#NEXUS 

[!References for rhabditid 18S rDNA sequences and male tail characters:

	Fitch, D. H. A., Bugaj-Gaweda, B., and Emmons, S. W.  1995.  18S
		ribosomal RNA gene phylogeny for some Rhabditidae related to
		Caenorhabditis.  Mol. Biol. Evol. 12:346-358.

	Fitch, D. H. A.  In press.  Evolution of male tail morphology and
		development in rhabditid nematodes related to Caenorhabditis
		elegans.  Syst. Biol.

OTUs:	Cbr = strain PB102 of Caenorhabditis briggsae (Dougherty and
			Nigon, 1949) Dougherty, 1955
		Cvu = strain EM464 of Caenorhabditis remanei (Sudhaus 1974)
			Andrassy, 1983 ssp. vulgaris (Baird, Fitch and Emmons, 1994)
			Sudhaus, in prep.
		Cel = strain CB4088 of Caenorhabditis elegans (Maupas, 1899)
			Dougherty, 1953
		Cre = strain CB5161 of Caenorhabditis sp. n. (misidentified for
			many years as C. remanei; Sudhaus, in prep.)
		Rbr = strain EM435 of Rhabditis myriophila Poinar, 1986
		Rbl = strain DF5010 of Rhabditis blumi Sudhaus, 1974
		Rax = strain DF5006 of Rhabditella axei (Cobbold, 1884) Chitwood,
			1933
		Pty = strain DF5026 of Pellioditis typica (Stefanski, 1922)
			Andrassy, 1983
		Tpa = strain DF5019 of Teratorhabditis palmarum Gerber and
			Giblin-Davis, 1990
		Pst = strain DF5022 of Pelodera strongyloides (Schneider, 1860)
			Schneider, 1866 ssp. dermatitica (Sudhaus and Schulte, 1988)
			Fitch, Bugaj-Gaweda and Emmons, 1995
]
[NOTE:	This is the data file used for the phylogenetic analysis of 18S rDNA and Male Tail
	characters alone or in combination.  When indels are EXCLUDED, the GAPMODE should be changed
	to =MISSING and the stepmatrices in the Assumptions Block should be changed to exclude the
	hyphens (indel "substitutions").  Also note that the Dependent adult male tail characters
	are excluded, the Cvu and Cre OTUs are deleted (as in the analysis presented in the second
	reference above), and Tpa and Pst are put into the outgroup before the program turns over
	control to the user.
	
	Note also that two separate symbols are used to designate alignment "gaps":  the hyphen (-)
	and the question mark (?).  This type of coding allows each "gap" to be counted as a single
	indel event, regardless of the length of the gap.  However, the position of the hyphen in
	the gap is crucial; hyphens at (assumed) homologous alignment positions will thus result in
	the represented gaps being treated as homologous characters.  Therefore, hyphens are only
	placed at homologous positions if the gaps are the same length.  If these precautions are
	taken, the requirement for a separate "indel matrix" is obviated.]


