#NEXUS

Begin DATA;
	Dimensions ntax=6 nchar=844;
	Format datatype=NUCLEOTIDE interleave gap=-;
	Matrix
	[                                  1         11        21        31        41        51        ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 ------------------------------------------------------------
	Chrysemys_picta_Intron4            GTCAGTTTCAAAATACATTTTAAATTAAATGAAGGCAGTTTGTATGAAAGACCAGAT-CA
	Pelodiscus_sinensis_Intron4        GTCAATTTTAAAATAAATTTTAAATTAAACTAAGGCACTGTGTGGGAAAGGCCAGAT-CA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  61        71        81        91        101       111       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 -----TGCCA-----------ATGTCTGGCAATGTTAAATGGTGTTTCAGAGAGAATGTA
	Chrysemys_picta_Intron4            TAG--TGCCATAAGACATGCCATACCAGATAAGGCCATTCAGCTATTCTGCCAATGGCTG
	Pelodiscus_sinensis_Intron4        TAC--TGC-------------ATAGGAGAGAAGGCCATTCATCTATCCTGCCAATGATTG
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  121       131       141       151       161       171       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 GTGT--TTCAGGGAAAGA-CAAAGAAATCCCATTGTACAGC-TAACAAATTGTGCAATGC
	Chrysemys_picta_Intron4            GTGCCATTAATTGGTATTTCAGAGGAAGACTAAGAAATCCCATCGTACATTGTGCAATGC
	Pelodiscus_sinensis_Intron4        GTAT--TTCAGAGG-----CAGGCAAATCCCATGGTACATC-TAGCGTATTGTGCAATGC
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  181       191       201       211       221       231       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 TATACAAGGGTAAGGATATAATCTCCAAGACCTTGTATCATGCATGAAAATGTAAACAAA
	Chrysemys_picta_Intron4            TGTACAAGGGGAAGAATATATTTTCCAGGACCTTGTATCTTGGATGAAAATGTAAACAAA
	Pelodiscus_sinensis_Intron4        TGTGCAAGGGGAAGAATATATTTTCCAGGACCTTGTATCTTGGATGAAAATGTAAACAAA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  241       251       261       271       281       291       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 CTGACAGCATAGCCTTTGTTACAGATATAGTTCATAACATACT-----AGCATATTT---
	Chrysemys_picta_Intron4            CTGACAACACAACCTTTGTAACAGATACAGTTAATAACATGCTGTCCTAATATGTTTTAA
	Pelodiscus_sinensis_Intron4        CTGACAACACGACCTTTGTAACAGATACAGTTAATAACGTGCTGTCCTAACATGTTTCAA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  301       311       321       331       341       351       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 ----AAAAAAATCATTGAATACAGTGAAGTTTCCTTACTACTTCAGAAGCAAAGTTTGAA
	Chrysemys_picta_Intron4            AAGAAAAAAAATCATCCAATACA-----GTAT----ACTTCTTCAGAAGGGCAAGA-GAA
	Pelodiscus_sinensis_Intron4        AAGAAAAAAAATCATCCAATATACAGTAGTAT----ACTGCTTCAGAAGGGCAAAA-GAA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  361       371       381       391       401       411       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 AGAAGCAAAAACTAAAAGACACCGCAGTCGCATCAGTTTAGTTCACAGATTTAGGTGATT
	Chrysemys_picta_Intron4            GAGAGCA--GTCACAAGTGAGTTGTTTACAAATCTATCTA-TAGATGA-CTGACATTCTA
	Pelodiscus_sinensis_Intron4        CAGAGCACAGTCCCAAGGAAGCTGTTTACAAATGTGTATA-TACATGAACTGACATTCTA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  421       431       441       451       461       471       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 AACAAATGTGCAAGTTTTTGCTATTTTTATACATAT-----CATT-TATTAATTCTTTTA
	Chrysemys_picta_Intron4            ACTGCATA-GCATGTTCTTGTAATTTATACTTATTT--TAAAGTTGTATTAATTCTTTTA
	Pelodiscus_sinensis_Intron4        ACTTTATA-GCACGTTTTTTCAATTTATACTTATATGTTAAAATGGTAT-AATTCTTTTA
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  481       491       501       511       521       531       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 TACCAAGAAATAAAA-------------GGAGTTCAAAATCATATCTTATCACTGGTT--
	Chrysemys_picta_Intron4            TTCCAAATATGAGAGTTCCACTCTTATCATGCCTTAGAACCATTTCTAATCACTAGCATT
	Pelodiscus_sinensis_Intron4        TTCCAAAAGTGAGAGCTCCACTTTTGCCATACCTTAGAACCATTTAGAATCACTAGTG--
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  541       551       561       571       581       591       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 ------------------TACCAG-GCAAA--------------ATACAAATTCTACCAA
	Chrysemys_picta_Intron4            AAAAAAAAAAAACCCTAAAACTAAAACAAACAAAAAACACGCACACACATAACCTACCAA
	Pelodiscus_sinensis_Intron4        ---------AACACCTGAAACCAACACAAATACA--ACACACAAATACACAACCTACTAC
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  601       611       621       631       641       651       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 CATGGTTTGAGAGTTC-TGCATGAGGCTGGTTTTAATTTAGTTCTTTTCCCTTTTCTTTC
	Chrysemys_picta_Intron4            TACTGT------GTTTATGTATGAAGCTGGTTTTAATTTAGTTCTTTTCCGTCTTCTTTC
	Pelodiscus_sinensis_Intron4        TACAGTATAAGCGTTTATATAAGATGCTGGTTTTAATTTA---CTTTTTCCCTTTTTTTC
	Alligator_mississippiensis_Exon5   ------------------------------------------------------------
	Chrysemys_picta_Exon5              ------------------------------------------------------------
	Pelodiscus_sinensis_Exon5          ------------------------------------------------------------

