#NEXUS BEGIN DATA; DIMENSIONS NTAX=19 NCHAR=663; FORMAT INTERLEAVE MISSING=N GAP=- DATATYPE=DNA; OPTIONS GAPMODE=newstate ; MATRIX [28 D1 segment] Drosophila NNNNNNNNGGATTTTCTTAGTAGCGGCGAGCGAAAAGAAAA-CAGTTCAGCACTAAGTCACTTTGTC-----TATAT----GGCAAATGTGAGATGCAGTGTAT-GGAGCGTCAATATTCTAGTATGAGAAATTAACG---ATTTAAGTCCTTCTTAAATGAGGC-CA-TTTACCCATAGAGGGTGCCAGGCCCGTATAACGTTAATGAT-----TACTA-GA-TGATGT----TTCCAAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATCTAAAACTAAATATAACC Tabanus NNNNNNNNGGATTTTCTTAGTAGCGGCGAGCGAAAAGAAAA-AAGTTCAGCACTAAGTTATTTTGTTA----TTTTT---TAACAAATATAAGATGCAGTGTAT-AGAATATCTATTATCTAGTATATTAAATTAATA---GTTCAAGTCCTTCTTAAATGGGGC-CA-TTTACCCATAGAGGGTGATAGGCCCGTAGAAACATTATTAAA----TACTA-GA-AGATAT----TTCTTAAGAGTCGTGTTGCTTGATAGTGCAGCACTAATTTGGTGGTAAACTCCATCTAAAACTAAATATAACC Bradysia ATTAACTAAGATTCCTTTAGTAGCGGCGAGCGAAACAGGAT-AAGCCCAGCACTAAGCTCTCCGGTC-----GTCCT----GACTGGTAGAGGATGCAGTGTAT-GGAAAGTCTATTATCTTATGCAACGATAATAT----GTTCAAGTCCATCTTGAATGGGGC-CATTAAACCCATAGAGGGTGCCAGGCCCGTAGCAGCTATTATCAG----TATAA-GA-AGGCTT----TTCCAAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTTGGTGGTAAACTCCATCTAAGGCTAAATATGACC Crinodiplosis ATTAAATAAGATTCCTTTAGTAGCGGCGAGCGAAACAGGAT-TAGCCCAGCACTAAGTCATCCAATT-----TTTAT----GATTGGTATGAGATGCAGTGTAT-GGAAAGTCTATTATCTGGTGTTGTATTCAATAC---GTTCAAGTCCATCTTGAATGGGGC-CAATATATCCACAGAGGGTGCCAGGCCCGTAGAAGCTATTGTTTTG---CATCA-GA-AGGCTT----TTCCAAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATAACC Bolitophila NNNNNCTAAGATTCCTTTAGTAGCGGCGAGCGAAACAGGAA-AAGCCCAGCACTAAGCCCTCCAGTC-----GTCCT----GGCTGGTAGGGGATGCAGTGTAT-GGGAAGTCTATTATCTTATATGACGGTAGCAC----GTTCAAGTCCATCTTGAATGGGGC-CATTTAACCCATAGAGGGTGCCAGGCCCGTAGCAACTGTTACCAG----TATAA-GA-AGATTT----TTCCGAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTTGGTGGTAAACTCCATCTAAGGCTAAATATAACC Anapausis ACTAACTAGGATTCCCTGAGTAGCGGCGAGCGAAATGGGAT-AAGCTCAGCACTAAGCCTTCTGGTT----CTAAAC----GACTAGTTAGGGATGCAGTGTAT-GGAAAATCTATTATCTTATATATATACAGCATAT--GTTCAAGTCCATCTTGAATGGGGC-CA-TTTACCCAAAGAGGGTGCCAGGCCCGTAGTAACTATTGTATTA---TATAG-GA-GGATTC----TTCCAAAGAGTCGTGTTGCTTGATAGTGCAGCACAAAGTTGGTGGTAAACTCGATCTAAAGCTAAATATTACC Dilophus NNNNNNNNNNNTTCCCNTAGTAGCGGCGAGCGAAACGGGAT-AAGTTCAGCACTAAGTCCTCTAA-------TTAAT------TTAG-AGGAGATTCAGTGTAT-GGAAAGTCTATTACTTTATATAAAGATGATAC----GTTCAAGTCCATCTTGAATGGGGC-CATTTAACCCGCAGAGGGTGCCAGGCCCGTAGTAACTATTATCAA----TATAAAGA-AGGCTC----TTCCAAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATCTAAAACTAAATATAACC