#NEXUS [written Mon Jun 09 19:32:00 PDT 2014 by Mesquite version 2.75 (build 566) at dhcp-206-87-197-53.ubcsecure.wireless.ubc.ca/206.87.197.53] BEGIN TAXA; TITLE 'Cystopteridaceae_gapCpSh_alleles'; DIMENSIONS NTAX=48; TAXLABELS 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' Cystopteris_bulbifera_5836_Arz_c1_5_7_627 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' Cystopteris_fragilis_5851_Ut_c10_576 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' Cystopteris_fragilis_5951_Col_c11_593 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' 'Cystopteris_fragilis 5951 col c6 [1]' 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' Cystopteris_fragilis_6380_Arg_c4_588_short 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' 'Cystopteris_fragilis 7248 Switz c2 [3_7]' 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' 'Cystopteris_fragilis 7625 Taiwan c1 [6]' 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' 'Cystopteris_montana 5839 NFD c1 [5_4_7]' 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' 'Cystopteris_protusa 5838 Mis c1 [4]' 'Cystopteris_protusa 5838 Mis c2 5 [3]' Cystopteris_tasmanica_6379_NZ_c1_603 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp Gymnocarpium_dryopteris_7981_Japan_c16_19_658 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' Gymnocarpium_remotepinnatum_4862_Tai_c3_658 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' ; END; BEGIN CHARACTERS; TITLE 'gapCpSh_alleles_Codonposition1'; DIMENSIONS NCHAR=99; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACATT Cystopteris_bulbifera_5836_Arz_c1_5_7_627 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Cystopteris_fragilis_5851_Ut_c10_576 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Cystopteris_fragilis_5951_Col_c11_593 AGGGAGCCGTAGACAGAGTCGTACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 5951 col c6 [1]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Cystopteris_fragilis_6380_Arg_c4_588_short AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGG----------------------- 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 7248 Switz c2 [3_7]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 7625 Taiwan c1 [6]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACATT 'Cystopteris_montana 5839 NFD c1 [5_4_7]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_protusa 5838 Mis c1 [4]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_protusa 5838 Mis c2 5 [3]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Cystopteris_tasmanica_6379_NZ_c1_603 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGCAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Gymnocarpium_dryopteris_7981_Japan_c16_19_658 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT Gymnocarpium_remotepinnatum_4862_Tai_c3_658 AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGAAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' AGGGAGCCGTAGACAGAGTCGCACAGTGGGTATCCGAGGTTGAAAGGGAGGTGGTAAGACGTAGGGGGTAGTGGGGATAATGGAGGAGCAGCTGACGTT ; END; BEGIN CHARACTERS; TITLE 'gapCpSh_alleles_Codonposition2'; DIMENSIONS NCHAR=98; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Cystopteris_bulbifera_5836_Arz_c1_5_7_627 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC Cystopteris_fragilis_5851_Ut_c10_576 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC Cystopteris_fragilis_5951_Col_c11_593 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 5951 col c6 [1]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Cystopteris_fragilis_6380_Arg_c4_588_short ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAA---------------------- 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 7248 Switz c2 [3_7]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_fragilis 7625 Taiwan c1 [6]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCAATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_montana 5839 NFD c1 [5_4_7]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Cystopteris_protusa 5838 Mis c1 [4]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_protusa 5838 Mis c2 5 [3]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC Cystopteris_tasmanica_6379_NZ_c1_603 ACTGATTCATAGGTCGTCTGTCCCATCTTATCGGTAAGTCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTGAGTTATTC 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' ACTGATTCATAGATCGTCTGTCCCATCTTATCAGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Gymnocarpium_dryopteris_7981_Japan_c16_19_658 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC Gymnocarpium_remotepinnatum_4862_Tai_c3_658 ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' ACTGATTCATAGATCGTCTGTCCCATCTTATCGGTAAGCCAACTACCTACCCAGCTAGTTGACAAATTCCATTGAAGCGTTACACGTCTAAGTTATTC ; END; BEGIN CHARACTERS; TITLE 'gapCpSh_alleles_Codonposition3'; DIMENSIONS NCHAR=99; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' CGAAAGCTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAATACCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' CGAAAGCTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAATACCGATGGTATATCGAATGACTATTTACTCTTTTAAACATTTAACTCCTTGTAGTTG Cystopteris_bulbifera_5836_Arz_c1_5_7_627 TGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' TGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTAAACACTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' CGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAAAACTCCGATGGCATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG Cystopteris_fragilis_5851_Ut_c10_576 CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTCAAACATTTGACTCCCTGTAGTTG 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG Cystopteris_fragilis_5951_Col_c11_593 CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 5951 col c6 [1]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTCAAACATTTGACTCCCTGTAGTTG 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' CGAAAGGTAGATAGCCAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTAAACACTTAACTCCTTGTAGTTG Cystopteris_fragilis_6380_Arg_c4_588_short CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATTACTATTTACTCTCTTA---------------------- 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTGCGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 7248 Switz c2 [3_7]' CGAAAGGTAGATGGCTAGACAGTCCTCGTGCGTCCAGAAAACTCCGATGGCATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTC 'Cystopteris_fragilis 7625 Taiwan c1 [6]' CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAAAACTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACACTTAACTCCCTGTAGTTG 'Cystopteris_montana 5839 NFD c1 [5_4_7]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTTCAGAGAATTCCGATGGTATATCGAATGACTATTTACTCTCTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTACTCTTTTAAACATTTAACTCCCTGTGGTTG 'Cystopteris_protusa 5838 Mis c1 [4]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCCTGTAGTTG 'Cystopteris_protusa 5838 Mis c2 5 [3]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCCTGTAGTTG Cystopteris_tasmanica_6379_NZ_c1_603 CGAAAGGTAGATAGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATAACTATTTACGCTCTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' CGAAAGGTAGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTTCGATGGTATATCGAATGACTATTTACCCTTTTAAACATTTAACTCCTTGTAGTTG 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' CGAAAGGTGGATGGCTAGACAGTCCTCATGCGTCCAGAGAACTCCGATGGTATATCGAATGACTATTTGCGCTCTTAAACATTTAACTCCTTGTAGTTG 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAATATTAAACTCCTTGTAGTTG 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG Gymnocarpium_dryopteris_7981_Japan_c16_19_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAATATTAAACTCCTTGTAGTTG 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTCTTAAGTATTAAACTCCTTGTAGTTG Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCTACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCTACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG Gymnocarpium_remotepinnatum_4862_Tai_c3_658 CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGTCACTCTCTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' CGAAAGGTAGATGGCTAGACAGTCCTCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTAGCCACTCTTTTAAACATTAAACTCCTTGTAGTTG 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' CGAAAGGTAGGCGGCTAGACAGTCCCCAGGCGTCCAGAGAACTCCGATGGTATATCGAATGACTACCCACTCTCTTAAACATTAAACTCCCTGTAGTTG ; END; BEGIN CHARACTERS; TITLE 'gapCpSh_alleles_noncoding'; DIMENSIONS NCHAR=449; FORMAT DATATYPE = DNA GAP = - MISSING = ?; MATRIX 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' GT-CACTGCCAACTTAACAATAACCTATA-AATTCCCTACT-----------------TATGCGGGGGCTACTCTATTGGGTTTGATGTCTTGTAAACATGTT-GTCTTTGTGGTAAACTGCAGTATGAACTTTACATGCTC-TACTCGTTGAAACGA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGGAGTTATT---------------CATAATACTGTCACAACTGATGCTGTCTAACCTATAGCTTTACCTGAAAGCTATATCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAGAAGGCAATTCCAATTATGCTCTCTCACATGCCTTA----------------------------------------------------------ATCGGTGGACTGGGTGATTTGC 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' GT-CACTGCCAACCGAACAATAACCTATA-ATGTCCCTACT-----------------CATGCGGGGGCTACTCTATTGGGTTTGATGTCTTGTAAACATGTT-GTCTTTGTGGTAAACTGCAGTATGAACTTTACATGCTC-TTCTTGTTGAAACGA-ATTTATT-GTCTAAATTAAT----------CAAGGGTGTTTTT---------------CGTAATACTGTCACAACTGATGCTGTCTAACCTATAGCTTAACCTGAAAGCTATATCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAAT---AGAAGGCAATTCCAATCATGCTCTCTCACATGCCTTA----------------------------------------------------------ATCGGTGGACTGGGTGGTGTGC