BEGIN DATA;
   DIMENSIONS NTAX=10 NCHAR=1831;
     FORMAT
       INTERLEAVE
       MISSING=?  GAP=-
       DATATYPE=DNA  SYMBOLS="12345";
	 OPTIONS
	   GAPMODE=NEWSTATE
	   MSTAXA=UNCERTAIN;
   CHARLABELS
        _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
        _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
        _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
		_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
	[1]	'Fan:_anterior_conformation'	[2]	'Fan:__anterior_position'	[3]	'Fan:__extension'	[4]	'Body_shape:__overall_shape'	[5]	'Body_shape:__tail_tip'
	[6]	'Phasmid:__position'	[7]	'Rays:__ray_8'	[8]	'Rays:__tip_position_for_1,2,4,8'	[9]	'Rays:__ray_6'	[10]	'Rays:__ray_3_position'
	[11]	Overall_retraction	[12]	'Terminal_cells:__retraction'	[13]	'Terminal_cells:__fusion'	[14]	'Ray_cell_associations:__ray_1'	[15]	'Ray_cell_associations:__ray_2'
	[16]	'Ray_cell_associations:__ray_3'	[17]	'Ray_cell_associations:__ray_4'	[18]	'Ray_cell_associations:__ray_5'	[19]	'Ray_cell_associations:__ray_6'	[20]	'Ray_cell_associations:__ray_7'
	[21]	'Ray_cell_associations:__ray_8'	[22]	'DV_position_of_Rnst:__ray_1'	[23]	'DV_position_of_Rnst:__ray_2'	[24]	'DV_position_of_Rnst:__ray_4'	[25]	'se-set_boundary_position'
	[26]	'Rn.p_position:__R1.p'	[27]	'Rn.p_position:__R2.p'	[28]	'Rn.p_position:__R6.p'	[29]	'Rn.p_position:__R9.p'	[30]	'Rn.p_cell_fusions:__R1.p'
	[31]	'Rn.p_cell_fusions:__R2.p'	[32]	'Rn.p_cell_fusions:__R3.p'	[33]	'Rn.p_cell_fusions:__R4.p'	[34]	'Rn.p_cell_fusions:__R5.p'	[35]	'Rn.p_cell_fusions:__R6.p'
	[36]	'Rn.p_cell_fusions:__R7.p'
	;
   STATELABELS  
	1796  '1:_open' '2:_closed',
	1797  '1:_near_base_of_spicules' '2:_near_cloaca',
	1798  '1:_broad' '2:_narrow',
	1799  '1:_blunt' '2:_elongate',
	1800  '1:_peloderan' '2:_leptoderan',
	1801  '1:_posterior' '2:_lateral',
	1802  '1:_present' '2:_absent',
	1803  '1:_at_margin' '2:_on_dorsal_or_ventral_surface',
	1804  '1:_narrow,_uniform,_open' '2:_broad,_tapered,_closed',
	1805  '1:_separate' '2:_tendency_to_fuse_with_ray_4',
	1806  '1:_strong' '2:_weak',
	1807  '1:_present' '2:_absent',
	1808  '1:_do_not_fuse' '2:_fuse',
	1809  '1:_R1.p' '2:_R1.p+R2.p' '3:_R2.p+R3.p' '4:_R3.p+R4.p',
	1810  '1:_R2.p' '2:_R2.p+R3.p' '3:_R3.p' '4:_R3.p+R4.p',
	1811  '1:_R3.p' '2:_R2.p+R3.p' '3:_R3.p+R4.p' '4:_R6.p',
	1812  '1:_R4.p' '2:_R4.p+R6.p' '3:_R6.p' '4:_R6.p+R7.p',
	1813  '1:_R5.p' '2:_R4.p+R6.p' '3:_R5.p+R6.p',
	1814  '1:_R6.p' '2:_R6.p+R7.p',
	1815  '1:_R7.p' '2:_R7.p+R9.p' '3:_migrates_into_R7.p',
	1816  '1:_R8.p' '2:_R7.p' '3:_(No_ray_8)',
	1817  '1:_seam-hyp_7_border' '2:_within_set',
	1818  '1:_seam-hyp_7_border' '2:_within_hyp_7',
	1819  '1:_seam-hyp_7_border' '2:_within_hyp_7',
	1820  '1:_near_base_of_spicules' '2:_near_cloaca',
	1821  '1:_within_seam' '2:_ventral_of_seam',
	1822  '1:_within_seam' '2:_ventral_of_seam',
	1823  '1:_ventral_of_seam' '2:_within_seam',
	1824  '1:_strictly_lateral' '2:_extends_to_dorsal_midline',
	1825  '1:_remains_unfused' '2:_fuses_with_R2.p+R3.p' '3:_fuses_with_set' '4:_fuses_with_se',
	1826  '1:_remains_unfused' '2:_fuses_with_R2.p+R3.p' '3:_fuses_with_set' '4:_fuses_with_se',
	1827  '1:_remains_unfused' '2:_fuses_with_R2.p+R3.p' '3:_fuses_with_set' '4:_fuses_with_se',
	1828  '1:_remains_unfused' '2:_fuses_with_set' '3:_fuses_with_se',
	1829  '1:_remains_unfused' '2:_fuses_with_R7.p' '3:_fuses_with_R6.p+R7.p' '4:_fuses_with_set' '5:_fuses_with_hyp7_or_maybe_se',
	1830  '1:_remains_unfused' '2:_fuses_with_R5.p+R7.p' '3:_fuses_with_se' '4:_fuses_with_hyp7',
	1831  '1:_remains_unfused' '2:_fuses_with_R5.p' '3:_fuses_with_R5.p+R6.p' '4:_fuses_with_hyp7',
   ;