Sylvicola NNNNNNNNGGATTCCCTTAGTAGCGGCGAGCGAAACGGGAA-AAGCCCAGCACTAAGTTCTCTAATCT----GTTGT---GGGTTAGTAGAAGATGCAGTGTAT-GGAGAGTCTACTATCTCATATGTTACGGCAATAC--GTTCAAGTCCTTCTTGAATGGGGCCCA-TTTACCCATAGAGGGTGCCAGGCCCGTAGTGACTGTTGTCCGTTTGCATGA-GA-AGACTT----CTCTTAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTTGGTGGTAAACTCCATCTAAGGCTAAATACAACC Psychoda ACTAACTAGGATTCCCTGAGTAGCGGCGAGCGAAACGGGAA-AAGCCCAGCACTTAGCCCATTGGCT----CATAAAC---GGCCAATTGGGGATGCAGTGTAT-GGAGTGTCCATTAACTCATTACAATAGATGATGTACGTTCAAGTCCATCTTGAATGGGGC-CATTTTACCCATAGAGGGTGCCAGGCCCGTGGAACTACCATCTGT----AATTT-GT-GGACTA----CTCTTAAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATTACC Tipula NNNNNNNNAGATTTCCTGAGTAGCGGCGAGCNAAATGGGAA-AAGTCCAGCATTAAGTCCTTTTACTG----ATTACT--CGGTAGAATGGAAATTCAATGTAAAGGAGTATCTATTATCCTAAATTTTTAATTATAT---GTCCAAGTCCATCTTGAATGGGGC-CA-TTTACCCACAGAGGGTGCCAGGCCCGTAGTGACTATAATCTTG---TTTAG-GA-AGATAT----CTCTAGAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTTGGTGGTAAACTCCATCTAAGACTAAATATGACC Limonia NNNNNNNNAGATTCCCTGAGTAGCGGCGAGCGAAACGGGAT-AAGCCCATCACAAAGTCCTCTTTC----TTTTAAC---GAGATTGTTGGAAATGCTGTGTCAATGTGAATTCATTATCTTATATGCATATGGTAC----GCTTAAGTTCATCTTGAATGGGGC-CA-TTTACCCACAGAGGGTGCCAGGCCCGTAT-AGCTACTATTGTA---TATTA-GA-GAATTT----TGCATCAGAGTCGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATAACC Trichocera NNNNNNNNNGATTCCCTTAGTAGCGGCGAGCGAAACGGGAT-TAGCCCAGCACCAAGTCCTCTAGCCT----TTAAC---GGGTTAGTAGGAGATGCGGTGTATAGGTAAATCTATATTCTTATATGTTCCAATAC-----GTTCAAGTCCATCTTGAATGGGGC-CATTTAACCCATAGAGGGTGCCAGGCCCGTGGTAACTATTGTTAT----TATAA-GA-AGATTT----TGCCTTAGAGTGGTGTTGCTTGATAGTGCAGCACTAAGTGGGTGGTAAACTCCATTTAAGGCTAAATATAANN Aedes ACTAACAAGGATTCCCTGAGTAGCTGCGAGCGAAACGGGAA-GAGCTCAGCACGCAGGGGCGATGCA-----CTGG-----TGTATCTGCCCGGTTCCGTGTACTGGAGAGTTCGTTATCTGCCGTAACCGGTCGCTG---GTTCAAGTTCAACTAGAATGTGGC-TTTTActCCCAGAGAGGGTGATAGGCCCGTAGAGCGGCGCACCGA----TGGTA-GA-AGATCT----TTCCATGGAGTCGTGTTGCTTGATAGTGCAGCACAAAGTGGGAGGTAAACTCCTTCTAAAGCTAAATATCACC Culex NNNNNNNMGGATTCCCCGAGTAGCTGCGAGCNAAAAGGGAA-GAGCTCAGCACGCAGGGGTGGCGC-----ACTACCC----GCGTCTACCCGGTTCCGTGTACTGGAAATTTTGTCATCTGCCATGCCCGGCGCAGT---GTCCAAGTTCAACTAGAATGTGGC-TTTTACTCCCATAGAGGGTGATAGGCCCGTAGGACGGCGCTGA------TGGTG-GA-AAATTT----TTCCATGGAGTCGTGTTGCTTGATAGTGCAGCACAAAGTGGGAGGTAAACTCCTTCTAAAGCTAAATATCACC