	[                                  661       671       681       691       701       711       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 AG----------------------------------------------------------
	Chrysemys_picta_Intron4            AG----------------------------------------------------------
	Pelodiscus_sinensis_Intron4        AA----------------------------------------------------------
	Alligator_mississippiensis_Exon5   --GATTAAAGAAACCAGGAAATCAGA-AAAAAGCAAAAGTATTCTAGGCATTCTCACTTG
	Chrysemys_picta_Exon5              --GATTAAAGAGACCAGGAAATCAGAAAAAAAGCAAAAGTATTCTAGGCATTTTCACTTG
	Pelodiscus_sinensis_Exon5          --GATTAGAGAAACCAGGAAA--AAATAATAAAAAAAAGTATTCTAAGCATTTTTACTTG

	[                                  721       731       741       751       761       771       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 ------------------------------------------------------------
	Chrysemys_picta_Intron4            ------------------------------------------------------------
	Pelodiscus_sinensis_Intron4        ------------------------------------------------------------
	Alligator_mississippiensis_Exon5   CTTTCAAGAATCCATCATTCCACTGGAGTCAGTGGTATGTCCTTCCATTAACTCTTCTTA
	Chrysemys_picta_Exon5              CTTTTAAGAATCCATCATTCCTCTGCAGTCAATGATGCATGCTTCCATTAACTCTACTTC
	Pelodiscus_sinensis_Exon5          CTTTCAAGAATCCATCATTCCACTGCAGTCAATGATGCATTTTTCCATTACCTCTACTTG

	[                                  781       791       801       811       821       831       ]
	[                                  |         |         |         |         |         |         ]
	Alligator_mississippiensis_Intron4 ------------------------------------------------------------
	Chrysemys_picta_Intron4            ------------------------------------------------------------
	Pelodiscus_sinensis_Intron4        ------------------------------------------------------------
	Alligator_mississippiensis_Exon5   TTAGTGAACGCTATAGCTAAAGAAAAACAAAAACAACTAGCAAATAAAAA-TGTTTAAAA
	Chrysemys_picta_Exon5              TTAGTGAATGCTATAGC-------------------------------------------
	Pelodiscus_sinensis_Exon5          TTAGCGAATGCAATAGCCAGAAAAAAAAGTA--CAACTAGCCAAAAAAAAATGTTTTAAA

	[                                  841    ]
	[                                  |    ]
	Alligator_mississippiensis_Intron4 ----
	Chrysemys_picta_Intron4            ----
	Pelodiscus_sinensis_Intron4        ----
	Alligator_mississippiensis_Exon5   AAAA
	Chrysemys_picta_Exon5              ----
	Pelodiscus_sinensis_Exon5          AATA

;
End;
begin paup;
charset PartialIntron4 = 1-662;
charset exon5 = 663-844;
charset stopcodon = 666-668; 
end;

[Ensembl coordinates and GenBank accession numbers as follows:
Alligator mississippiensis: AKHW01000355
Chrysemys picta: scaffold:ChrPicBel3.0.1:JH584884.1:1335730:1336500:-1
Pelodiscus sinensis: scaffold:PelSin_1.0:JH208023.1:2414184:2414930:-1]