Cystopteris_bulbifera_5836_Arz_c1_5_7_627 GTACACTGCTAACTTAACAAAAACCTAAA-AACATCCTACT-----------------AATGCCGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGACCTTTACATGCTC-TACTCATTGAAACAA-CTTTTTTTGTCTAAATTAATTTATTCTAGTCTAGGGAATTATTTG-------------CAAATTACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTAT-----------TAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTCCAGTCATGCTCTCTCAGCTGCCTTA----------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' GTACACTGCTAACTTAACAAAAACCTAAA-AACATCCTACT-----------------AATGCCGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACTTTACATGCTC-TACTCATTGAAACAA-CTTTTTTTGTCTAAATTAATTTATTCTAGTCTAGGGAATTATTTG-------------CAAATTACTGTCACAACTGATGCTGTCTAACCTTAAGCTT-ACCTGAAAGCTACATCTAATGTGATTTAT-----------TAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTCCAGTCATGCTCTCTCAGCTGCCTTA----------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' GTACACTGCTAACTTAACAAAAACCTTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAATTTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACATTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCTCAAGTTAGTTTCAGTCATGCTTGCTCAAATTCCTTAGCATTTATTTTACCTATAGATACCATAAATGTAATTTTGAAATTTGTATTTTTAAACTAACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' GTAGACTGCTAACTTAACCAAAACCTAAA-AACATCCTACT-----------------AATGTGGTGGCTATT---TTG---------CCTTGTTAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTCGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGGTCGCTCAAATTCCTTCA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC Cystopteris_fragilis_5851_Ut_c10_576 GTACACTGCTAACTTAACAAAAACCTTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCCTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTA-------------------------------TATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' GTACACTGCTAACTTAACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' GTACACTGCTAACTTCACAAAAACCTTTAAAACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTACGAACATTACATTCTC-TACTCATTGAAACAA-ATTTTTTTGTCTAAATTTATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTACAATTGCAGAAGGCAGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC Cystopteris_fragilis_5951_Col_c11_593 GTACACTGCTAACTTAACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TATTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TATTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 5951 col c6 [1]' GTACACTGCTAACTTAACAAAAACCTTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCCTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTA-------------------------------TATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCGGTCATGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' GTACACTGCTAACTTAACAAAAACCTTCA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------GCTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACATTTCTTGTAGGAGGTAACTTCCACTTCCACTTTAGAATTGCTCAAGTTAGTTTCAGTCATGCTTGCTCAAATTCCTTAGCATTTATTTTACCTATAGATACCATAAATGTAATTTTGAAATTTGTATTTTTAAACTAACGGTGGACTGGGTTGTTTGC Cystopteris_fragilis_6380_Arg_c4_588_short GTACACTGCTAACTTAACAAAAACCTTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAATTTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACATTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCTCGAGTTAGTTTCAGTCATGCTTGCTCAAATTCCTTAGCATTTATTTTACCTATAGATACCATAAATGTAATTTTGAAATTTGTATTTTTAGACTAACGGTGGACTGG--------- 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 7248 Switz c2 [3_7]' GTAGACTGCTAACTTAACCAAAACCTAAA-AACATCCTACT-----------------AATGTGGTGGCTATT---TTG---------CCTTGTTAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTCGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGCTTCAGTCATGGTCGCTCAAATTCCTTCA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 7625 Taiwan c1 [6]' GTACACTGCTAACTTAACAAAAACCTTCA-AACATCCTACT-----------------AATGTGGTGGCTGTTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATTCTC-TACTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTACAATTGCAGAAGGCAGTTTCAGTCATGCTCGCTCAAATTCCTTA----------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' GTACACTGCTAACTTAA--------TTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACCTGCTC-TACTCATTGAAACAA-ATTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTTTTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCACAAGTTAGTTTCAGTCATGCTCGCTCAAATTCCTTAGCATTTATTTTACCTATAGATACCATAAATGTAATTTTGAAATTTGTATTTTTAAACTAACGGTGGACTGGGTTGTTTGC 'Cystopteris_montana 5839 NFD c1 [5_4_7]' GTACACTGCCAACTTAACCAAAACCTAAA-AACACCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTT-GTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATTTTTTTGTCTAAATTAATTTAATCTAGTCTAAGGAGTTATTTG-------------CAAATTGCTGTCACAACTGATGCTGTCTAACCTTGAACTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTCCAGTCATGCGCTCTCAAATACCTTAA---------------------------------------------------------AACGGTGGACTTGGTTGTTTGC 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' GTACACTGCTAACTTAACAAAAACCCAAA-AACACCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTAATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCTAGTCTAGGGAATTATTTG-------------CAAATTACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACTTGAAAGCTACATCTAATGTGATTTTTTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAAAATTGCAGAAGGTAGTTCCAGTCATGGTTTTTCAGCTGCCTTA----------------------------------------------------------AACGGTGGACTGGGCTGTTTGC 'Cystopteris_protusa 5838 Mis c1 [4]' GTACACTGCTAACTTAA--------TTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCGTTGAAACAA-ATTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGCTCTCTCAAATGCCTTAA---------------------------------------------------------AA--GTGGACTGGGTTGTTTGC 'Cystopteris_protusa 5838 Mis c2 5 [3]' GTACACTGCTAACTTAA--------TTT------------------------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TTCTCATTGAAACAA-TTTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------TCTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATCACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGCTCTCTCAAATGCCTTA----------------------------------------------------------AA--GTGGACTGGGTTGTTTGC Cystopteris_tasmanica_6379_NZ_c1_603 GTACACTGCTAACTTAACCAAAACCT-AA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAGCTGCAGTATGAACATTACATGCTC-TAGTCATTGAAACAA--TTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAATTTTTAGCCT-AACTGAAAGCTACATCTAATGTGATTTATTACACTTTTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGCTCGCTCAAATTCCTCT----------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' GTACACTGCTAACTTAA--------TTTA-AACATCCTACT-----------------AATGTGGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAACTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATTTTTTTGTCTAAATTAATTTATTCT----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTAGTTTCAGTCATGCTCTCTCA?ATGCCTTA----------------------------------------------------------AA--GTGGACTGGGTTGTTTGC 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' GTACACTGCTAACTTCACAAAAACCTTTA-AACGTCCTACT-----------------AA---GGTGGCTATTTTATTG---------CCTTGTAAACATGTTGGTCTTTGTGGTAAATTGCAGTATGAACATTACATGCTC-TACTCATTGAAACAA-ATT----------AATTAATTTATTCA----------------------------------------------ACTGATGCTGTCTAACCTTTAGCTT-ACCTGAAAGCTACATCTAATGTGATTTATTACACTTCTTGTAGGAGGTA------ACTTCCACTTTAGAATTGCAGAAGGTGGTTTCAGTCAAGCTCGCTCAAATTCCTTAA---------------------------------------------------------AACGGTGGACTGGGTTGTTTGC 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTATAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACTTGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTATTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGTGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACACGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATCGGGTGTGATCCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACGTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC Gymnocarpium_dryopteris_7981_Japan_c16_19_658 GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTACATTAATTTAATCTAGTCAAGGTAATTATTTGCGAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACGTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATCCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCATGACTGATGATGTCTAACGTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTGGAATTGCAAAAGGCAGCTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTACATTAATTTAATCTAGTCAAGGTAATTATTTGCGAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 GTACACTGCCAACTTAACAATAACCTATA-AGCACCCTACT-----------------TACGTGGTGTCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-TTTTATT-GTCTAAATTAATTTAATCTAGTCAGGGTAATTATTTGCAAAGTAGTTATTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTCCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTCACTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' GTACACTGCCAACTTAACAATAACCTATA-AGCACCCTACT-----------------TACGTGGTGTCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-TTTTATT-GTCTAAATTAATTTAATCTAGTCAGGGTAATTATTTGCAAAGTAGTTATTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTCCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTCACTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTAAGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTACATTAATTTAATCTAGTCAAGGTAATTATTTGCGAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTTGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC Gymnocarpium_remotepinnatum_4862_Tai_c3_658 GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGTCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-TTTTATT-GTCTAAATTAATTTAATCTAGTCAGGGTAATTATTTGCAAAGTAGTTATTCAAAATACTGTCACAATTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTCCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' GTACACTGCGAACTTAACAAAAACCTTTA-AACACCCTACT-----------------TAAGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCCTTGTGGCAAACTCCAGTATGAACTTTACATGCTCTAACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTAATCTAGTCAAGGTAATTATTTGCAAAGTAGTTGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' GTACACTGCGAACTTAACAATAACCTATA-AACACCCTACT-----------------TATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-TTTTATT-GTCTAAATTAATTTAATCTAGTCAGGGTAATTATTTGCAAAGTAGTAGTTCAAAATACTGTCACAACTGATGCTGTCTAACCTTTAGCTT-ACATGAAAGCTACACCTAATGTGATTTATTACTTTTCTTTTAGGAGGTA------ACTTCCATTTTAGAATTGCAAAAGGCAGTTCCAATCATGCTCGCTCACATCCCTTA----------------------------------------------------------ATCGGTGGACTGGGTTGTCTGC 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' GTACACTGCCAACTTAACAATAACCTATA-AACACCCTACTTGTGCGGACACCCTACTTATGCGGTGGCTACTTTATTGGGTGTGATGCCTTGTAAACATGTT-GTCTTTGTGGTAAACTCCAGTATGAACTTTACATGCTC-AACTCATTAAAACAA-ATTTATT-GTCTAAATTAATTTTATCTAGTCAAGGTAATTATTTGCAAAGT---AGTTCAAAATACTGTCACAACTGATGCTTTCTAACCTTTAGCTT-ACCTGAAAGCTACACCTAATGTGATTTATTACATTTCTTTTAGGAGGTA------ACTTCCATTTTAGGATTGCAAAAGGCAGTTCCAATCGTGCTTGCTCACATCCCTTA----------------------------------------------------------ATTGGTGGACTGGGTTGTCTGC ; END; BEGIN CHARACTERS; TITLE 'gapCpSh_alleles_recodedindels'; DIMENSIONS NCHAR=28; FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1"; MATRIX 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]' 100011000111001001??000101?0 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]' 100011000111001101??000111?0 Cystopteris_bulbifera_5836_Arz_c1_5_7_627 0000110010110000001?011101?0 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]' 0000110010110000001?011101?0 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]' 00001100101000001???01010000 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]' 00001110101101?01???01010010 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]' 00001101101100001???01010010 Cystopteris_fragilis_5851_Ut_c10_576 00001100101100001???1?010010 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]' 00001110101101?01???01010010 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]' 00000100101100001???01010010 Cystopteris_fragilis_5951_Col_c11_593 00001110101101?01???01010010 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]'00001110101101?01???01010010 'Cystopteris_fragilis 5951 col c6 [1]' 00001100101100001???1?010010 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]' 00001100101100001???01000000 Cystopteris_fragilis_6380_Arg_c4_588_short 00001100101000001???01010000 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]' 00001110101101?01???01010010 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]' 00001110101101?01???01010010 'Cystopteris_fragilis 7248 Switz c2 [3_7]' 00001101101100001???01010010 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]' 00001110101101?01???01010010 'Cystopteris_fragilis 7625 Taiwan c1 [6]' 00001100101100001???010101?0 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]' 01001100101100001???01010000 'Cystopteris_montana 5839 NFD c1 [5_4_7]' 0000110011110000001?01010010 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]' 0000110010110000001?010101?0 'Cystopteris_protusa 5838 Mis c1 [4]' 01001100101100001???01010011 'Cystopteris_protusa 5838 Mis c2 5 [3]' 0101??00101100001???010101?1 Cystopteris_tasmanica_6379_NZ_c1_603 00101100101?10001???010101?0 'Cystopteris_tenuis 6387 VT c10 [7_11_12]' 01001100101100001???010101?1 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]' 00001110101101?01???01010010 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]' 00001100011100100000010101?0 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]' 00001100011100100000010101?0 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]' 00001100011100100000010101?0 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]' 00001100011100100000010101?0 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]' 00001100011100100000010101?0 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]' 00001100011100100000010101?0 Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp 00001100011100100000010101?0 Gymnocarpium_dryopteris_7981_Japan_c16_19_658 