#NEXUS [!This data set was downloaded from TreeBASE, a relational database of phylogenetic knowledge. TreeBASE has been supported by the NSF, Harvard University, Yale University, SDSC and UC Davis. Please do not remove this acknowledgment from the Nexus file. Generated on May 17, 2024; 5:24 GMT TreeBASE (cc) 1994-2008 Study reference: Steppan S., Adkins R., Spinks P., & Hale C. 2005. Multigene phylogeny of the Old World mice, Murinae, reveals distinct geographic lineages and the declining utility of mitochondrial genes compared to nuclear genes. Molecular Phylogenetics and Evolution, null. TreeBASE Study URI: http://purl.org/phylo/treebase/phylows/study/TB2:S1366] BEGIN TAXA; TITLE AP5; DIMENSIONS NTAX=37; TAXLABELS Aethomys_namaquensis Anisomys_imitator Apodemus_agrarius Apodemus_semotus Apomys_datae Apomys_hylocoetes Archboldomys_luzonensis Arvicanthis_somalicus Batomys_granti Chrotomys_gonzalesi Conilurus_penicillatis Dacnomys_millardi Gerbillus_gerbillus Hybomys_univattus Hylomyscus_parvus Leggadina_forresti Lemniscomys_barbarus Malacomys_longipes Mastomys Maxomys_bartelsii Mus_musculus Niviventer Oenomys Parotomys_sp Phloemys Praomys_jacksoni Praomys_tullbergi Pseudomys_australis Rattus_exulans Rattus_norvegicus Rhynchomys_isarogensis Stochomys_longicaudatus Sundamys_muelleri Thallomys_paedulcus Uranomys_ruddi Uromys_caudimaculatus Zelotomys_hildegardeae ; END; BEGIN CHARACTERS; [! TreeBASE Matrix URI: http://purl.org/phylo/treebase/phylows/matrix/TB2:M1458] TITLE AP5; LINK TAXA = AP5; DIMENSIONS NCHAR=446; FORMAT DATATYPE=DNA SYMBOLS= "A C G T" MISSING=? GAP= -; MATRIX [ 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 280 290 300 310 320 330 340 350 360 370 380 390 400 410 420 430 440 450 ] [ . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ] Aethomys_namaquensis CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATTGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACCGGAGTGCATGATGCCAATGATAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAG-----AGGTCACTCCACACT-GGGACCTTCCTCT----GGGGAGGGCAGAAGGCAAGT---CTCCTAC----------CTGTAACTCGGGCATCC-AATGGTTTCCTT-CCATTGGATTCTGATTCGGGGGAAGCAGCTGAGTGGCTGTTGACCCCAGAGGAGGG-----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGA{CT}GTGTTCTCTGACCGTGCCCTCCACAACATCCCCTGGTACGTGCTGGCTGGAAACCATGATCACCTT Anisomys_imitator CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAGTGGGGAGGTCACTCCAAGAT-GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTAT----------GGGGACCTTGGACTGCC-GATAGTTCCCTT-CCCTTGGTTTGTGATTCGGTGGAAGCAGCAGAGTGGTTGCTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCATGATCACCTT Apodemus_agrarius -------CCCGGGAAATGGCCAACGCGAAAGAAATCGCCAGAACCGTGCAGATGATGGGCGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACCGGCGTGCATGATGCCAATGATAAGAGGTTCCAGGTA-CGT-GCTCCTCAG---AGTCGGAGGGGACAGC-GGGAGGT--CCCCACGCT-GGGACCTGCCTCT-----GGGAGGGCAGGAGGCAGAGG-ACACCTTC----------AGGCACCTCGGACTCCC-GATGGCTCCCTGGCCCTCGGTTTCTGATCCGGTGGAAGCTGCAGAGTGCCTGGTGACAC-------------GACGCCCTTTCTGTCTGTCTGTCACAGGAGACCTTCGAGGACGTGTTCTCTGACCGCGCCCTTCGCAACATCCCCTGGTACGTGCTGGCTGGAAACCACGATCA---- Apodemus_semotus ------------------------------------------------------ATGGGCGCCGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGTGTGCATGATGCCAATGATAAGAGGTTCCAGGTA-CGT-GCTCATCAG---AGTCAGAGGGGACAGC-GGGAGGT--CCCCACACT------------------GGGGAGGGCAGGAGCCAGAGG-ACCCCTTC----------AGGCACCTCGGACTCCC-GATGGTGCCCTTGGCCTCGGTTTCTGACCCGGTGGAAGCTGCAGAGTGGCTGGTGACCCCAGCGGAGGGAGGGACGCCCTTACTGTCTGTCTGTCACAGGAGACCTTCGAGGACGTGTTCTCTGACCGCGCCCTTCGCAACATCCCCTGGTACGTGCTGGCTGGAAACCACGATCA---- Apomys_datae ????????CCGGGAAATAGCCAATGCAAAAGAAATCGCCAGAACGGTGCAGATCATGGGTGCCGATTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-GC{CT}{CT}AACAG---AGTCAGAGGTGACAGTCGGGAGGTCACTCCATGAT-GGGACCTTCCTCT----GGGGAGGGCAGAAG{AG}-------ACCTCTGC----------GGGGACCTTGGACTCCC-GATAGTTCCCTT-CCCTTGGTTTCTGACTGGGTGGACGCAGCAGAGTGATTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTTTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCAT--------- Apomys_hylocoetes ----------------TAGCCAATGCAAAAGAAATCGCCAGAACGGTGCAGATTATGGGTGCCGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-GCCCAACAG---AGTCAGAGGTGATAGTCGGGAGGTCACTCCATGAT-GGGACCTTCCTCT----GGGGCGGGCAGAAGG-------ACCTCTAC----------GGGGACCTTGGACTCCC-GATAGTTCCCTT-CCCTTGGTTTCTGACTCGGTGGAAGCGGCAGAGTAGTTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTTTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCATGAT------ Archboldomys_luzonensis -----AGCCCGGGAAATAGCCAATGCAAAAGAAATCGCCAGAACGGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAGTCAGGAGGTCACTCCACAAT-GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTAC----------GGGGACCTTGGACTCCC-GATAGTTCCCTT-CCCTTAGTTTCTGATTCGGTGGAAGCAGCAGAGTGGTTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTTTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAA---------------------------------------- Arvicanthis_somalicus -CCACAGCCCGGGAAATTGCCAATGCTAAAGAAATTGCCAGAACCGTTCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACGGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAGTGGGGAGGTCACTCCACACT-GGGACCTTCCTCT----GGCGAGGGCAGAAGGCAGGG---CTCCTAC----------CTGTAACTTGGGCATCC-AGTCGTTTCCTT-CCACTGGACTCTGATTCTGTGGAAGCAGCTGAGGGGCTGTTGA-CCCAGAGGAGGG-----TGCCCTTACTGTCCGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGAAACATCCCCTGGTATGTGCTGGCTGGAAACCACGATCACCTT Batomys_granti CACACAGCCCGGGAAGTGGCCAATGCTAAAGAAATGGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACTGGAGTGCATGATGTCAGCGACAAGAGGTTCCAGGTA-TGT-GCTCAGCAG---AGTCAGAGGTGATAGAGGAGGAGCCGCTCCATGCA-GGCACCTTCCTCT----GGGGAGGGGAGAGGGCAGAAGGACTCCT{AG}C----------AGGGACCTCGGACATCC-GATTGTTCCCTTGTCCTTGGTTTCTGATTCGGTGGAAGCAGCTGAGTGGCTGTTGACCTCAGAGGAGGGA----CGTCCTAACTGTCTATC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGCGCCCTCCGCAACATTCCCTGGTACGTGCTGGCTGGGAACCACGACCACCTT Chrotomys_gonzalesi -----AGCCCGGGAAATAGCCAACGCAAAAGAAATCGCCAGAACGGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAGTCGGGAGGTCACTCCACGAA-GGGACCTTACTGT----GGGGAGGGCAGAAGG-------ACCTCTACGGGGACCTTGGGGGACCTTGGACTCCC-AGGAGTTCCCTT-CCCTTAGTTTCTGATTCCGTGGAAGCAGCAGAGTGGTTCTTGACCCCAGAGGAGGGA----TGCCCTTACTGTTTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAAC--------------------------------------- Conilurus_penicillatis --------------------------------------------CGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGT{GT}CATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGACAGTGGGGAGGTCACTCCACCAT-GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTGA----------GGGGACCTTGGACTT{CT}C-GATAG{GT}TCCCTT-CCCTTGGTTTCTGATTCGGTGGAAGCAGCAGAGTGGTT{GT}TTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTCGAGGACGTGTTCTCTGACCGTGTCCTACGCAAC--------------------------------------- Dacnomys_millardi ------------------GCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGCGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGACAGT-GGGAGACCACTCCACACT-GGGGTCTTTCCCT----GGGGAGGGCAGAAGG-----------------------------ACCTCGGACTCCC-GATGGTTCCGTTGCCCTTGGTTTCTAATTTGGTAGAAGCAACAGAGTGACTGTTGACCCCAGAGTGGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTACGTGCTGGCCGGAAACCATGAT------ Gerbillus_gerbillus ----------------TGGCCAATGCTAAAGAGATGGCCAGAACGGTGCAGATTATGGGTGCTGACTTCATCCTGTCCCTGGGGGACAACTTCTACTTCACTGGCGTGCACGATGCCAACGACAAGAGGTTCCAGGTA-TGT-TCTCGACAG---GGTCAGAGGTGACAGT-GGACAGTCACTCTGCGC{CT}-GGGGCCTTCCTCC----GGGGAAGGCAGAGGGCAGAAGGGCTCCCAC----------AGCGGCCCTGGACACCC-AATGGCTCCCTTCTCGTTGGTCTCTAACTTGGTGGGAGCAGCAGGGTGGCTGTTGGCCTCAGAGGAGGGG----TGCCCTCTCTGTCTGCC----ACAGGAGACCTTCGAGGATGTGTTCTCCGAC{CG}GTGCCCTCCGCAACATTCCCTGGTACGTGCTGGCTGGAAACCATGACC----- Hybomys_univattus -------CCCGGGAAATGGCCAATGCTAAAGAAATTGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTATTTCACCGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-TCTCAACAG---AGTCAGAGGTGATAGTGGGGATGTCACTCCACACT-GGGACCTTCCTCT----GGGGAGGGCAGAAGGCAGGA---GTCCCAC----------CTGTAACTTGGGCATCC-AATGGTTTCCTT-CCATTGGATTCTGATTCGGTGGAAGCAGCTGAGTGGCTGTTGACCCCAGAGGAGGG-----TGCCCTTACTGTCCATC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCACGATCA---- Hylomyscus_parvus ----------GGGAAATGGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATGATGGGCGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACATGATGCTAATGACAAGAGGTTCCAGGTA-CGTGGCTCACCAG---GGTCAGAGGGGATAGTAAGGAGGCCGCTCCATGCT-GGGACCTTCTTCT----GGGGAGGGCGGAAGGCAGGAGGATGCCTCC----------GAGTACCTCGGACTCTG-GATGGTTCCCTCACCCTTGGTTTCTGATTTGGTGGAAGCAGCAGAGTGGCTGTTGACCCCAGGGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTTCGCAATGTCCCCTGGTATGTGCTGGCTGGAAACCATGACCA---- Leggadina_forresti ------------------GCCAATGCTAAAGAAATCGCCAGAACGGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTATTGT-GCTCAACAG---AGTCAGAGGTGATAGTGGGGAGGTCACTCCACGAT-GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTGA----------GGGGACCTTGGACTTTC-GATAGTTCCCTT-CTCTTGGTTTCTGATTCGGTGGAAACAGCAGAGTGGTTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACGTCCCCTGGTATGTGCTGGCTGGA--------------- Lemniscomys_barbarus -----------------------TGCTAAAGAAATTGCCAGAACAGTTCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACCGGGGTGCATGATGCCAGTGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGAGAGTGGGGAGGTCACTCCACACT-GGGACCTTCCTCT----GGGGAGGGCAGAAAGCAGGA---CTCCTAC----------CTGTAACTTGGGCA{CT}CC-AGTCGTTTCCTT-CCACTGGACTCTGCTTCCGTGGAAGCAGCTGAG{GT}GGCTGTTGA-CCCAGAGGAGGG-----TGCCCTTACTGTCCGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCACGAT------ Malacomys_longipes -------------------CCAATGCTAAAGAAATTGCCAGAACCGTGCAGATCATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAACGACAAGAGGTTCCAGGTA-TGT-GCTCACCAG---AGTCAGAGGTGACAGAGGGGAGGCCACTCCGTGCT-GGGACCTTCCTCT----GGGGAGGGCAGAAGTCAGAAGGACTCCTTC----------CGGTACCTCGGACTCCCCGATGGTTTCCTTGCCCTTGGTTTCTGATTCAGTGGAGGCCAAAGAGTGGCTGTTGACCCCAGAGGAGGAA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTTCGAAACATCCCCTGGTATGTGCTG--------------------- Mastomys CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATGATGGGCGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACACGATGCCAATGACAAGAGGTTCCAGGTA-CGT-GCTCAACAG---GGTCAGAGGTGATAGTGAGGGGGCCACTCCATGCT-GGGACCTTCTTCT----GGGGAGGGTAGAAGGCAGAAGGATGCCTCC----------CGGTACCTCGGACTCCC-GATGGTTCCCTCGCCCTTGGTTTCTGATTCGGTGGAAGCAGCAGAGTGGCTGTTGACCCCAGAGGAGGGA----TGCCCTTCCTGTCTGTC----ACAGGAGACCTTTGAGGATGTGTTCTCTGACCGTGCCCTTCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCACGATCACCTT Maxomys_bartelsii CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACTGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATAGTGGGGA----------------GGGCCTTCTCCT----GGGGAGGGCAGAAGGCAG----------------------AAGGACCTCGGACTCCC-GATGGTTCCCTTGCCCTTGGTTTCTGATCCGGTAGAAGCAACAGAGTAACTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCATGATCACCTT Mus_musculus -C{CT}ACAGCCCGGGAAATGGCCAATGCCAAAGAGATCGCCAGAACCGTGCAGACGATGGGCGCTGACTTCATCATGTCTCTGGGGGACAATTTCTACTTCACTGGAGTGCACGATGCCAGCGACAAGAGGTTCCAGGTA-TGT-GCTCAACAGCAGGGTCAGAGGTGACAGCGGTGAGGTCACTTCACACT-GGGACCTTCCTCT----GGGGAGAGCAGAAGGCAGAAGGAT----------------GGGTACCTCGGGCTTCC-ATTGGTTCCCTTGCCCTTGATTTCTGATTCGGTGGAAGCTGCAGAGTGGCTGTTGACTCCAGAGGAGGGA----TGCCCTTACTGTCTGCC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTTCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCATGATCACCTG Niviventer ----CAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGCGCTGACTTCATCATGTCCCTCGGGGACAACTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTTGACAG---AGTCAGAGGTGACAGT-GGGAGGCCACTCCACACC-AGGGCCATTCCCT----GGGGAGGGCAGAAGG-----------------------------ACCTCAGACCCCC-GAGGGTTCCGTTGCCTTTGATTTCTGATTCGGTAGAAGCAACAGAGTGACTGTTGACCCCAGAGGGGGGA----TGCCCTTGCTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGAAACATCCCCTGGTACGTGCTGGCTGGAAACCATGATCACCTT Oenomys ----------------------ATGCTAAAGAAATCGCCAGAACTGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGGTGATGGTGGGGATGTCACTCCGCACT-GGGAC-TTCCTCT----GGGGAGGGCAGAAGGCAGGA---CTCCTAC----------CTGTAA---------------------------------------CTCGGTAGAAGCAGCTGAGTGGCTGTTGACCTCAGAGGAGGG-----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGAAACATCCCCTGGTATGTGCTGGCTGGAAACCACGA------- Parotomys_sp CACACAGCCAGGGAAATAGCCAATGCTAAAGAAATTGCCAGAACCGTGCAGGTTATGGGTGCTGACTTTATCATGTCCCTGGGGGACAATTTCTACTTCACCGGAGTGCATGATGCAAATGACAAGAGGTTTCAGGTA-TGT-GCCCAGCAG---AGTCAGAGGTGACAGT{AG}GGAGGGT----------------------------------GGGCAGAAGGCAGGA---CTCCCAC----------CCGTAA----------------------CT-CCATTGGATTCTGATTCGGTGGAAGCAGCTGAGTAGCTGTTGACCCCAGAGGAGGG-----TGCTTTTACTGTCTGTC----ACAGGAGACCTTTGAAAACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCATGATC----- Phloemys CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATGGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCTCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAACGACAAGAGGTTCCAGGTA-TGT-GCCCAACAG---AGTCAGAGGTGATAGAGGAGAGGCTGCTCCACGCC-GGCACCTTCCTCT----GGGGAGGGGAGAGGGCAGAA--------------------------------------GATTGTTCCCTTGTCCTTGGTTTCTGTTCCG-TGGAAGCAGCTGAGTAGCTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTATC----ACAGGAGACCTTCGAGGATGTGTTCTCTGACCGTGCCCTCCGCAACATTCCCTGGTATGTGCTGGCTGGAAACCACGACCACCTT Praomys_jacksoni ------------------------GCTAAAGAAATCGCCAGAACTGTGCAGATGATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACACGATGCCAATGACAAGAGGTTTCAGGTA-CGT-GCTCAACGG---GGTCAGAGATGATAGTAAGGAGGC?GCTCCATGCT-GGGACCTTCTTCT----GGGGAGGGCAGAAGACAGAAGGAAACCTCC----------GGGTACCTGAGACTCCC-GATGGTTCCCTCGCCTTTGTTTTCTGACTCGGTGGAAGCAGCAGAGTGGCTGTTGACCCCAGAGGAGGGA----TGCCCTTTCTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCTCTTCGCAACATCCCCTGGTATGTGC----------------------- Praomys_tullbergi ---------------------------AAAGAAATCGCCAGAACCGTGCAGATGATGGGCGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACACGATGCCAATGACAAGAGGTTCCAGGTA-CGT-GCTCAACAG---GGTCAGAGGTGATAGTAAGGAGGCCACTCCATGCT-GGGACCTTCTTCT----GGGGAGGGCAGAAGACAGAAGGAAACCTCC----------GGGTACCTGGGACTCCT-GATGGTTCCCTCGCCCTTGGTTTCTGATTCGGTGGAAGCAGCAGAGTGGCTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGATGTGTTCTCTGACCGTGCCCTTCGAAACATCCCCTGGTATGTGCTGGCTGGAAACCACG-------- Pseudomys_australis ------GCCCGGGAAATAGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-G{CT}TCAACAG---AGTCAGAGGTGATAGTGGGGAGGTCACTCCACGAT-GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTGA----------GGGGACCTTGGACTTC--GTTAGTCCCCTT-CCCTTGG{CT}TTCTGATTCGGTGGAAGCAGCAGAGTGGTTGTTGACCCCGGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACATCCCCTGGTATGTGCTGGC------------------- Rattus_exulans CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACGGTGCAGATTATGGGCGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-CCTTGGCAG---AGTCAGAGGTGACAGT-GGGAGGCCACTCCACACC-GGGGCCTTCCCCT----GGGGAGGGCAGAAGGCAG----------------------AAGGACCTCGGACTCCC-GATGGTTCCGTTGCCCTTGGTTTCTGATTCGGTAGAAGCAACAGAGTGACTGTTGACCCCAGAGGGGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTACGTGCTGGCTGGAAACCATGATCACCTT Rattus_norvegicus CACACAGCCCGGGAAATGGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGCGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACTGGAGTGCATGACGCCAATGACAAGAGGTTCCAGGTA-TGT-CCTTGGCGG---AGTCAGAGGTGACAGT-GGGAGGCCACTCCACATG-GGGGCCTTCCCTT----GGGGAGGGCAGAAGGCAG----------------------AAGGACCTCAGACTCCC-GATGGTTCCCTTGCCCTTGGTTTCTGATTCAGTAGAAGCAACAGAGTGACTGTTGACCCCAGAGGGGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGATGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTACGTGCTGGCTGGAAACCATGATCACCTT Rhynchomys_isarogensis -----------------------------------------------GCAGATTATGGGTGCTGACTTCATCATGTCCCTTGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCCGAGGTGATAGTCAGGAGGTCACTCTACGAT-GAGACCTTCCTC-----GGGGGGGGGGGGG---------ACCTCTAT----------GGGGACCTTGGACTCCC-GATAGTTCCCTT-CCCTTAGTTTCTGATTCGGTGGAAGCAGCAGAGTGGTTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTTTGTC----ACAGGAGACCTTTGAGGATGTGTTCTCTGACCGTGTC---CGCAAC--------------------------------------- Stochomys_longicaudatus --------------------CAATGCTAAAGAAATTGCCAGAACTGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACCGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCCCAACAG---AATCAGAGGTGATACTGGGGGTGTCACTCCATACT-GGGACCTTCCTCT----GGGGAGGGCAGATGGCAGGA---CTCCTAC----------CTGTAACTCGGGCATCC-AATGGTTTCCTT-CCATTGGATTCTGATTTGGTGGAAGCAGCTGAGTGGCTGTTGACCCCAGAGGAGGG-----TGCCCTTACTGTCCGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCACGATCACC-- Sundamys_muelleri ----------------TGGCCAATGC{GT}AAAGAAATCGCCAGAACCGTGCAGATTATGGGCGCTGACTTCATCATGTCCCTGGGGGACAACTTCTACTTCACTGGAGTGCATGACGTCAATGACAAGAGGTTCCAGGTA-TGT-CCTTGGCGG---AGTCAGAGGTGACAGT-GGGAGGCCACTCAACACC-GGGGCCTTCCCCT----GGGGAGGGCAGAAGGCAG----------------------AAGGACCTCGGACTCCC-GATGGTTCCGTTGCCCTTGGTTTCTGATTTG-TAGAAGCAACAGAGTGACTGTTGACCCCAGAGGGGGG-----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAATATCCCCTGGTACGTGCTGGCCGGAAACCATGATCA?--- Thallomys_paedulcus -------------------------CTAAAGAAATTGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-CGT-GCTCAATAG---ACTCAGAGGTGATAGTGGGGAGGTCACGCCACACT-GGGACCTTCCTCT----GGGGAGGGCAGAAGGCAGGA---CTCCCAC----------CTGTAACTCGGCCATCC-GGTGGTTTCCTT-CCATTGGATTCTGATTCGGGGGAAGCAGCTGAGTGGCTATTGACCCCAGGGGAGGG-----TGCCCTTACTGTCCGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTCCGCAACATCCCCTGGTATGTGCTGGCTGGAAACCACGATCA---- Uranomys_ruddi -----------------GGCCAATGCTAAAGAAATCGCCAGAACTGTGCAGATTATGGGTGCTGACTTTATCATGTCCCTGGGAGACAACTTCTACTTCACGGGCGTGCATGATGCCAACGACAAAAGGTTCCAGGTG-TGT-GCTCAGCTG---GGCCAGAGATGACAGCCAGGAGGTCACTCTACCCT------------------GGGGAAGGCGGCGGGCACAAGGGCTCCT-----------------------ACATCC-AGTGGTTTCCTGGCCCTCTGCCTCTAATTTGGTGGGAACAAGAGGTTGGCTGTTGACCTCAGCGGAGGGG----TGCCCTCTCTGTCTGTC----ACAGGAGACCTTTGAGGATGTGTTCTCTGACCGTGCCCTCCGCAGCGTCCCCTGGTACGTTTTGGCTGGAAACCATG-------- Uromys_caudimaculatus ---ACAGCCCGGGAAATAGCCAATGCTAAAGAAATCGCCAGAACCGTGCAGATTATGGGTGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTGCATGATGCCAATGACAAGAGGTTCCAGGTA-TGT-GCTCAACAG---AGTCAGAGCTGATAGCGGGGAGGTCACTCCACAT--GGGACCTTCCTCT----GGGGAGGGCAGAAGG-------ACCTCTGA----------GGGGACCTTGGACTTCC-GATAGTTCCCTT-CCCTTGGTTTCTGATTCGGTGGAAGCAGCAGAGTGGTTGTTGACCCCAGAGGAGGGA----TGCCCTTACTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGTCCTCCGCAACATCCCCTGGTATGTGCTGGCCGGAAACCATGATCACC-- Zelotomys_hildegardeae -----------------------TGCTAAAGAAATCGCCAGAACCGTGCAGATGATGGGCGCTGACTTCATCATGTCCCTGGGGGACAATTTCTACTTCACTGGAGTACACGATGCCAATGACAAGAGGTTCCAGGTA-CGT-GCTCAACAA---GGTCAGAGGTGACAGTGAGGGGGCCA-TCCATGCT-GGCACCTTCTTCT----GGGGAGGGCAGAAGGCTGAAGGACGCCCCC----------GGGTACCTCGGACTCCT-GATGGTTCCCTCGCCCTTGGTTTCTGATTTGGTGGAAGCAGCAGAGTGGCTGTTGACCCCAGAGGAGGGA----TGCCCTTCCTGTCTGTC----ACAGGAGACCTTTGAGGACGTGTTCTCTGACCGTGCCCTTCGCAACATCCCCTGGTATGT------------------------- ; END; BEGIN CODONS; CODONPOSSET * CodonPositions (CHARACTERS = AP5) = N: 136-362, 1: 1-135\3 363-444\3, 2: 2-136\3 364-445\3, 3: 3-137\3 365-446\3; CODONPOSSET CodonPositions (CHARACTERS = AP5) = N: 136-362, 1: 1-135\3 363-444\3, 2: 2-136\3 364-445\3, 3: 3-137\3 365-446\3; END;