Chironomus NNNNNNNNNNNNNCCCTTAGTAGTGGCGAACGAAACGGGAT-CAGCCCATCACGTAGGATCATAGGC-----TTAATT---GTCTATTGATCGATTCCGTGTAAAGGAGGGTCCATTATCTTGCACATATAAACATCAT--ATTTAAGTCCAGCTTGAATGCGGCTCAATATACCCACAGAGGGTGCCAGGCCCGTATATGTATGATGCTTG---TGTAA-GT-GGGCTATCAACTCCTAGGAGTCATGTTGCTTGATAGTGCAGCATTAAGTGGGAGGTAAACTCCTTCTAAGGCTAAATATTACC Simulium ACTAAATAGGATTCCCCTAGTAGCGGCGAGCGAAAAGGGAA-AAGTCCAGCACGTAGAATCGCAACT-----GTTAT----GGTTGTTGATTGATGCCGTGTACAGGTTCGGCCATTATCTCATATTATAATTAGTAT---GTTCAAGTCCTTCTTGAATGAGGC--AATATACCCACAGAGGGTGATAGGCCCGTATAACTGCTATGATA----TATGA-GA-GGTTGT----TACCTAGGAGTCGTGTTGCTTGAAAGTGCAGCACTAAGCGGGAGGTAAACTCCTTCTAAGACTAAATATTACC Panorpa NCTAACTAGGATTCCCTTAGTAGCGGCGAGCGAACAGGGAA-GAGCCCAGCACTGAATCCCCTAGCCG----ATTT----CGGATAGTGGGAAATGTAGTGTATAGGAGGATTCATTTATCCTGAGATCATGTAGCGC---GTTTAAGTCCATCTTGAATGGGGC-CA-ATTACCCATAGAGGGTGCCAGGCCCGTAA-AACTGTTACTGAT---CTTGG-GA-GGATCT----CTCCTTTGAGTCGGGTTGCTTGAGAGTGCAGCTCTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATAACC Archaeopsylla NNNNNNNNNNNNNNCCTCAGTAGCGGCGAGNGAACAGGGAA-GAGCCCAGCACTAAATCCCGCGGCCG----GAGA----CGGACCGTGGGAAATGTAGTGTTAGGGAGGATCCAATTATCTCGGTGCGTCGCGGCGA---GTTCAAGTCCATCTTGAATGGGGC-CA-TTTACCCATAGAGGGTGCCAGGCCCGTAGCGACCGTTGCGCGT---ATCGA-GA-GGATCT----CTCCTCAGAGTCGAGTTGCTTGAGAGTGCAGCTCTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATGACC Manduca NNNNNNNNGNATTTCCTTAGTAGCGGCGAGCGAACAGGAATATAGCCCAGCACTGAATCCCGCTGTTG----TAA------CGGCAGCGGGAGATGTGGTGTTCGGGAGGTTCCG-CTTTCTCGTCACCGATACTCCT---GTCCAAGTTCGTCTTGAACGGGGC-CG-TTTTCCCGAAGAGGGTGCCAGGCCCGTAGCGACGGAGGGCGGT---GGCGA-GA-GGGACT----CTCCTCAGAGTCGGGTTGCTTGAGAGTGCAGCCCTAAGTGGGTGGTAAACTCCATCTAAGGCTAAATATTACC [28S D7 segment] Drosophila GAACGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATCCGTTTGTTATTAAATA-----TGGGCCTCGT-----------------------------GCTCATCCTGGCAACAGGAACG---ACCATAAAGAAGCCGTCGAGAGATATCGGAAGAGTTTTCTTTTCTGTTT-TATAGCCGTA-CTACCATGGAAGTCTTTCGCAGAGAGATATGGTAGATG-GGCTAGAAGAGCATGACATATACT-GTTGTGTCG-ATATTTTCTCCTCGGACCTTGAAAATTTATGGTGGGG--ACACGCAAAC--TTCTCAACAGGCCGTACCAATATCCGCAGCTGGTCTCCA Tabanus GAACGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-AAGTATACGTTTGTTATTAAAAAA----TGGGCTTTAAT----------------------------GCTCATCGTGGCAACACAAACA---ATCATAAAGAAACCGTCGAGAGGTATCGGAAGAGTTTTCTTTTCTGTTT-TATAGTTGTA-TTACCATGGAAGTCTTTCGAAGAGAGATATGGTAAATG-AACTAGAAGAGCATAGCATATACT-GCTGTGTCG-ATATTTTCTCCTCGGGCCTTGAAAATTTATGGTAGGG--TTACGCAAAC--TTCTTAACAGGCCGTACCAATATCCGCAGCTGGNCTCCA