00001100011100100000010101?0 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]' 00001100011100100000010101?0 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]' 00001100011100100000010101?0 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]' 00001100011100100000010101?0 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]' 00001100011100100000010101?0 Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658 00001100011100100000010101?0 Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658 00001100011100100000010101?0 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]' 00001100011100100000010101?0 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]' 00001100011100100000010101?0 Gymnocarpium_remotepinnatum_4862_Tai_c3_658 00001100011100100000010101?0 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]' 00001100010100100000010101?0 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]' 00001100011100100000010101?0 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]' 00001000011100100001010101?0 ; END; BEGIN TREES; Title 'Trees from "3.3bnoxcysto.best.tre"'; LINK Taxa = 'Cystopteridaceae_gapCpSh_alleles'; TRANSLATE 1 'Acystopteris_taiwaniana 4870 c2 3 4 6 [5]', 2 'Acystopteris_tenuisecta 4831 Tai c1 4 6 [3]', 3 Cystopteris_bulbifera_5836_Arz_c1_5_7_627, 4 'Cystopteris_bulbifera 6116 On c12 [2_4_5_9_14_10_11_15_1_3_8_7]', 5 'Cystopteris_fragilis 5316 CR c1 2 9 [12_14 5 6 8 11_4_7_10]', 6 'Cystopteris_fragilis 5840 Swd c2 4 [1_9]', 7 'Cystopteris_fragilis 5840 Swd c6 8 10 [3_5_7]', 8 Cystopteris_fragilis_5851_Ut_c10_576, 9 'Cystopteris_fragilis 5851 Ut c1 2 12 13 [3_4_5_9]', 10 'Cystopteris_fragilis 5851 Ut c7 11 14 16 [6_8]', 11 Cystopteris_fragilis_5951_Col_c11_593, 12 'Cystopteris_fragilis 5951 col c4 5 8 12 13 17 18 20 22 23 [9_10_12_14_15_19_3_21]', 13 'Cystopteris_fragilis 5951 col c6 [1]', 14 'Cystopteris_fragilis 6380 Arg c1 [2_5_6]', 15 Cystopteris_fragilis_6380_Arg_c4_588_short, 16 'Cystopteris_fragilis 7009 Iceland c10 15 [9_19]', 17 'Cystopteris_fragilis 7009 Iceland c7 12 13 14 16 [3_6_8_17_2_11_4_5]', 18 'Cystopteris_fragilis 7248 Switz c2 [3_7]', 19 'Cystopteris_fragilis 7248 Switz c4 5 6 [1]', 20 'Cystopteris_fragilis 7625 Taiwan c1 [6]', 21 'Cystopteris_fragilis 7625 Taiwan c2 4 [3_5]', 22 'Cystopteris_montana 5839 NFD c1 [5_4_7]', 23 'Cystopteris_moupinensis 4861 Tai c4 [1_2_3_5]', 24 'Cystopteris_protusa 5838 Mis c1 [4]', 25 'Cystopteris_protusa 5838 Mis c2 5 [3]', 26 Cystopteris_tasmanica_6379_NZ_c1_603, 27 'Cystopteris_tenuis 6387 VT c10 [7_11_12]', 28 'Cystopteris_tenuis 6387 VT c1 4 8 14 [3_6]', 29 'Gymnocarpium_appalachianum 7639 Virg c2 4 6 10 [1_5_7_9]', 30 'Gymnocarpium_appalachianum 7800 Virg c9 12 [1_11_10_14_8_15_2_16_17]', 31 'Gymnocarpium_disjunctum 4710 ALSK c2 [1_3_4]', 32 'Gymnocarpium_disjunctum 7751 Wash c2 5 9 13 [11_12]', 33 'Gymnocarpium_disjunctum 7751 Wash c6 [1_10_14_15]', 34 'Gymnocarpium_dryopteris 5837 Fin c1 2 [3]', 35 Gymnocarpium_dryopteris_5837_Fin_c4_5_6_7_658bp, 36 Gymnocarpium_dryopteris_7981_Japan_c16_19_658, 37 'Gymnocarpium_dryopteris 7981 Japan c2 5 10 12 [1_4_7_11_13_18]', 38 'Gymnocarpium_dryopteris 7981 Japan c3 6 [8_9_15_17]', 39 'Gymnocarpium_dryopteris 8031 Ont c1 2 7 10 12 [3_13_14_15_16_8_11]', 40 'Gymnocarpium_dryopteris 8031 Ont c6 [4_5]', 41 Gymnocarpium_jessoense_parvulum_6979_Ont_c1_658, 42 Gymnocarpium_jessoense_parvulum_6979_Ont_c3_c4_658, 43 'Gymnocarpium_jessoense_parvulum 8120 Russia c1 2 3 7 10 12 [5_11]', 44 'Gymnocarpium_jessoense_parvulum 8120 Russia c6 8 9 [4]', 45 Gymnocarpium_remotepinnatum_4862_Tai_c3_658, 46 'Gymnocarpium_remotepinnatum 4862 Tai c4 6 7 [1_2_5]', 47 'Gymnocarpium_robertianum 7945 Norw c4 12 13 14 [3_7_10_9_11]', 48 'Gymnocarpium_robertianum 7945 Norw c5 8 [1]'; TREE bestREP8 = (2:0.02573387,((((23:0.02008764,(3:0.00156399,4:0.00309186):0.01027038):0.00376545,((((10:0.01125033,20:0.00537611):0.00534494,26:0.03021952):0.00289796,((7:1.0E-8,18:0.00162956):0.02087247,((9:1.0E-8,11:0.00338457,((17:1.0E-8,28:1.0E-8):0.00168345,16:1.0E-8,19:0.00168736,6:1.0E-8,12:0.00168638):0.00169172):0.01693221,(8:1.0E-8,13:0.00171576):0.00752476):0.00322827,(21:0.00884436,((5:1.0E-8,15:0.00317197):0.00147412,14:0.00598446):0.01239145):0.00849381):0.00162811):0.00356693,(25:0.00762146,(24:0.00336153,27:0.00165731):0.00110335):0.00849437):0.00766397):0.00798375,22:0.01925564):0.03310884,(((((35:1.0E-8,40:1.0E-8,38:1.0E-8):0.0014601,33:1.0E-8,31:0.00145871):0.00145824,37:1.0E-8,32:0.0029255):0.00898605,((45:0.00290535,(42:1.0E-8,43:1.0E-8):0.00742784):0.00450862,47:0.00295211):0.00444533):0.00291819,(29:0.00293219,48:0.02288728,((39:1.0E-8,34:0.0014599):0.00146189,30:0.00292719,(36:1.0E-8,44:1.0E-8,41:1.0E-8):0.00293321):0.0014635):0.00146239,46:0.0103779):0.02745514):0.0316323,1:0.00327107); END; BEGIN