#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 May 13, 2026; 23:59 GMT

TreeBASE (cc) 1994-2008

Study reference:
Bonito G.M. 2010. A global meta-analysis of Tuber ITS rDNA sequences: species diversity,
host associations and long-distance dispersal. Molecular Ecology, 19(22):
4994-5008.

TreeBASE Study URI:  http://purl.org/phylo/treebase/phylows/study/TB2:S13538]

[ The following blocks are input data for analysis step 10283 ]
BEGIN TAXA;
        TITLE  TaxaForAnalysisStep10283;
        DIMENSIONS NTAX=31;
        TAXLABELS
            Tuber_ITCV142_Mexico_2
            Tuber_ITCV4026_Mexico
            Tuber_ITCV4739_Mexico
            Tuber_ITCV885_Mexico
            Tuber_beyelerii_JT32597_Oregon_3
            Tuber_foetidum_AJ557544_Hungary
            Tuber_foetidum_JT9769_Nepal
            Tuber_lauryi_JT26987_Oregon_13
            Tuber_linsdalei_L63_Type_2
            Tuber_maculatum_AJ557519_2
            Tuber_multimaculatum_A200_Spain_Paratype
            Tuber_rapaeodorum_AJ557522_Hungary_42
            Tuber_sancarloensis_Type_ITCV181_Mexico_7
            Tuber_setatus_Type_ITCV180_Mexico_3
            Tuber_shearii_JT12498_North_Carolina
            Tuber_sp._ex._132b_Carya_Georgia_3
            Tuber_sp._ex._Epipactis_J8_New_York_3
            Tuber_sp._ex._Epipactis_helleborine_California_7
            Tuber_sp._ex._Epipactis_helleborine_California_AY634172
            Tuber_sp._ex._Epipactis_helleborine_California_AY634177
            Tuber_sp._ex._Epipactis_helleborine_Japan_2_AB428786
            Tuber_sp._ex._Populus_Germany_5_AJ510273
            Tuber_sp._ex._Populus_tremula_Austria_2_EF644167
            Tuber_sp._ex._Quercus_Missouri_2_EU202710
            Tuber_sp._ex._Quercus_Missouri_3_EU202706
            Tuber_sp._ex._Quercus_garryana_Oregon_AY969006
            Tuber_sp._ex._Quercus_robur_Hungary_3_DQ355246
            Tuber_sp._ex._Salix_alba_Neatherlands_4_AJ920009
            Tuber_sp._ex._Salix_alba_Neatherlands_AJ920011
            Tuber_sp._ex._clone_Alaska_2_EU2922221
            Tuber_whetstonense_JT25783_Oregon_Paratype_10
            ;
END;

BEGIN CHARACTERS;
[! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M14945]

	TITLE Fig3_Maculatum;
	LINK TAXA = TaxaForAnalysisStep10283;
	DIMENSIONS NCHAR=928;
	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       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940]
[                                                                    .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .         .]
Tuber_ITCV142_Mexico_2                                      ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????G-CCCCTA-ACCAGGG---CTCTC--------------------------------------------------------------------------------------------------------------------------------TATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACTTTTTAAAACCTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCACAAAAGAGTGTGGTTTTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-C-ACCACTCTGCTGGAATG---AATGGGCCGGAAATGTATACCATGGTCACAGACTTTCAGAGTATTTTGGAAT-GCTAA-ACTAGTTTGT-AGGCTTGGTCAGAA-TCTAGGCCATTTGGACCCCCTATTCTGTGTAAAGCAGTAAATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCCAGTAA????????????????????????????????????????????????????????????????????????????????????
Tuber_ITCV4026_Mexico                                       ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????G-CCCTTA-ACAGGGG---CCTACT------------------------------------------------------------------------------------------------------------------------------CTAGAAAA---CTCTA----AAC-TTGCAGTCTGAGAAGGCCATGGGCCATAATC-T-TTACAATTTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGCATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AACCAGTGTGGTATTGGCGGAAGTGGATAG--------GGCT-GGC-----TGTGCTGG-C-CCCACTCTGCTAGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATCTCGTCAT-GCTAA-ATTAGTTTGT-AGGC-TGGTCAGAA-TCCAGGCTG-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCCAGTAA????????????????????????????????????????????????????????????????????????????????????