Bradysia AAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTTATTAAAAA----TGGGTCTTATTAC--------------------------ACTCATCCTGGCAACAGGAACG---ACCATAGAGAAGCCTTCGAGAGATACTGGAAGAGTTTTCTTTTCTGCTA-AACAAACGTA-CCACCATGGAAGTCTTTTATAGAGAGATATGGTGGATG-GCTTGGAAGAGCATGACATTTACT-GTTGTGTCA-GTATTTTCTCCTTGGACCTTGAAAATCTATGGTGGGG--CCACGCAAAC--TTCTCAACAGACCGTACCGATATCCGCAGCCGGTCTCCA Crinodiplosis GGGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTTATTAAAAG----TGGGTCTTGTTAC--------------------------ACTCATCCTGGCAACAGGAACA---ACCATAGAGAAGCCTTCGAGAGATATTGGAAGAGTTTTCTTTTCTGTTG-AACAATCGTA-TAACCATGGAAGTCTTTCACAGAGAGATATGGTTAATG-GATTGGAAGAACATGACATTTACT-GTTGTGTCA-ATATTTTCTCCTTGGACCTTGAAAATCTATGGTAGGG--CCANGCAAAT--TTCTCAACAGACCGTACCGATATCCGCAGCCGGTCTCCA Bolitophila GAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTTATTAAAAA----TGGGTCTTATTAC--------------------------ACTCATCCTGGTAACAGGAACA---ACCATAGAGAAGCCTTCGAGAGATACTGGAAGAGTTTTCTTTTCTGTTG-AACAATCGTA-TCACCATGGAAGTCTTTCACAGAGAGATATGGTGAATG-GATTGGAAGAGCATGACATTTACT-GTTGTGTCA-GTATTTTCTCCTTGGACCTTGAAAATCTATGGTAGGG--CCACGCAAAC--ATCTCAACAGACCGTACCGATATCCGCAGCCGGTCTCCA Anapausis GAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTTTGAGTATACGTTTGTTGATAAAAA-----TGGGTTCATTATATATGC---------------------ACTCATCCTGGTAACAGAAACA---ACCATAGAGAAGCCTTCGAGAAATACTGAAAGAGTTTTCTTTTCTGTTG-AACAATTGTA-TCACCATGGAAGTCTTTTACAGAGAGATATGGTGAATG-AATTGGAAGAGCATGACATTTACT-GTTGTGTCA-GTATTATCTCCTTGGACCTTGAAAATCTATGGTAGGG--CCACGCAAAC--ATCTCAACAGACCGTACCGATATCCGCAGCCGGTCTNNA Dilophus AAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTTATTAAAAA----TGGGTCTCGTTAC--------------------------ACTCATCCTGGTAACAGGAACA---ACCATAGAGAAGCCTTCGAGAGATACTGGAAGAGTTTTCTTTTCTGTTG-AACAATCGTA-TCACCATGGAAGTCTTTCATAGAGAGATATGGTGAATG-GATTGGAAGAGCATGACATTTACT-GTTGTGTCA-GTATTATCTCCTTGGACCTTGAAAATCTATGGTGGGG--CCACGCAAAC--ATCTNAACAGACCGTACCGATATCGGCAGCCGGTCTNNA Sylvicola GAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTTAATAAAATA---TGGGTCCCTTAGT--------------------------ACTCATCCTGGCAACAGGAACA---ACCATAGAGAAGCCTTCGAGAGGTACTGGAAGAGTTTTCTTTTCTGTTGTAACAACTGTA-TAACCATGGAAGTCTTTAAAAGAGAGATATGGTTAATG-AGTTGGAAGAGCATGACATTTATT-GTTGTGTCA-GTACTTTCTCCTTGGACCTTGAAAATCTATGGTGGGG--CCACGCAAAC--ATCTCAACAGACCGTACCGATATCCGCAGCCGGTCTCCA