ASSUMPTIONS; TYPESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition1') = unord: 1 - 99; TYPESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition2') = unord: 1 - 98; TYPESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition3') = unord: 1 - 99; TYPESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_noncoding') = unord: 1 - 449; TYPESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_recodedindels') = unord: 1 - 28; END; BEGIN CODONS; CODESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition1') = universal: 1 - 99; CODESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition2') = universal: 1 - 98; CODESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition3') = universal: 1 - 99; CODESET * UNTITLED (CHARACTERS = 'gapCpSh_alleles_noncoding') = universal: 1 - 449; END; BEGIN MESQUITECHARMODELS; ProbModelSet * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition1') = 'Jukes-Cantor': 1 - 99; ProbModelSet * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition2') = 'Jukes-Cantor': 1 - 98; ProbModelSet * UNTITLED (CHARACTERS = 'gapCpSh_alleles_Codonposition3') = 'Jukes-Cantor': 1 - 99; ProbModelSet * UNTITLED (CHARACTERS = 'gapCpSh_alleles_noncoding') = 'Jukes-Cantor': 1 - 449; ProbModelSet * UNTITLED (CHARACTERS = 'gapCpSh_alleles_recodedindels') = 'Mk1 (est.)': 1 - 28; END; Begin MESQUITE; MESQUITESCRIPTVERSION 2; TITLE AUTO; tell ProjectCoordinator; timeSaved 1402367520863; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; setID 0 5180263693110769223; endTell; getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters; tell It; setID 0 8816985453473565207; checksumv 0 2 2511544813 null getNumChars 99 numChars 99 getNumTaxa 48 numTaxa 48 short true bits 15 states 15 sumSquaresStatesOnly 87436.0 sumSquares 87436.0 NumFiles 1 NumMatrices 5; setID 1 907253005242443764; checksumv 1 2 3158658265 null getNumChars 98 numChars 98 getNumTaxa 48 numTaxa 48 short true bits 15 states 15 sumSquaresStatesOnly 109619.0 sumSquares 109619.0 NumFiles 1 NumMatrices 5; setID 2 5100956844801500198; checksumv 2 2 430272491 null getNumChars 99 numChars 99 getNumTaxa 48 numTaxa 48 short true bits 15 states 15 sumSquaresStatesOnly 107258.0 sumSquares 107258.0 NumFiles 1 NumMatrices 5; setID 3 2372869975187167161; checksumv 3 2 2638171176 null getNumChars 449 numChars 449 getNumTaxa 48 numTaxa 48 short true bits 15 states 15 sumSquaresStatesOnly 428984.0 sumSquares 428984.0 NumFiles 1 NumMatrices 5; setID 4 5832395693245348311; checksumv 4 2 4130214513 null getNumChars 28 numChars 28 getNumTaxa 48 numTaxa 48 short true bits 3 states 3 sumSquaresStatesOnly 2593.0 sumSquares 2593.0 NumFiles 1 NumMatrices 5; endTell; getWindow; tell It; suppress; setResourcesState false false 100; setPopoutState 400; setExplanationSize 0; setAnnotationSize 0; setFontIncAnnot 0; setFontIncExp 0; setSize 752 685; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; desuppress; endTell; getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa; tell It; showTaxa #5180263693110769223 #mesquite.lists.TaxonList.TaxonList; tell It; setTaxa #5180263693110769223; getWindow; tell It; newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder; newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; endTell; showWindow; getEmployee #mesquite.lists.ColorTaxon.ColorTaxon; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel; tell It; togglePanel off; endTell; endTell; endTell; getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord; tell It; makeTreeWindow #5180263693110769223 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker; tell It; suppressEPCResponse; setTreeSource #mesquite.trees.StoredTrees.StoredTrees; tell It; setTreeBlock 1; toggleUseWeights off; endTell; setAssignedID 976.1402366940675.2027803023664400311; getTreeWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.reroot; endTell; getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator; tell It; suppress; setTreeDrawer #mesquite.trees.SquareTree.SquareTree; tell It; setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard; tell It; branchLengthsToggle on; toggleScale on; toggleBroadScale off; toggleCenter on; toggleEven on; endTell; setEdgeWidth 6; orientUp; setCornerMode Right_Angle 50; endTell; setBackground White; setBranchColor Black; showNodeNumbers off; showBranchColors on; labelBranchLengths off; centerBrLenLabels on; showBrLensUnspecified on; showBrLenLabelsOnTerminals on; setBrLenLabelColor 0 0 