAGTT-----TA-CG-CTCTAC-AACCCTTTGTGAAC--ATACCTATAACTG-TTGCTTCGGCGGGTAGGGTCTCCGC-----GAC---CCTCCCGGCCTC-------CCGC-----CT-CCGGGCGGGTCGGCGCCCGCCGGAGGATA-ACCAAACTCTGATTTAACGACGTTTCTTCTGAGTG--GTACAAGC-AAAT-A-ATCAAAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGC-AAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCGCCAGCATTCTGGCGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTC--AAGCTCTGCTTGG--TGTTGG-----GGCCCTACAGCTGATG-------TA------------------GGCCCTCAAAGGTAGTCGCGAACCCTCTCGGGAGCCTCCTTTGCGTAGTAAC---------TT-TACGTCTCGCACTGGGGATCCGGAGGGACTCTTGCCGTAAA------ACCCCC-AACTTTCCAAAGG Phaeocryptopus_gaeumannii AAGGGTTA---TTCGTAGCC-CGACCTCCAA{AC}CCTTTGTTGTTATAACTACCTCGTTGCTTTGGCGGGACC--GCTCGGTC-TC--------GAGCTG-CTGG-------TCTT-----CGGCCCGGCAA----GTGCCCGCCAGAGT-CTACTCAAACTCTTGTTTT-AA-CCGGTCGTCTGAGT---TAAACTTTTAATTAA-ATTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAAATCTTTGAAACGCACATTGCGCTCCCTGGTATTCCGGGGGAGCATGCCTGTTCGAGCGTCATTACACCACTC--AAGCACT-----G---CTTGGTATTAGGCC----ATCGTCCCCC----GAAAGGTG----------GGCGTGCCTCAAACACCTCGGCGGAACCT---CACCGGCTTTGG-GCGTAATAAAATTTC----TC-AACGTCT-TATAAGTACCGGTTCTGACTCCTTTGCCGTTAAACCCCA-------AACTTTTAAA-GG Saccharomyces_cerevisiae TGTGCTTTTGTTATAGGACTTAAA--ACCG-TTTCAATACAACACACTGTGGAGTTTTCATATCTTTG-CAACTTTTTCTTTGGG----------CATTCG-A-----GCAATCGGGGCCAGAGGTAACAAACACAAACAATTTTATTTATTCATTAAATTTTTGTCAAAAACAAGAATTTTCGTAACTGGAAATTTTAAAATA-TTAAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTG-?CCCCTTGGTATTCCAGGGG-GCATGC-TGTTTGAGCGTCATTTC-CTTCTCA-AACA--TTCT--G---TTTGGTAGTGAGTGATACTCTTTG----------GAGTTAACTTGAAATTGCTGGCCTTTTCA-----TTG--GATGTTTTTTT--TT-TCCAAAGAGAGGTTTCTCT------GCGTGCTTGA-GGTATAATGCAAGTACGGTCGTTTTAGGTTTTACCAACTGCGGCTAATCTTTTTTATAC Torulaspora_delbrueckii ACTGTTTCTCTGTCTGCGGTTCAC---TGCCTAAAAATTATACACACACTGGAGTTTTCTTTTAAAACACTTCTTCTTCTTTGGG----------C-TT---------GCAA--GAGCCCGGAGTTGACAAACACAAACAATTTTGTT-AT--ATTATAATCAAGTCAAAACCAA----TTTCGTTA-T-GAAATAC-AAATAA-TTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCCTTGGTATTCCAGGGG-GCATGCCTGTTTGAGCGTCATTTC-CTTCTCA-AAGAACTCTT--C---TTTGGTAGTGAGTGACACTCTTTCT--------AGAGTTAACTTGAAATTGCTAGCCATATAA-----TAGCTGTTGATTGCTGACTT-TGGACGGAGCGATTTGTCCA-----GTCTGCT-G-----ATACCG--ATT---GTCGTATTAGGTTTTACCAACTTCGACGG-ACGTAGTGTTAG Xylaria_hypoxylon AAGAGTTT---TGATAAACTCCCA-AACCCATGTGAA-C--TTACCT--T-CTG-TTGCCTCGGCAGGTCGC-GTCTACCCTGTGGGCAC-CTACCCTGTAGGAC----CCGACCTGGTGGTCGCGGTCATG--CCTGCCGGTGGCCCTTTAAACTTTCTGTGTATTCTAT---GTTATTCTGAGTT--GGCAACTA-AAATAA-GTTAAAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAA-TCTTTGAA-CGCACATTGCGCCCATTAGTATTCTAGTGG-GCATGCCTGTTCGAGCGTCATTTCAACCCTT--AAGCCCCT----GTCGCTTAGTGTTGGGAGCCTACAGTC--------------------TT---CTGTAGCTCCCTAAAGTTAGTGGCGGAGTCG--GTTTGTACTCTAG-ACGTAGTAGA---------TTCTATCTCG---TCTAT-AGTTAAGCCGGTCTCTTGCCGTAAAA------CCCCCTAATTTCTCAA-GG ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P2-6') = N: 1-580; CODONPOSSET CodonPositions (CHARACTERS = 'ITS1 5.8S ITS2 with P2-6') = N: 1-580; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M2269] TITLE '5.8S P1-9'; LINK TAXA = Taxa2; DIMENSIONS NCHAR=158; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 ] [ . . . . . . . . . . . . . . . ] 'Ceratobasidium oryzae-sativae' AAAGTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCTTGGAGCATGCCTGTTTGAGTATCATGA