Tuber_ITCV4739_Mexico                                       ??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TTACTGTCTGAGAAGGCCATGTGCCGTATTC-T-TTAAACTTTTTAAAACCTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAA-AACGCA-CGAAATGCGATAAGTAATGTGAATTGCA-AATTCA-TGAATCATC-AATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTC-AGCGTCACTAACAACCCCA-TCAC-AAAAAGTGTGGTTTTGGCAAA--TGGGTAG---------GCT-AGC-----AGTGCTGG-C-ACCACTCTGCTGGAATG---AATGGGCCGGAAATGTAA-CCATGGTCACAGACTTTCA-AGTATTTTGGAAT-GCTAA-ACTA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_ITCV885_Mexico                                        ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????G-CCCTTA-ACAGGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTAGAAAA---CTCTA----AAC-TTAAAGTCTGAGAAGGCCATGGGCCATAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGCATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AACGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-GGC-----TGTGCTGG-C-CCCACTCTGCTAGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATCTCGTGAT-GCTAA-ATTAGTTTGT-AGGC-TGGTCAGAA-TCCAGGCTG-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCCCAGTAA????????????????????????????????????????????????????????????????????????????????????
Tuber_beyelerii_JT32597_Oregon_3                            ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????TCATTATTATAATGCGTGGAAATG-CCCCTA-ACAAGGG---CTCTC--------------------------------------------------------------------------------------------------------------------------------TATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAAAAACCTCA-TCAC-AAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGCAAGGAAGTGCTGG-C-CCCACTCTGCT{AG}GAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATCGTCAAAT-GCTAA-ATTAGTTTGT-ATGCTTGGTCAGAA-TCTAGGCCA-TTGGACCCCC-ATTCTGTATAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_foetidum_AJ557544_Hungary                             ???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????T-CAATATTTGGG-GTG---CTTG-ACACTGG---CTCCCAATA-AAACCCATCCATGAGTACTC-TGCCATGTTGCTTCCCCAGGCCAGTGGCCACT-GCTGCCAGCCAGGCCGTTATTCGGTCACTTGGTTG------------AGGTGCCTGGGGAAGGGCCAATTAGTAAA---CTTTACATTAAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAAAACC-AGA-TCAC-CAAGAGTGTGGTATTGGCAGAAGTGGGTGG--------GACT-ATA-----AGGGACCCTT--CCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGATCGGAA-CCCAGGCCA-TTAGACCCCC-ATCCTGTGTAAAGCAGT-AAGG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_foetidum_JT9769_Nepal                                 ???????????????????????????????????????????????????????????????????????????????AGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAAGGCGTGGAAAGG-CCCCTGTGACCGTC---CTCACA----------------------------------------------------------------------------------------------------------------------AGGGCCTAATAGAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCACGTGCCGTAATC-T-TTAAACATTTTAAAACCTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AATGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----ATTGCTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAAACTTTCAGAGTATTTTAAGAT-GCTAA-ATTAGTTTGT-AGGC-TGGTCAGAA-TCCAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTT???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_lauryi_JT26987_Oregon_13                              ?????????????????????????????????????????????????????????????????????????????????????????GTATCAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAT--AAATATATGGGA----TGCTCA-ATATGAG---TTCTCAACA-AAACACTTTCATGTGTATCC-TTCCATGTTGCTTCCTCAGGCCAGTAGCCATT-GCTACCAGCCAGGCCGATCTTCGGTCACTAGGTTG------------AGGTGCCTGGGGAAGGGTCAATCATGAAA---CTTTACATTGAC-TTATTGTCTGACAAGGCCATGTGCCATTATA-T-TTAAATATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCATATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAACAACC-AA-TCAC-CTTATGTGTGGTATTGGCAGATGTGGGTTGAGTACAA-AGCTTAGC-----AGTGATACTCTCCCACACTGTTGGAATG---AATAGGCTAGAAAAGTAGATCATAGCAACAGACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGGTCAGAA-TCTAGGCCA-TTTGACCCCC-ATTCTGTGTAGAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTAACGCCT-CTGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCCGGA
Tuber_linsdalei_L63_Type_2                                  AGGCCTTCGGAGCGCTCGATGGAGGTCGGCAACGACCACCGCCAGGTGCAAAGTTGGTCAAACTTGGTCATTTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAATG-CCCCTA-ATAAGGG---CTCTCATGA--------------------------------------------------------------------------------------------------------------------------------AAA---CTCTA----AAC-CTACAGTCTGAGAAGGCCATGTGCCGTAAAC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACG{CT}ACAT{CT}GCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCACAAAGTAGTGTGGTATTGGCAGAAGTGGGTAG--------GGGTAAGC-----AGTGCTGC-C-TCCACTCTGCTGGAATA---AATAGGCCGGAAATGTAGACCATGATAACAAACTTTCAGAGTATCGTCATAT-GCTAA-ATTAGTTTGG-AAGC-TGGTCAGAA-TCCAGGCCA-TTGGACCCCC-ATCCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CC{CT}{CT}AGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAACCTGGTACCTCTG?????????????????????????????????????
