NEXUS [File created by TreeBASE: 7/26/07 21:13:59] [Matrix accession#: M2834] BEGIN TAXA; TITLE M2834; DIMENSIONS NTAX=39; TAXLABELS Tuber_puberulum_AJ557537 Tuber_puberulum_AJ557536 Tuber_puberulum_AJ557533 Tuber_oligospermum Tuber_maculatum_AY558809 Tuber_maculatum_AJ557520 Tuber_maculatum_AJ557519 Tuber_maculatum_AJ557518 Tuber_maculatum_AF106889 Tuber_maculatum_AF003919 Tuber_liui Tuber_foetidum_AJ557544 Tuber_foetidum_AJ557543 Tuber_dryophilum Tuber_californicum_xb11 Tuber_californicum_hr12 Tuber_californicum_hr08 Tuber_californicum_AY558807 Tuber_borchii_kd08 Tuber_borchii_AJ557542 Tuber_borchii_AJ557541 Tuber_borchii_AJ557540 Tuber_borchii_AF132505 Tuber_borchii_AF003920 'Tuber asa-foetida' Tuber_rufum Tuber_rapaeodorum_kd05 Tuber_rapaeodorum_kd04 Tuber_rapaeodorum_kd03 Tuber_rapaeodorum_kd01 Tuber_rapaeodorum_AJ557529 Tuber_rapaeodorum_AJ557528 Tuber_rapaeodorum_AJ557526 Tuber_rapaeodorum_AJ557524 Tuber_rapaeodorum_AJ557523 Tuber_rapaeodorum_AJ557522 Tuber_rapaeodorum_AJ557521 Tuber_puberulum_it Tuber_puberulum_AJ557538 ; END; BEGIN CHARACTERS; TITLE M2834; DIMENSIONS NCHAR=271; FORMAT DATATYPE = DNA MISSING = ? GAP = - ; MATRIX Tuber_puberulum_AJ557537 CAAAATGTTATGGG-ATGTCC-TA---ACGGGCACCCAAGCAAA-CACATCCAT---------------------------------------------------------------------------------------------------------ATT--AAAACTTTTGAAACAATTACTAGTCTGATAAGGCCATATG-CTGTAAAAATTTAAA-TATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_puberulum_AJ557536 CAAAATGT-ATGGG-ATGCCC-TA---TCGGGCTCCTAAGCAAAACAC-CTTCCTGTGTACTCTCTCCCTTT--------------------------------------------------------------------------------------------AAAACTTTTGAACCAATTAGTAGTCTGAGAAGGCCATGTG-CCATAAAA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_puberulum_AJ557533 CAAAATGT-ATGGG-ATGCCC-TA---TCGGGCTCCCAAGCAAAACACA-TTCCTGCGTACTCTCTCCC------------------------------------------------------------------------------------------ATT--AAAACTTTTGAACCAATTAGTAGTCTGAGAAAGCCATGTG-CTGTAAAA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_oligospermum CATA-TGT-CCGGG-ATGTCC-AA---TGGGGCTCCCAAGCAAAACACATCCAT-GTGTA--CACTCCCATGTTGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCTGCC-CTTCATG-GCATTTCGG-GTTGAGGTGTCTGGGGAAGGGTCCAATATCAAACTTTTGAACAAATCAGTTGTCTGAGAAGGCCATCCG-CCGCAAATTTTTAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_maculatum_AY558809 -AAA-TAT-CTGGG-ATGTCC-AA--TCGGG-CCCCCAAGT-AAACACATCCAT-GNGC---CACTCCCATGTGGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCAACCCCTTGATTGGGGTCCTGG-GTTGAGGTGTCTGGGGAAGGGCCCAATAACAAACCTTTGAACCAATTAGTTGTCTGAGTAGGCCACCTG-CCGCAA-TCTTTAAAACATGTTAAAACTTTC----------------------------------- Tuber_maculatum_AJ557520 -CAA-TAT-CTGGG-ATG-CAAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-TCAGGCCGTT--ATTCGGTTACTTGGTT-GAGGTGCCTGGGGAAGGGCCAATTATCAAAC-TTTACATTAACTTACTGTCTGAGAAGGCCATGTG-CCGTAATA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_maculatum_AJ557519 -CAA-TAT-CTGGGCATG-CAAAAGACACATGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-TCAGGCCGTT--ATTCGGTTACTTGGTT-GAGGTGCCTGGGGAAGGGCCAATTATCAAACTTT-ACATTAACTTACTGTCTGAGAAGGCCATGTG-CCGTAATA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_maculatum_AJ557518 -CAA-TAT-CTGGGCATG-CAAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTAC-TCCTCCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-TCAGGCCGTT--ATTCGGTTACTTGGTT-GAGGTGCTTGGGGAAGGGCCAATTATCAAAC-TTTACATTAACTTACTGTCTGAGAAGGCCATGTG-CCGTAATA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_maculatum_AF106889 CCAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGCGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATAGGTTGAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATCGTCTGAGAAGGCCATGTG-CCGTAATC-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_maculatum_AF003919 ---------------------------------TCCC-GATAAAACACATTTAT-GCGTA--TTCTCCCATGTTGCTTTCCCAGGCCAGCGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAATC-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_liui CAAA-TGT-CTGGG-ATGTCC-AA--TCGGG-CTCCCAAGT-AAACACATTCAT-GTGTA--CTCTTCCATGTTGCTTCCCCAGACCAGCAGCCATTAAGCCTGCCAG-CCTACCCCCTT-ATGG-GTTATTGG-GTTGAGGTGTCTGGGGAAGGACCCCATATCAAACTTTTGAACAAATTCATAGTCTGAGAAGGCTATATG-CCGCAA-TCTTTAAA-TATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_foetidum_AJ557544 TCAA-TAT-TTGGG-GTG-CTT--GACACTGGCTCCC-AATAAAACCCATCCAT-GAGTA--CTCTGCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-CCAGGCCGTT--ATTCGGTCACTTGGTT-GAGGTGCCTGGGGAAGGGCCAATTAGTAAAC-TTTACATTAACTTACTGTCTGAGAAGGCCATGTG-CCGTAATC-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_foetidum_AJ557543 TCAA-TAT-TTGGG-GTG-CTT--GACACTGGCTCCC-AATAAAACCCATCCAT-GAGTA--CTCTGCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-CCAGGCCGTT--ATTCGGTCACTTGGTT-GAGGTGCCTGGGGAAGGGCCAATTAGTAAAC-TTTACATTAACTTACTGTCTGAGAAGGCCATGTG-CCGTAATC-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_dryophilum -----------------------------------------------------------------TCCCATGTTGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCTGCC-CTTCATG-GCATTTCGG-GTTGAGGTGTCTGGGGAAGGGTCCAATATCAAACTTTTGAACAAATCAGTTGTCTGAGAAGGCCATCCG-CCGCAAATTTTAAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_californicum_xb11 ------------------------------GACTCCCACAT-AAACACATTCCT-GTGTA--TTCTTCCATGTTGCTTTCCCAGACCAGTGGCCATTG---CTGCCAG-TTCCAGCCCTTAACC-GGTCACTGG-GCTGAGGTGTCTGGGAGAGGGCTCATTGCTAAACTATTATACAAATTGGTTGTCTGAGATGGCCATGTG-CCGTAAATTTT--AAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_californicum_hr12 ------------------------------GACTCCCACAT-AAACACATTCCT-GTGTA--TTCTTCCATGTTGCTTTCCCAGACCAGTGGCCATTG---CTGCCAG-TTCCAGTCCT-AACC-GGTCACTGG-GCTGAGGTGTCTGGGAGAGGGCTCATTGCTAAACTATTATACAAATTGGTTGTCTGAAATGGCCATGTG-CCGTAAATTAT--AAACATGTTAAAACTTACAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_californicum_hr08 --CA-ATATCTGGG-ATGTCC-T---TCAGGACTCCCACAT-AAACACATTCCT-GTGTA--TTCTTCCATGTTGCTTTCCCAGACCAGTGGCCATTG---CTGCCAG-TTCCAGCCCT-AACC-GGTCACTGG-GCTGAGGTGTCTGGGAGAGGGCTCATTGCTAAACTATTATACAAATTGGTTGTCTGAGATGGCCATGTG-CCGTAAATTTT--AAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_californicum_AY558807 -------------------------------------------------------GTGTA--CTCTCCCATGTTGCTTCCCCAGACCAGTGGCCACTG---CTGCCAG-TCCGGCCTCTTAACG-GGTTTCTGG-TCTGAGATGTCTGGGGAAGG-TCCATTATTAAACTTTTAAACCAATTGCCAGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAAATATATTAAAACTTTC----------------------------------- Tuber_borchii_kd08 -----------------------A--CATGGGCTCCCAAGC-AAACTCATACCC-GGGTC--CTTTTCCTTGGTGCT--------------------------GCCAGTCCATGTC--CTACCCG-GTCATTGGAGCTGAGGTGTCTTGGGCAGGATCTATTATCAAACATTT-ACCCAATATGTCGTCTGAGAAGGCTTTGTG-CCGAAA-TCATTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_borchii_AJ557542 CATA-TGT-CCGGG-ATGTCC-AA---TGGGGCTCCCAAGCAAAACACATCCAT-GTGTA--CACTCCCATGTTGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCTGCC-CTTCATG-GCATTTCGG-GTTGAGGTGTCTGGGGAAGGGTCCAATATCAAACTTTTGAACAAATCAGTTGTCTGAGAAGGCCATCCG-CCGCAAATTTTTAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_borchii_AJ557541 CATA-TGT-CCGGG-ATGTCC-AA---TCGGGCTCCCAAGCATAACACATCCAT-GTGTA--CACTCCCATGTTGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCTGCC-CTTCATG-GCTTTTCGG-GTTGAGGTGTCTGGGGAAGGGTCCAATATCAAACTTTTGAACAAATCAGTTGTCTGAGAAGGCCATCCG-CCGCAAATTTTTAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_borchii_AJ557540 CATA-TGT-CCGGG-ATGTCC-AA---TCGGGCTCCCAAGCAAAACACATCCAT-GTGTA--CACTCCCATGTTGCTTCCCCAGATCAGTGGCCACTG---CTGCCAG-CCCTGCC-CTTCATG-GCATTTCGG-GTTGAGGTGTCTGGGGAAGGGTCCAATATCAAACTTTTGAACAAATCAGTTGTCTGAGAAGGCCATCCG-CCGCAAATTTTAAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_borchii_AF132505 CAAAATGT-ATGGG-ATGCCCCTA---TCGGACTCCCAAGCAAAACACACTTCCGGTGTA--CTCTCCC----------------------------------------------------------------------------------------TCATT---AAACTTTTGAACCAATTAGTAGTCTGAGAAGGCCATGTG-CCGTAAAA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_borchii_AF003920 CAAAATGT-ATGGG-ATGCCC-TA---TCGGACTCCCAAGCAAAACACA-TTCCTGTGTA--CTCTCCC----------------------------------------------------------------------------------------TCATT---AAACTTTTGAACCAATTAGTAGTCTGAGAAGGCCATGTG-CCGTAAAA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA 'Tuber asa-foetida' --AA-TGT-GCGGG-ATATCCC-ATC-GGGGACTCCTTAGCGAAACACATCCTTGAAGTA--CCCTTCCATGTTGCTTTCCCAGATCAGTGGCCACTG---CTGCCAA-CCCAGTCCCTTAATG-GGTTCTTGG-GTTGAGATGTCTGGGGAAGGGCTCAGTATCAAACTTTTGAAACAATTAGTCGTCTGAGAAGGCCATCCG-CCGCAA-TATTTAAAACATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rufum --------------------------------------TAC-AAACCCTCTC-T-GTGTA--CCAATCCATGTTGCTTTCCCAGGTGGTTGGTTTCAGTTGATGCCAATCCTGCATGCTAGCTGAGTTAATATCACTAAGTGGGTCCCGGGAAAGGGACCAATGCAAACATTTGAA----TCAGCCGTCTGAGTTGGCCCAGTG-CCG-TA-TTATT-GAATAAGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_kd05 CAAA-TGT-TCGGG-ATGTCC-TA--CATGG-CTCCCAAGC-AAACTCATACCC-GGGTC--CTTTCCCTTGGTGCT--------------------------GCCAGTCCATGTC--CTACCCG-GTCATTGGAGCTGAGGTGTCTTGGGCAGGATCTATTATCAAACATTT-ACCCAATATGTCGTCTGAGAAGGCTTTGTG-CCGAAA-TCATTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_kd04 ----------CGGG-ATGTCC-TA--CATGG-CTCCCAAGC-AAACTCATACCC-GGGTC--CTTTCCCTTGGTGCT--------------------------GCCAGTCCATGTC--CTACCCG-GTCATTGGAGCTGAGGTGTCTGAGGCAGGATCTATTATCAAACATTT-ACCCAATATGTCGTCTGAGAAGGCTTTGTG-CCGAAA-TCATTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_kd03 CAAA-TGT--CGGG-ATGTCC-TA--CATGG-CTCCCAAGC-AAACTCATACCC-GGGTC--CTTTTCCTTGGTGCT--------------------------GCCAGTCCATGTC--CTACCCG-GTCATTGGAGCTGAGGTGTCTTGGGCAGGATCTATTATCAAACATTT-ACCCAATATGTCGTCTGAGAAGGCTTTGTG-CCGAAA-TCATTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_kd01 CAAA-TGT-TCGGG-ATGTCC-TA--CATGG-CTCCCAAGC-AAACTCATACCC-GGGTC--CTTTCCCTTGGTGCT--------------------------GCCAGTCCATGTC--CTACCCG-GTCATTGGAGCTGAGGTGTCTTGGGCAGGATCTATTATCAAACATTT-ACCCAATATGTCGTCTGAGAAGGCTTTGTG-CCGAAA-TCATTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557529 -CAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGCGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557528 -CAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGTGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557526 -CAA-TAT-CTGGGCATG-CCAAAGGCACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGTGGCCACTG---CTGCCAG-CCATGCCG-TTTCTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTAATTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557524 -CAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGCGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557523 -CAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGCGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557522 -CAA-TAT-CTGGG-ATG-CCAAAGACACAGGCTCCC-GATAAAACACATTTAT-GCGTA--TCCTCCCATGTTGCTTTCCCAGGCCAGTGGCCACTG---CTGCCAG-CCATGCCG-TTTTTC-GGTTACATGGTT-GAGGTGCTTGGGGAAGGGCTAATTATCAAAC-TTTACTTCACCTTATTGTCTGAGAAGGCCATGTG-CCGTAA-TCTTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_rapaeodorum_AJ557521 -CAA-TATCCTGGG-ATG-CAAAAGACACAGGCTCCC-GATAAAACACATTCAT-GCGTA--TCCTTCCATGTTGCTTCCCCAGGCCAGTGGCCACTG---CTGCCAG-CCAGGCTA-CTACTC-GGTGACCTGGTT-GAGGTGCCTGGGGAAGGCCCAATTATCAAAC-TTTACATTAACTTACAGTCTGAGAAGGCCATGTG-CCGTAA-TCTTCAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_puberulum_it CAAA-TAT-CTGGG-ATGTTC-TA--C-TGAACTCCCTTGT-AAACACATTCAT-GTGTA--CCCATCCATGTTGCTTCCCCAGACCAGTGGCTACCG-GCCTGCCAG-CCTAGTACATAATTGAGACTTCTGG-GTTGAGGTGTTTGGGGAAGGATTCATTATCAAACTTTTAAACAAATTAGTTGTCTGAGAGGGCCATGTGTCCGAAA-TATTTAAAATATATTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA Tuber_puberulum_AJ557538 CAAAATGT-ATGGG-ATGCCC-TA---TCGGGCTCCTAAGCAAAACAC-CTTCCTGTGTACTCTCTCCCTTT---------------------------------------------------------------------------------------------AAACTTTTGAACCAATTAGTAGTCTGAGAAGGCCATGTG-CCATAAAA-TTTAAA-CATGTTAAAACTTTCAACAACGGATCTCTTGGCTCTCGCATCGATGAAGA ; END; BEGIN CODONS; CODONPOSSET * CodonPositions = N: 1 - 271 ; CODESET * UNTITLED = Universal: all ; END; BEGIN ASSUMPTIONS; OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS ; END;