Cystofilobasidium_capitatum TAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCTCTTTGGTATTCCGAAGAGCATGCCTGTTTGAGTGTCATGA Gigaspora_albida AAACTTTCAACAATGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCAAAATGCGATAAGTAATATGAATTGCAGAATTCCGTGAATCATCAAATTTTTGAACGCAAATTGCACTTCTTGGTATTCCAAGGAGTACACATGCTTGAGGGTCGTTA Glomerella_graminicola AAACTTTTAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGCATTCTGGCGGGCATGCCTGTTCGAGCGTCATTT Glomus_mosseae TCACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAGTGTGAATTGCATAATTTTGTGAATCATCGAATCTTTGAACGCAAATTGCACTCCCTGGTATTCCGGGGAGTATGCCTGTTTGAGGGTCGTTA Hypocrea_rufa AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCGCCAGTATTCTGGCGGGCATGCCTGTCCGAGCGTCATTT 'P1-9' TAACTTTTGACAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCTTGGAGCATGCCTGTTTGAGTGTCATGA Phaffia_rhodozyma AAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATGA Pleospora_herbarum CAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATACGTAGTGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCAAAGGGCATGCCTGTTCGAGCGTCATTT Saccharomyces_cerevisiae AAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATACGTAATGTGAATTGCAGAATTCCGTGAATCATCGAATCTTTGAACGCACATTG-?CCCCTTGGTATTCCAGGGGGCATGC-TGTTTGAGCGTCATTT Sorosporium_saponariae CAACTTTCGGCAACGGATCTCTAGGTTCTCCTATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGACATCAGTGAATCATCGAATCTTTGAACGCATCTTGCGCCCTTTGGTATTCCTTAGGGCATGCCTGTTTGAGTGTCACGA Sporisorium_sorghi CAACTTTTGGCAACGGATCTCTTGGTTCTCCCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGA----AGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCCTGCTAATCTGGGGAGCATGCCTGTTTGAGGGCCGCGA Thanatephorus_cucumeris TAAGTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCTTGGAGCATGCCTGTTTGAGTATCATGA Ustilago_vaillantii CAACTTTCGGCAATGGACCTCTTGGTTCTCCTATCGATGAAAAACCCAGCGAATTGCAATAAGTAATGTGAATTGCAAAATTCATTGAACCATTGATTTTTTGAACGCATCTTGCCCCCTTTGGTATTCCTTAGGGCATGCCTGTTTGAGTGTCATGA Xanthophyllomyces_dendrorhous AAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAATTGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACCTTGCGCTCCTTGGTATTCCGAGGAGCATGCCTGTTTGAGTGTCATGA Xylaria_hypoxylon AAACTTTCAACAACGGATCTCTTGGTTCTGGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCATTAGTATTCTAGTGGGCATGCCTGTTCGAGCGTCATTT ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = '5.8S P1-9') = N: 1-158; CODONPOSSET CodonPositions (CHARACTERS = '5.8S P1-9') = N: 1-158; END; BEGIN TREES; TITLE Tb5802; LINK TAXA = Taxa4; TRANSLATE 1 Gelasinospora_nigeriensis, 2 Hypocrea_rufa, 3 Glomerella_graminicola, 4 Xylaria_hypoxylon, 5 Exophiala_spinifera, 6 Rhinocladiella_atrovirens, 7 Exophiala_jeanselmei, 8 Capronia_pilosella, 9 Capronia_pulcherrima, 10 Capronia_coronata, 11 'P4-4', 12 Trimmatostroma_cordae, 13 Coniosporium_perforans, 14 Phaeococcomyces_catenatus, 15 Dothidea_hippophaeos, 16 Phaeocryptopus_gaeumannii, 17 Elsinoe_australis, 18 Saccharomyces_cerevisiae, 19 Torulaspora_delbrueckii, 20 Candida_glabrata; TREE Fig._5 = [&R] (((((((5,6),7),((8,9),10)),(((11,12),13),14)),((15,16),17)),((1,2,3),4)),((18,19),20)); END; BEGIN TREES; TITLE Tb5803; LINK TAXA = Taxa1; TRANSLATE 1 Phaeosphaeria_avenaria, 2 Ophiosphaerella_herpotricha, 3 Pleospora_herbarum, 4 Dothidea_hippophaeos, 5 