Tuber_maculatum_AJ557519_2                                  ????????????????????????????????????????????????????????????????????????????????????????????????GGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAC--CAATATCTGGGCATG-CAAAAG-ACACA{GT}G---CTCCCGATA-AAACACATTTATGCGTATCC-TCCCATGTTGCTTCCCCAGGCCAGTGGCCACT-GCTGCCAGTCAGGCCGTTATTCGGTTACTTGGTTG------------AGGTGCCTGGGGAAGGGCCAATTATCAAA---CTTTACATTAAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATA-T-TTAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCGCTAAAACCCAGA-TCAC-CTAGAGTGTGGTATTGGCAGAAGTGGATAT--------GGCT-ACTA--TCAGGGCTGT-T-CCCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTGTTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGATCGGAA-CCCAGGCCA-CTTGACCCCC-ATCCTGCGTGAAGCAGT-AAGGTTGACCTCGGATCAGGTAGG?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_multimaculatum_A200_Spain_Paratype                    ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????CATTAATATATT---TGGGA-TA-CCCTTA---CAGGTTCCCTATCCTTTAAACCTCTCTGTGTACCAATCCATGTTGCTTTCCTCAGATCAGCAGCCACTGCTGCCTGTATAGTTCACAATGGGCTAATATACAGAGGTATCTGGGGGAGGGTCTTCTTATAACTC-----------ATAT---TGTT----AACCATGCAGTCTGAGTTGGCTGAATACCATACATATCTTGAATAAGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGTATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGCATTCCTCAGGGCA----TGCCTGTTCGAGCGTCACTACAAACCTCACTCAC-AACAATTGTGGTAATGGTAGGAGTGGATTATTAT----GACAAAGTC----AC--CAGT-C--ACACCCTACCGAAATGC---ATTGGGCGGACTTTTAGGCTTAGTGAAGAGACTT--AGTACATGTTCAAAGAATATATAATAGTCTCA--TGCTAGGTTAGGT--CCTGCCTGCCTGGACCTCC-ATCTGGTTTATAT-ACT--GGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCCGGAGGAA?GAA????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_rapaeodorum_AJ557522_Hungary_42                       ?AGCTATCATCCACGCGTGGAGCTCTCCATAGGTCGACCTGCAGGCGGCCGCACTAGTGATTCTTGGTCCATTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAC--CAATATCTGGG-ATG-CCAAAG-ACACAGG---CTCCCGATA-AAACACATTTATGCGTATCC-TCCCATGTTGCTTTCCCAGGCCAGCGGCCACT-GCTGCCAGCCATGCCGTTTTTCGGTTACATGGTTG------------AGGTGCTTGGGGAAGGGCTAATTATCAAA---CTTTACTTCACC-TTATTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCGCAAAAACCCAGA-TCAC-CTAGAGTGTGGTATTGGCAGAAGTGGCCGG--------GGCT-ATC-----AGCGCTGC-T-GCCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCACAGTATTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGATCGGAA-CCTAAGCCA-TTTGACCCCC-ATCCTGCGTAAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTAACGCCT-CTGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCCGGA
Tuber_sancarloensis_Type_ITCV181_Mexico_7                   ???????????????????????????????????????????????????????????????????????TTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGAAAATG-CCCCTA-ACACGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTAGAAAA---CTCTA----AAC-TTACAGTCTGAGAAGGCCATGGGCCATAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGCATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-GGC-----AGTGTTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATGATAACAGACTTTCAGAGTATCCCCTGAT-GCTAA-ATTAGTTTGT-AGGC-TGGTCAGAA-TCCAGGCCG-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTGCCCCCAGTAA????????????????????????????????????????????????????????????????????????????????????
Tuber_setatus_Type_ITCV180_Mexico_3                         ????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GCCCCTA-ACCAGGG---CTCTC--------------------------------------------------------------------------------------------------------------------------------TATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACTTTTTAAAACCTTCAACAACGGATCTCTTGGCTCTCGCTTCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCAA-TCACCAAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-C-TCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATTTTGGAAT-GCTAA-ATTAGTTTGT-AGGCTTGGTCAGAA-TCTAGGCCATTTGGACCCCC-ATTCTGCATAGAGCAGTAAATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCCCAGTAA????????????????????????????????????????????????????????????????????????????????????