Psychoda GTGCGAAAGGGAATACGGTTCCAATTCCGTAACCTATT-GAGTATACGTTTATTG------------TGGGTACTGGGCCTTGCTTGCAAGTGTTCCGGTTTT---ACTCATCCTGGCAACAGAAGCT---GGCATAGAGAAGCCGTCGAAGCGTACCGAAAGAGTTTTCTTTTCTGTTT-TATAGTCGTA-TTACCATGGAAGTCTTTCGAAGAGAGATATGGTAAATG-GACTAGAAGAGCATGGCCTATATT-GCTGTGTCGCGTACGTCTTCCTCGGACCTTGAAAATCTATGCCAGGG--CCACGTAAACA-TTCTCAATAGACCGTACCAATATCCGCAGCAGGTCTCCA Tipula GAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTGTACGCTTTTAAGAT---------TGGATATTAACATTTTAAGATGANT--------------ATTCATCCTGGTAACAGGAACT---GCCGTAGAGACGCCGTCGGGATATACCGAAAGAGTTTTCTTTTCTGTTT-CATAGACATA-CTACCATGGAAGTCTTTCGCAGAGAGATATGGTAAAAA-GTCTAGAAGAGCATGACATTTACT-GTTGTGTCG-GTATTCTCCCTTCGGACCTTGAAAATCTATGGAAGGG--TTACGCAAAT---TCTCAACAGACCGTACCGATATCCGCAGCTGGTCTCCA Limonia GACCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGCTTAAAAGAT---------TGGATATTAACATGCAATGATGAAT--------------ATTCATCCTGGTAACAGGAACA---ACCATAGAGACGCTGTCGGGATATATCGAAAGAGTTTTCTTTTCTGTTT-TATAGAAGCA-TAACCATGGAAGTTTTTCGCAGAGAGATATGGTTAATA-GTCTAGAAGAGCATGACATTTACT-GTTGTGTCG-ATATTCTCCCCTCAGACCTTGAAAATCTATGGTAGGG--CTACGCAAAT---TCTCAACAGACCGTACCGATATCCGCAGCTGGTCTCCA Trichocera GAGCGAAAGGGAATACGGTTCCAATTCCGTAACCTGTT-GAGTATACGTTTGTTAAAT---------TGGGTTCTTTTAATTACTNTAATTAAGGT----------ACTCATCCTGGTAACAGGAACA---ACCATAGAGAAGCCGTCGAGAGATATCGGAAGAGTTTTCTTTTCTGTTT-TATAGTCGCA-TCACCATGGAAGCCTTTCGAAGAGAGATATGGTGAATT-GTCTAGAAGAGCATGGCATTTACT-GCTGTGTCG-ATATTTTCTCCTCGGACCTTGAAAATCTATGGTAGGG--CCACGCAAAT---TCTCNACAGACCGTACCGATATCCGCAGCTGGTCTCCA Aedes GAGCGAAAGGGAATCCGGTTACAATTCCGGAGCCTGTT-GGGTATACGTTTGCA-------------TTGGCGTCCCATACCGGCAACGGTAGCGCCTT-------TGTAATCATGGCAACATGAATCCTTTTCTTCGAGAAGCCAACAAGAGATATCGGAAGAGTTCTCTTTTCTGTTT-TACAGTCACACTAGCCATGGAAGTCTTTCATAGAGAGATATGGTTGGACAGGCTGGTAGAGCATGGTATTAAATTGCTGTGTCG-ATATTCTCTTCTTGGACCTTGAAAATCGAAGACTGGG--GCACGCAAAC---TCCCAACAGCTTGTACCG-AATCCGCAGCAGGTCTCCA Culex GAGCGAAAGGGAATCCGGTTACAATTCCGGAGCCTGTT-GGGTATACGTTTGCA-------------TTGGCGGTAATACCGGTAACACGGTAGCGCCTT------TGTAATCATGGCAACATGAATCCTTTCCTTCGAGAAGCCAACAAGAGATATCGGAAGAGTTTTCTTTTCTGTTT-TACAGCCACACTGGCCATGGAAGTCTTTCATAGAGAGATATGGTCGGACAAGCTGGTAGAGCATGGTATTAAATTGCTGTGTCG-ATATTCTCTTCTTGGACCTTGAAAATCGAAGACTGGG--GCACGCAAAC---TCCCAACAGCTTGTACCG-AATCCGCAGCAGGTCTCCA Chironomus