Phaeocryptopus_gaeumannii, 6 Elsinoë_australis, 7 Cladosporium_tenuissimum, 8 Cladosporium_cladosporioides, 9 Cladosporium_sp., 10 Cladosporium_herbarum, 11 Cladosporium_oxysporum, 12 Cladosporium_sphaerospermum, 13 'P4-5', 14 Cladosporium_fulvum, 15 'P4-7', 16 MS594, 17 Mycosphaerella_graminicola, 18 Botryosphaeria_dothidea, 19 Saccharomyces_cerevisiae, 20 Torulaspora_delbrueckii, 21 Candida_glabrata; TREE Fig._6 = [&R] (((((((((7,8),9),(10,11)),12),((15,16,17),(13,14))),18),((4,5),6)),((1,2),3)),((19,20),21)); END; BEGIN TREES; TITLE Tb5801; LINK TAXA = Taxa6; TRANSLATE 1 Colletotrichum_coccodes, 2 Colletotrichum_acutatum, 3 Colletotrichum_musae, 4 Colletotrichum_fragariae, 5 'P2-6', 6 Glomerella_cingulata, 7 Glomerella_graminicola, 8 Colletotrichum_orbiculare, 9 Hypocrea_rufa, 10 Elsinoë_australis, 11 Saccharomyces_cerevisiae; TREE Fig._4 = [&R] (((((((3,4,5,6),1,7),2),8),9),10),11); END; BEGIN TREES; TITLE Tb5799; LINK TAXA = Taxa3; TRANSLATE 1 Candida_glabrata, 2 Torulaspora_delbrueckii, 3 Saccharomyces_cerevisiae, 4 Claviceps_purpurea, 5 Hypocrea_rufa, 6 Glomerella_graminicola, 7 'P2-6', 8 Gelasinospora_nigeriensis, 9 Ophiostoma_ulmi, 10 Amphisphaeria_umbrina, 11 Xylaria_hypoxylon, 12 Elsinoë_australis, 13 Phaeocryptopus_gaeumannii, 14 Dothidea_hippophaeos; TREE Fig._2 = [&R] (((((7,6),(5,4),(9,8)),(11,10)),((14,13),12)),((3,2),1)); END; BEGIN TREES; TITLE Tb5798; LINK TAXA = Taxa5; TRANSLATE 1 Chlorella_ellipsoidea, 2 'P3-2', 3 Pteridium_aquilinum, 4 Lilium_parryi, 5 Ginkgo_biloba, 6 Cicer_reticulatum, 7 Phytophthora_ilicis, 8 Achlya_bisexualis, 9 Glomus_mosseae, 10 Lentinula_edodes, 11 Xylaria_hypoxylon, 12 Gelasinospora_nigeriensis, 13 'P2-6', 14 Glomerella_graminicola, 15 'P4-5', 16 Mycosphaerella_graminicola, 17 Eurotium_rubrum, 18 Pleurotus_pulmonarius, 19 'P1-9', 20 Tremella_foliacea, 21 Puccinia_caricina, 22 Morchella_crassipes, 23 'P4-7', 24 'P4-4'; TREE Fig._1 = [&R] (((((((14,13),12),11),(24,23),22,17,16,15),21,20,19,18,10,9),((((6,4),5),3),2,1)),(8,7)); END; BEGIN TREES; TITLE Tb5800; LINK TAXA = Taxa7; TRANSLATE 1 Colletotrichum_coccodes, 2 Colletotrichum_trichellum, 3 Colletotrichum_dematium, 4 Colletotrichum_destructivum, 5 Colletotrichum_linicola, 6 Colletotrichum_capsici, 7 Colletotrichum_musae, 8 Colletotrichum_fragariae, 9 Colletotrichum_kahawae, 10 Colletotrichum_fuscum, 11 Glomerella_cingulata, 12 'P2-6', 13 Colletotrichum_sublineolum, 14 Glomerella_graminicola, 15 Colletotrichum_acutatum, 16 Colletotrichum_trifolii, 17 Colletotrichum_orbiculare, 18 Colletotrichum_lindemuthianum, 19 Hypocrea_rufa, 20 Elsinoë_australis, 21 Saccharomyces_cerevisiae; TREE Fig._3 = [&R] (((((((((5,4),3),2,1),((13,14),15)),(((((12,11,10),9),8),7),6)),((16,17),18)),19),20),21); END; BEGIN TREES; TITLE Tb5804; LINK TAXA = Taxa2; TRANSLATE 1 Glomerella_graminicola, 2 Hypocrea_rufa, 3 Xylaria_hypoxylon, 4 Pleospora_herbarum, 5 Saccharomyces_cerevisiae, 6 Glomus_mosseae, 7 Gigaspora_albida, 8 'Ceratobasidium oryzae-sativae', 9 Thanatephorus_cucumeris, 10 Phaffia_rhodozyma, 11 Xanthophyllomyces_dendrorhous, 12 Cystofilobasidium_capitatum, 13 Sorosporium_saponariae, 14 Ustilago_vaillantii, 15 Sporisorium_sorghi, 16 'P1-9'; TREE Fig._7 = [&R] ((((8,9),(13,14),10,11,12,15,16),(5,(4,(3,(2,1))))),(6,7)); END;