Tuber_shearii_JT12498_North_Carolina                        ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????T?TGGG---TTCCCAAAACAAACACATTCATGTGTATCC-TCCCATGTTGCTTTCCCAAGCCAGTGGCCACT-GCTACCAGCCAGTCCATTATTTGGTCTTCAGGTTG------------AGGTGCTTGGGAAAGGGTCATTTAACAAA---CTTTATATTAAC-CTATTGTCTGATGAGGCTATATGCCATAATA-T-GTAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACAAACAATCTGA-TCAC-CATATGTGTGGTATTGGCAGAAGTGGATAT--------AGTC-ATG-----AGTTTCAGAC-TCCACTCCGCTGGAATA---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTATTTTGGAAT-ACTAA-ATTAGTTTA--GAGC-AGATCAGAA-TCCAGGCCA-GTTGACCCCC-ATCCTGTGTAATGCAGT-AAGGTTG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._132b_Carya_Georgia_3                          ???????????????????????????????????????????????????????????????????????????????????????????????AGGTTTC?GTAGGTGAAC?TGCGGAAGGATCATTA{AT}CACAATATGTGGGA----TGCTCA-ATATGAG---CTCCCAAAATAAACACATTCATGTGTATCC-TTCCATGTTGCTTTCCCAGGCCAGTGGCCACT-GCCACCAGCCAGTCCATTATTTGGTCTTCAGGTTG------------AGGTGCTTGGGAAAGGGCCAATTATCAAACTTCTTTATATTAAC-CTATTGTCTGATGAGGCTATATGCCGTAATA-T-GTAAATATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCATAAACAATCTGA-TCAC-CATATGTGTGGTATTGGCAGAAGTGGATAT--------AGTC-AAG-----AGTATTAGAC-TCCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATGGCAATAGACTTTCAGAGTATTTTAGAAT-GCTAA-ATTAGTTTG--GAGC-TGATCAGAA-CCCAGGCCA-GTTGACCCTC-ATCCTGTGTAAAGCAGT-AAGAATGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGACATCT-CTGATGTTCGAGTTGTAATTTGGAGAGACATCTTCTGGA
Tuber_sp._ex._Epipactis_J8_New_York_3                       ??????????????????????????????????????????????????????????????????????????????????????????????????GGTTCGTAGGTGA-CCTGCGGAAGGATCATTAC{AG}A-AATATCTGGGA----TGCTCA-ATATGAG---TTCCCAACA-AAACACATTTATGCGTATTC-TTCCGTG-TGTTTCCCCAGGCCAATGGCCAGTATGTACCATCTTGGCCCATAACAGGGTATCCAGCTGGTGTACAGCCGCGTGTGTCTGGGAAGGCCCAAATTGGCAAAA--CTTTATGTTAAC-TTACTGTCTGACAAGGCCATGTGCCCCTGTATT-TTAAATATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAAAAACCCCA-TCAC-ATTATGTGTGGTATTGGCAGAAGTGGGTAC------------------------------T-CCCACCCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCGTAGCAACAGACTTTCAGAGTGTTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGGTCGGAACCCCAGGCCA-TTTGACCCCC-ATTCTGCACAAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAATAAG{CG}CGGAGG???????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Epipactis_helleborine_California_7            ?????????????????????????????????????????????????????????????????????CATTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAATG-CCCCTA-ACAAGGG---CTGTCT------------------------------------------------------------------------------------------------------------------------------CTATAAAA---CTCTA----AAC-TTACAGTCTGAGAAGGCCATGTGCCATAATC-T-TTAAACTTTTTAAAACCTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCACAAAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATTTTGCAAT-GCTAA-ATTAGTTTGT-AGGCTTGGTCAGAA-TCTAGGCTATTTGGACCCCC-ATTCTGCGTAAAGCAGTAAATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGACACCT-TTGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCTGGA
Tuber_sp._ex._Epipactis_helleborine_California_AY634172     ????????????????????????????????????????????????????????????????????????TAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAT--CAATATCTGGGA----TGCTCA-ATATGAG---CTCCCAACA-AAACACATCCATGCGTATCC-TTCCATGTTGCTTTCCCAGGCCTGTGGCCACT-GCTACCAGCCCGGCCATTATTTGGTTATCAGGTTG------------AGGTGCCTGGGGAAGGGTCAATCATGAAA---CTTTACATTACA-TTACCGTCTGAAAAGGCCATGTGCCGTTATA-T-ATAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCTGA-TCAC-CTCATGTGTGGTATTGGCAGAAGTGGGTAGAGCATAGTTGCT-AGT-----AG-------T-CCCACCCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--GAGC-TGGTCGGAA-CCCAGGCCA-TTTGACCCCC-ATTCTGTGTAAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Epipactis_helleborine_California_AY634177     ??????????????????????????????????????????????????????????????????????ATTAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGATAGGCCCCCTA-ACAGGGG---CTCCC--------------------------------------------------------------------------------------------------------------------------------TAGAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTTAACTTTTTAAAACCTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAAAAGACCCA-TCACACAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-GGC-----AGTGCTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTGGACCACGGTAACAGACTTTCAGAGTATTTTGAAAT-GCTAGTTTTAGTTTGT-AGGCTTGGTCAGAA-TCTAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGA??????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Epipactis_helleborine_Japan_2_AB428786        ???????????????????????????????????????????????????????????????????????????????????????????????????????GTAGGTGAACCTGCGGAAGGATCATTAT--CAATATTTGGGG----TGCTTG-ACACTGG---CTCCCAATA-AAAC{AC}CATCCATGAGTACTC-TGCCATGTTGCTTCCCCAGGCCAGTGGCCACT-GCTGCCAGCCAGGCC{AG}TTATTCGGTCACTTGGTTG------------AGGTGCCTGGG{CG}AAGGGCCAATTAGTAAA---CTTTACATTAAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAA-AACCAGA-TCAC-CAAGAGTGTGGTATTGGCAGAAGTGGGTGG--------GACT-ATA-----AGGGACCC-T-TCCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGATC{AG}GAA-CCCAGGCCA-TTAGACCCCC-ATCCTGTGTAAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGACACCT-CTGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCAGGA
Tuber_sp._ex._Populus_Germany_5_AJ510273                    ????????????????????????????????????????????????????????????????????????TAGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAAAGCCCCCTT-ACAGGGG---CTCTC--------------------------------------------------------------------------------------------------------------------------------TAGAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCTACGTGCCATAATC-T-TTAAATATTTTAAAACCTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-GGC-----ATTGCTGG-T-CCCACTCTGCTGGAATG---AATAGGCCGGAACTGTAGACCATAGTAACAGACTTTCAGAGTATTTTAAGAT-GCTAA-ATCAGTTTGT-ATGC-TGGTCAGAA-TCCATGCCA-TTGGACCCCC-ATACTGTGGAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCATA?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Populus_tremula_Austria_2_EF644167            ????????????????????????????????????????????????????????????????????????????????????????????????????TCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAATGCCCCCTA-ACAGGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTAGAAAA---CTCTA----AAC-TTACAGTCTGAGAAGGCCATGGGCCATAACC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGCATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-GGC-----AGTGCTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCA{GT}GGTGACAGACTTTCAGAGTATCTCGTAAT-GCTAA-ATTAGTTTGT-AGGC-CGGTCAGAA-TCCAGGCTG-{GT}TGGACCCCC-ATT{AC}TGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-A???????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Quercus_Missouri_2_EU202710                   ?????????????????????????????????????????????????????????????????????TTAGAGGAAAGTAAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAC--AAATATCTGGGA----TGCTCA-ATATGAG---TTCCCAACA-AAACACATTCATGCGTATCC-TTCCATGTTGCTTCCCCAGGTCAATGGTCAGTAGTTACCGTCTTGGC{CT}CATAACAGGGTATCCAGCTGGTCTACGGCCGCGTGTGCCTGGGAAGGTCCAAATTGGCAAAA--CTTTATATTAACTTTAC{CT}GTCTGACAAGGCCATGTGCCACTGTA-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCACTAAAAACCCC{AG}-TCAC-ATTAT{GT}TGTGGTATTGGCAGAAGTGGGTAG------------------------------T-CCCACCCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAACAGACTTTCAGAGTGTTTTGAAAT-GCTAA-ATTAGTTTG--AAGC-TGGTCGGAACCCCAGGCCA-TTTGACCCCC-ATTCTGCATGAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGACGCCT-CCGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCTGGA
Tuber_sp._ex._Quercus_Missouri_3_EU202706                   ?????????????????????????????????????????????????????????????????????????AGAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAATATA-TATATGGGA----TGCTTA-ATATGAG---CTCTCAAAATAAACACATTCATGTGTATAC-TTCCATGTTGCTTTCCCAGGCCAGTGGCCACT-GCCACCAGCCAGTCCATTATTCTGTCTTCAGGTTG------------AGGTGCTTGGGAAAGGG{CT}CAATTATCAAACTTCTTTATATTAAC-CTATTGTCTGATGAGGCTATATGCCGTAATA-T-GTAAATATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCTTTTGGTATTCCTTAGGGCA----TGCCTGTTCGAGCGTCATAAACAATCTGA-TCAC-CATATGTGTGGTATTGGCAGAAGTGGATAT--------AGTC-AAG-----AGTATTGGAC-TCCACTCTGCTGGAATG---AATAGGCTGGAAAAGTAGATCATAGCAATAGACTTTCAGAGTATCTTAGAAT-GCTAA-ATTAGTTTG--GAGC-TGATCAGAA-CCCAGGCCA-GTTGACCCTT-ATCCTGTGTAAAGCAGT-AAGAATG??????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Quercus_garryana_Oregon_AY969006              ????????????????????????????????????????????????????????????????????????????????????????????????????????????????TATGCGGA?AGAATTTTAT--AATTCCTCGGAAATG-----CAAATAAGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTATAAAA---CTCTA----AAC-TTACTGTCTGA?AAGGCCACGTGCCGTAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCTTTTTTCACTAACAACCCCA-TCATACAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-T-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGCAGACCATGGCAACAAACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--GAGC-TGGTCGGAA-TCCAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT?AAGCGGAGGAAAA???????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Quercus_robur_Hungary_3_DQ355246              ????????????????????????????????????????????????????????????????????????????????????????????????GGTTTCCGTAGGTGAACCTGCGGAAGGATCATTAT--CAATTTCTGGAAATG-CCCCTA-ACCCGGG---CTCTCAAGA-AAACACATCCATGCGTATTC-TGCCATGTTGCTTCCCCAGGCCAGTGGCCACT-GCCACCAGTCAGGCATCCATAGGGGAGCTAGACTG------------AGGTGCCTGGGGAAGGGTCATCTATTAAA---CTTTACATTAAC-TTACAGTCTGAGAAGGCAATGTGCCGAAATT-A-TCAAATATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAATAACCTCA-TCAC-CAACTGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----ATTGCTGG-T-CCCACTCTGCTGGAATA---AATAGGCCGGAAATGTAGACCACAGTAACAGACTTTCAGAGTAT-TTGAGAT-ACTAA-ACTAGTTTG--AAGC-TGGTCAGAA-TCCAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AAGGTTGACCTCGGATCAGGTAGGGATACCCGC????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????
Tuber_sp._ex._Salix_alba_Neatherlands_4_AJ920009            ????????????????????????????????????????????????????????????????????????????????????????????????GGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAAGGCGTGGAAATG-CCCCTA-ACAAGGG---CATACT------------------------------------------------------------------------------------------------------------------------------ATATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGTATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAAAAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----GGTGCTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATTGTCACAGACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTGT-AGGCTTGGTTGGAA-TCTAGGCCA-TTCGACCCCT-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGCGACCTCCGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCTGGA
Tuber_sp._ex._Salix_alba_Neatherlands_AJ920011              ?????????????????????????????????????????????????????????????????????????????????????????????????????????????????????GGAAGGATCATTATTATAAGGCGTGGAAATG-CCCCTA-ACAAGGG---CATACT------------------------------------------------------------------------------------------------------------------------------ATATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCATGTGCCGTAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGTATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCATGACTGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAAAAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-C-CCCACTCTGCTGGTATATGTAATAGGCCGGAAATGTAGACCATTGTCACAGACTTTCAGAGTATTTTGAAATCGCTAA-ATTATTGTGTCAGGCTTGGTTGGAATGCCAGGCCA-TTCGACCCCT-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGAATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGCACCCATGCC???????????????????????????????????