GAGCGAAAGGGAATACGGNTCCAATTCCGTAACCTATT-GAGTATACGTT-----------------TGTTATTTGAATTCGTTTCGAA-----------------TAACATCTCGGTAACGAGAAGCT--CTCATAGAGACGTCAATGGGAGGTATCGAAAGAGTTTTCTTTTCTGTTT-TACAATCGTACGTACCATGGAAGTCTTTCATAGAGAGATATGGTATAACAGATTGGTAGAGCATGACATTAAATTGTTGTGTCG-GTATACTCTCATTGGACCTTGAAAATCTATGAAAGGG--ACACGATAAA--TTCTCAATAGCCTGTACCCGAATCCGCAGCAGGTCTCCA Simulium GAGCGAAAGGGAATCCGGTTACAATTCCGGAACCTGTT-GAGTATACGTTTGCATTATGTGACCGCCTACATTTATGTAGGTTATCCATT----------------ATGTATCTCGGCAACGAGAAGCC--AATATAAAGAAGCTATCGGGATGTAACAAAAGAGTTTTCTTTTCTGTTT-TACAGTTGTACGCACCATGGAAGTCTTTCATAGAGAGATATGGTGTAATAGGCTGGTAGAGCATGGCATTCAGTTGCTGTGTTG-TTACAATCTCCTTAGACCTTGAAAATTTATATTGGGG--TCACGCAAAC---TCTCAACAGACCGTACCG-AATCCGCAGCAGGTCTCCA Panorpa GGGCGAAAGGGAATCCGGTTCCTATTCCGGAACCCGGCAGCGNAACCGTTAACAAGT----------CGGGCCCTCGAAAGAGA----------------------GTTCGTCGGGGTAACCCAAAAA---GACCTGGAGACGCCGTCGGGAGATCCAGAAAGAGTTTTCTTTTCTGTAT-GAGCATTCGA-GTTCCCTGGAATCCTTTAGCAGGGAGATAGGGTTTGG--AATGCGAAGAGCAC-GCAGTTGCG-GCGGTGTCT-GGATCTTCCCCTCGGACCTTGAAAATCCAGGAGAGGG--CCACGTGGAGGTGTCGCGCCGGTTCGTACCCATATCCGCAGCAGGTCTCCN Archaeopsylla NNNNNAAAGGGAATCCGGTTCCTATTCCGGAACCCGGCAGCGGAACCGTTTACAAGT----------CGGGCCCTCGCAAGAGA----------------------GTTCGTCGGGGTAACCCAAAAT---GACCTGGAGACGCCGTCGGGAGATACGGGGAGAGTTTTCTTTTCTGTAT-GAGCGTTCGA-GTTCCCTGGAATCCTCTAGCAGGGAGATAGGGTTTGG--AACGCGAAGAGCAC-GCAGTTGCG-GCGGTGTCC-GTATCTTCCCCTCGGACCTTGAAAATCCAGGAGAGGG--CCACG-GGAGGTGTCGCGCCGGTTCGTACCCATATCCGCAGCAGGTCTCCA Manduca GAGCGAAAGGGAATCCGGTTCCTATTCCGGAACCCGGCAGCGGAACCGTTTCAATAAT---------CGTTCCCTCGTTTAATAGCGAGT----------------GTTCGACGGGGTAACCCAAAGT---GGCCTGAAGACGCCGCCGAGAGGTCCGGGAAGAGTTTTCTTTTCTGCCT-GAGCGTTCGA-GTTCCATGGAATCCTATAGAAGGGAGATATGGTTCGG--AACGCGAAGAGCAC-GCATTTGCG-GCGGTGTCC-GGATACTCTCTGCGGACCTTGAAAATTCAGGTGAGGGATGTACGTGGAAATGTCGCGCCGGTTCGTACCCATATCNGCAGCAGGTCTCCA ; END; [!Assumptions saved by PAUP on Tuesday, October 6, 1992 16:17] begin assumptions; typeset *saved [AllUnord] = unord: all; wtset *saved [equal] = 10:all, 8:23 24 30 31 36-40 44-47 50-54 58-67 82-87 89-92 98-102 106-114 119-125 131-138 143-146 149-153 159-163 182-184 192-194 199-210 216-229 235-238 247-253 262-268 274-278 281-291 294-297 308-311 316-317 321-325 334-349 375-379 414-423 428-432 439-446 451-453 456-472 477-482 491-495 500-507 512-514 520-522 527-534 539-543 549-556 562-588 599-606 627-634 636-638 640-642 648 649 656 657 659-662; exset *saved = 1-18 41-43 61-90 104-106 121-141 166-170 198-215 221 224 231-234 346 358-374 380-413 435-439 488 499 537-539 563 573 611-612 622-625 644 ; end; usertype V = 4 [weights transversions only] a c g t [a] . 