255; setNumBrLenDecimals 6; desuppress; getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames; tell It; setColor Black; toggleColorPartition on; toggleShadePartition off; toggleShowFootnotes on; toggleNodeLabels on; toggleCenterNodeNames off; toggleShowNames on; namesAngle ?; endTell; endTell; setTreeNumber 1; setTree '(((((23:0.02008764,(3:0.00156399,4:0.00309186):0.01027038):0.00376545,((((10:0.01125033,20:0.00537611):0.00534494,26:0.03021952):0.00289796,((7:1.0E-8,18:0.00162956):0.02087247,((9:1.0E-8,11:0.00338457,((17:1.0E-8,28:1.0E-8):0.00168345,16:1.0E-8,19:0.00168736,6:1.0E-8,12:0.00168638):0.00169172):0.01693221,(8:1.0E-8,13:0.00171576):0.00752476):0.00322827,(21:0.00884436,((5:1.0E-8,15:0.00317197):0.00147412,14:0.00598446):0.01239145):0.00849381):0.00162811):0.00356693,(25:0.00762146,(24:0.00336153,27:0.00165731):0.00110335):0.00849437):0.00766397):0.00798375,22:0.01925564):0.03310884,(2:0.02573387,1:0.00327107):0.0316323):0.01372757,(((((35:1.0E-8,40:1.0E-8,38:1.0E-8):0.0014601,33:1.0E-8,31:0.00145871):0.00145824,37:1.0E-8,32:0.0029255):0.00898605,((45:0.00290535,(42:1.0E-8,43:1.0E-8):0.00742784):0.00450862,47:0.00295211):0.00444533):0.00291819,(29:0.00293219,48:0.02288728,((39:1.0E-8,34:0.0014599):0.00146189,30:0.00292719,(36:1.0E-8,44:1.0E-8,41:1.0E-8):0.00293321):0.0014635):0.00146239,46:0.0103779):0.01372757);'; setDrawingSizeMode 0; toggleLegendFloat on; scale 0; toggleTextOnTree off; showWindow; endTell; desuppressEPCResponse; getEmployee #mesquite.trees.ColorBranches.ColorBranches; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.ornamental.BranchNotes.BranchNotes; tell It; setAlwaysOn off; endTell; getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition; tell It; colorByPartition off; endTell; getEmployee #mesquite.ornamental.DrawTreeAssocDoubles.DrawTreeAssocDoubles; tell It; setOn on; setDigits 4; writeAsPercentage off; toggleCentred on; toggleHorizontal on; setFontSize 10; setOffset 0 0; endTell; getEmployee #mesquite.trees.TreeInfoValues.TreeInfoValues; tell It; panelOpen false; endTell; endTell; endTell; getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord; tell It; showDataWindow #907253005242443764 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #5100956844801500198 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #2372869975187167161 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.ColorByState.ColorByState; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges off; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames off; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize off; toggleColorsPanel off; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.align.AlignToDropped.AlignToDropped; tell It; gapCosts 8 3 2 2; subCosts 10 5 10 10 10 5 5 10 10 10 5 10; endTell; getEmployee #mesquite.molec.ColorByAA.ColorByAA; tell It; emphasizeDegeneracy off; endTell; getEmployee #mesquite.molec.SequenceInfoEditor.SequenceInfoEditor; tell It; panelOpen false; endTell; endTell; showDataWindow #5832395693245348311 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker; tell It; getWindow; tell It; setExplanationSize 30; setAnnotationSize 20; setFontIncAnnot 0; setFontIncExp 0; setSize 652 618; setLocation 8 22; setFont SanSerif; setFontSize 10; getToolPalette; tell It; endTell; setActive; setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow; colorCells #mesquite.charMatrices.NoColor.NoColor; colorRowNames #mesquite.charMatrices.TaxonGroupColor.TaxonGroupColor; colorColumnNames #mesquite.charMatrices.CharGroupColor.CharGroupColor; colorText #mesquite.charMatrices.NoColor.NoColor; setBackground White; toggleShowNames on; toggleShowTaxonNames on; toggleTight off; toggleThinRows off; toggleShowChanges on; toggleSeparateLines off; toggleShowStates on; toggleAutoWCharNames on; toggleAutoTaxonNames off; toggleShowDefaultCharNames off; toggleConstrainCW on; toggleBirdsEye off; toggleAllowAutosize on; toggleColorsPanel off; toggleDiagonal on; setDiagonalHeight 80; toggleLinkedScrolling on; toggleScrollLinkedTables off; endTell; showWindow; getWindow; tell It; forceAutosize; endTell; getEmployee #mesquite.charMatrices.ColorCells.ColorCells; tell It; setColor Red; removeColor off; endTell; getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel; tell It; togglePanel off; endTell; getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip; tell It; showStrip off; endTell; getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector; tell It; autotabOff; endTell; getEmployee #mesquite.categ.SmallStateNamesEditor.SmallStateNamesEditor; tell It; panelOpen true; endTell; endTell; endTell; endTell; end;