Tuber_sp._ex._clone_Alaska_2_EU2922221                      ????????????????????????????????????????????????????????????????????????????????????AAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAATG-CCCCTA-ACAAGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTATAAAA---CTCTA----AAC-TTACAGTCTGAGAAGGCCATGTGCCGTATTC-T-TTAAACCTTTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCA{CT}CGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCAC-AAATAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----ACGGTTGG-C-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGTAGACCATGGTAACAGACTTTCAGAGTATTTTCAAAT-GCTAA-ATTAGTTTGT-AGGCCTGGTCAGAA-TCCAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGGCACCT-CTGGTGCTCGAGTTGTAATTTGGAGAGGCATCTTCTGGA
Tuber_whetstonense_JT25783_Oregon_Paratype_10               ??????????????????????????????????????????????????????????????????????????GAGGAAGTAAAAGTCGTAACAAGGTTTCCGTAGGTGAACCTGCGGAAGGATCATTATTATAATGCGTGGAAATG-CCCCTA-ATAAGGG---CATACT------------------------------------------------------------------------------------------------------------------------------CTATAAAA---CTCTA----AAC-TTACTGTCTGAGAAGGCCACGTGCCGTAATC-T-TTAAACATTTTAAAACTTTCAACAACGGATCTCTTGGTTCTCGCATCGATGAAGAACGCAGCGAAATGCGATAAGTAATGTGAATTGCAGAATTCAGTGAATCATCGAATCTTTGAACGCACATTGCGCCCTTTGGTATTCCATAGGGCA----TGCCTGTTCGAGCGTCACTAACAACCCCA-TCATACAAGAGTGTGGTATTGGCAGAAGTGGGTAG--------GGCT-AGC-----AGTGCTGG-T-CCCACTCTGCTGGAATG---AATAGGCCGGAAATGCAGACCATGGCAACAAACTTTCAGAGTATTTTGAAAT-GCTAA-ATTAGTTTG--GAGC-TGGTCAGAA-TCCAGGCCA-TTGGACCCCC-ATTCTGTGTAAAGCAGT-AATGTTGACCTCGGATCAGGTAGGGATACCCGCTGAACTTAAGCATATCAAT-AAGCGGAGGAAAAGAAACCAACAGGGATTG-CCTTAGTAACGGCGAGTGAAGCGGCAAAAGCTCAAATTTGAAATCTGACACCT-CTGGTGTTCGAGTTGTAATTTGGAGAGGCATCTTCTGGA
;
END;

BEGIN SETS;
	CHARSET excluded (CHARACTERS = Fig3_Maculatum) =  1-121 131-136 146-149 155-166 172-179 230-247 265-277 288-299 307-309 315-318 545-548 576-584 592-597 604-608 696-699 802-928;
END;
BEGIN CODONS;
CODONPOSSET * UNTITLED (CHARACTERS = Fig3_Maculatum) = 
		N: 1-928;
CODONPOSSET  CodonPositions (CHARACTERS = Fig3_Maculatum) = 
		N: 1-928;
END;
[ The following blocks are output data for analysis step 10283 ]
BEGIN TREES;
      TITLE Fig3_Maculatum;
      LINK TAXA = TaxaForAnalysisStep10283;
      TREE Fig._3a = [&R] (Tuber_multimaculatum_A200_Spain_Paratype,((((Tuber_linsdalei_L63_Type_2,Tuber_beyelerii_JT32597_Oregon_3),((Tuber_sp._ex._Populus_Germany_5_AJ510273,Tuber_foetidum_JT9769_Nepal),(Tuber_sp._ex._Epipactis_helleborine_California_AY634177,((Tuber_sp._ex._Epipactis_helleborine_California_7,Tuber_setatus_Type_ITCV180_Mexico_3),(Tuber_ITCV142_Mexico_2,Tuber_ITCV4739_Mexico))))),(((Tuber_sp._ex._Salix_alba_Neatherlands_4_AJ920009,Tuber_sp._ex._Salix_alba_Neatherlands_AJ920011),((Tuber_sp._ex._Populus_tremula_Austria_2_EF644167,((Tuber_ITCV4026_Mexico,Tuber_ITCV885_Mexico),Tuber_sancarloensis_Type_ITCV181_Mexico_7)),Tuber_sp._ex._clone_Alaska_2_EU2922221)),(Tuber_sp._ex._Quercus_garryana_Oregon_AY969006,Tuber_whetstonense_JT25783_Oregon_Paratype_10))),Tuber_sp._ex._Quercus_robur_Hungary_3_DQ355246),((((Tuber_sp._ex._132b_Carya_Georgia_3,Tuber_sp._ex._Quercus_Missouri_3_EU202706),Tuber_shearii_JT12498_North_Carolina),((Tuber_sp._ex._Epipactis_helleborine_California_AY634172,Tuber_lauryi_JT26987_Oregon_13),(Tuber_sp._ex._Quercus_Missouri_2_EU202710,Tuber_sp._ex._Epipactis_J8_New_York_3))),((Tuber_sp._ex._Epipactis_helleborine_Japan_2_AB428786,Tuber_foetidum_AJ557544_Hungary),(Tuber_maculatum_AJ557519_2,Tuber_rapaeodorum_AJ557522_Hungary_42))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr58372]