1 0 1 [c] 1 . 1 0 [g] 0 1 . 1 [t] 1 0 1 . ; usertype T = 4 [weights transitions only] a c g t [a] . 0 1 0 [c] 0 . 0 1 [g] 1 0 . 0 [t] 0 1 0 . ; usertype 100 = 4 [AT transversions downweighted] a c g t [a] . 5 5 1 [c] 1 . 5 1 [g] 1 5 . 1 [t] 1 5 5 . ; usertype 10 = 4 [weights transversions 10 times transitions except A/T] a c g t [a] . 10 1 1 [c] 10 . 10 1 [g] 1 10 . 10 [t] 1 1 10 . ; usertype 2 = 4 [weights transversions 2 times transitions] a c g t [a] . 2 1 2 [c] 2 . 2 1 [g] 1 2 . 2 [t] 2 1 2 . ; typeset user_V = V: 23 24 30 31 36-40 44-47 50-54 58-67 82-87 89-92 98-102 106-114 119-125 131-138 143-146 149-153 159-163 182-184 192-194 199-210 216-229 235-238 247-253 262-268 274-278 281-291 294-297 308-311 316-317 321-325 334-349 375-379 414-423 428-432 439-446 451-453 456-472 477-482 491-495 500-507 512-514 520-522 527-534 539-543 549-556 562-588 599-606 627-634 636-638 640-642 648 649 656 657 659-662; typeset user_T = T: all; typeset user_100 = 100: all; typeset user_10 = 10: ; typeset user_2 = 2: all; end; [ambiguous sites: 1-18 41-43 61-90 104-106 121-141 166-170 198-215 221 224 231-234 346 358-374 380-413 435-439 488 499 537-539 563 573 611-612 622-625 644 + ds regions, leaves ss regions: 23 24 30 31 36-40 44-47 50-54 58-67 82-87 89-92 98-102 106-114 119-125 131-138 143-146 149-153 159-163 182-184 192-194 199-210 216-229 235-238 247-253 262-268 274-278 281-291 294-297 308-311 316-317 321-325 334-349 375-379 414-423 428-432 439-446 451-453 456-472 477-482 491-495 500-507 512-514 520-522 527-534 539-543 549-556 562-588 599-606 627-634 636-638 640-642 648 649 656 657 659-662 + ss regions only, leaves ds regions: 1-22 25-29 32-35 41-43 48 49 55-57 68-81 88 93-97 103-105 115-118 126-130 139-142 147-148 154-158 164-181 185-191 195-198 211-215 230-234 239-246 254-261 269-273 279-280 292 293 298-307 312-315 318-320 326-333 350-374 380-413 424-427 433-438 447-450 454-455 473-476 483-490 496-499 508-511 515-519 523-526 535-538 544-548 557-561 589-598 607-626 635 639 643-647 650-655 658 663 ]