END;
BEGIN TREES;
      TITLE Fig3_Maculatum;
      LINK TAXA = TaxaForAnalysisStep10283;
      TREE Fig._3c = [&R] (Tuber_multimaculatum_A200_Spain_Paratype,((((Tuber_linsdalei_L63_Type_2,Tuber_beyelerii_JT32597_Oregon_3),(((Tuber_sp._ex._Salix_alba_Neatherlands_4_AJ920009,Tuber_sp._ex._Salix_alba_Neatherlands_AJ920011),((Tuber_sp._ex._Populus_tremula_Austria_2_EF644167,((Tuber_ITCV4026_Mexico,Tuber_ITCV885_Mexico),Tuber_sancarloensis_Type_ITCV181_Mexico_7)),Tuber_sp._ex._clone_Alaska_2_EU2922221)),(Tuber_sp._ex._Quercus_garryana_Oregon_AY969006,Tuber_whetstonense_JT25783_Oregon_Paratype_10))),((Tuber_sp._ex._Populus_Germany_5_AJ510273,Tuber_foetidum_JT9769_Nepal),(Tuber_sp._ex._Epipactis_helleborine_California_AY634177,((Tuber_sp._ex._Epipactis_helleborine_California_7,Tuber_setatus_Type_ITCV180_Mexico_3),(Tuber_ITCV142_Mexico_2,Tuber_ITCV4739_Mexico))))),Tuber_sp._ex._Quercus_robur_Hungary_3_DQ355246),((((Tuber_sp._ex._132b_Carya_Georgia_3,Tuber_sp._ex._Quercus_Missouri_3_EU202706),Tuber_shearii_JT12498_North_Carolina),((Tuber_sp._ex._Epipactis_helleborine_California_AY634172,Tuber_lauryi_JT26987_Oregon_13),(Tuber_sp._ex._Quercus_Missouri_2_EU202710,Tuber_sp._ex._Epipactis_J8_New_York_3))),((Tuber_sp._ex._Epipactis_helleborine_Japan_2_AB428786,Tuber_foetidum_AJ557544_Hungary),(Tuber_maculatum_AJ557519_2,Tuber_rapaeodorum_AJ557522_Hungary_42))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr58374]


END;
BEGIN TREES;
      TITLE Fig3_Maculatum;
      LINK TAXA = TaxaForAnalysisStep10283;
      TREE Fig._3b = [&R] (Tuber_multimaculatum_A200_Spain_Paratype,(((Tuber_linsdalei_L63_Type_2,Tuber_beyelerii_JT32597_Oregon_3),(((Tuber_sp._ex._Populus_Germany_5_AJ510273,Tuber_foetidum_JT9769_Nepal),(Tuber_sp._ex._Epipactis_helleborine_California_AY634177,((Tuber_sp._ex._Epipactis_helleborine_California_7,Tuber_setatus_Type_ITCV180_Mexico_3),(Tuber_ITCV142_Mexico_2,Tuber_ITCV4739_Mexico)))),(((Tuber_sp._ex._Salix_alba_Neatherlands_4_AJ920009,Tuber_sp._ex._Salix_alba_Neatherlands_AJ920011),((Tuber_sp._ex._Populus_tremula_Austria_2_EF644167,((Tuber_ITCV4026_Mexico,Tuber_ITCV885_Mexico),Tuber_sancarloensis_Type_ITCV181_Mexico_7)),Tuber_sp._ex._clone_Alaska_2_EU2922221)),(Tuber_sp._ex._Quercus_garryana_Oregon_AY969006,Tuber_whetstonense_JT25783_Oregon_Paratype_10)))),Tuber_sp._ex._Quercus_robur_Hungary_3_DQ355246),((((Tuber_sp._ex._132b_Carya_Georgia_3,Tuber_sp._ex._Quercus_Missouri_3_EU202706),Tuber_shearii_JT12498_North_Carolina),((Tuber_sp._ex._Epipactis_helleborine_California_AY634172,Tuber_lauryi_JT26987_Oregon_13),(Tuber_sp._ex._Quercus_Missouri_2_EU202710,Tuber_sp._ex._Epipactis_J8_New_York_3))),((Tuber_sp._ex._Epipactis_helleborine_Japan_2_AB428786,Tuber_foetidum_AJ557544_Hungary),(Tuber_maculatum_AJ557519_2,Tuber_rapaeodorum_AJ557522_Hungary_42))));
[!  TreeBASE tree URI: http://purl.org/phylo/treebase/phylows/tree/TB2:Tr58373]


END;