   MATRIX

    [18S rDNA characters:                                                                                
                                                                                                        1
              1111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTGTTCGGAA-TC
Cvu  GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTGTTCGGAA-TC
Cel  GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTATCCGGGA-TC
Cre  GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAGCAGATATCACCTTATTCGGAA-TC
Rbr  GATTAAGCCATGCA-???????TGT-AAAAGTTCAACTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAGCAGCTATCATTCTCTTCGGAT-AT
Rbl  GACTAAGCCATGCA-???????TGT-CTCAGATCCCCATTTCACGGA-?ATCGGCGAA-CGG-???CTCAATATTACAGCTATCACT-TATTCGGTG-AT
Rax  GATTAAGCCATGCA-???????TGT?-ATAGTTCATTTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAGCAGATTTTAC-CTATTCCGAA-AT
Pty  ????????????????????????????????????????????GAA-?ACTG-CGAA-CGG-???CTCATTAGAGCTTATACTAAGCTAG-CACCT-GC
Tpa  GATTAAGCCATGCA-???????TGTATTCGAACGGTCATTTTATGGCCCATCTGCGAA-CGG-???CTCATTACAACAGTTAAAATTCGCATGACGA-TT
Pst  GATTAAGCCATGCAAGTAAAAGTGCCAACTTGTTCGTTCTTCGGAACTAAGTTGAACTACGGACTACTCATTGCAATGTTTTGAAAAAAGCTGAAAAGAC


    [                                                                                                    
     1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  CTAATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTAAACCCCAACGTAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGG
Cvu  CT-ATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTAAGCCCCAACGTAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGG
Cel  CTCATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTATACCCCAACGCAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTTTCGG
Cre  CT-ATATGGATAACTGCGGAAATACTGGAGCTAATACATGCAACTATACCCCAACGCAAGGCGGGGTGCAATTAT-TAG-AACAGACCAAACGTTCTCGG
Rbr  CCTTTATGGATAACTGCGGAAATTCTGGAGCTAATACATGCAACAAAACCTCGACTT-TGAAGAGGTGCAGATAT-TAG-TACAAACCAATCGTCTTCGG
Rbl  CCTT-?TGGATAACTGCGGAAATACTGGAGCTAATACATGCAACAT-GCCGTGTCTT-TGACACGGTGCAATTAT-TAG-TACAAATCAATCGCTTTCGG
Rax  CTTATTTGGATAACTGCGGTAATTCTGGAGCTAATACATGCAATAAAGCCCATCCTTACGGGTGGGTGCAGATAT-TAG-TACAAACCAATCGTCTCTG-
Pty  CTTTTA-GGATATCTTCGACAA-ATTGAAGCTAATACATGCAACCATGGCTC-?CTTCGGG-?GGTCGCA-ATAT-TAG-AACT-ACCAGT-?TTACTGG
Tpa  GTTTCTTGGATACTTTCAGTAATTCTGGAGCTAATACGT-?AAGCGTGCTTCGGCAC-??????????CACTTAT-TAG?-ATCGACCAACCGCTT-?AG
Pst  GTGAAAGGGATATATACGGCAAATCTGGGTCTAATACAGAATACGTA-????????????????????CACCTAGCTATGGATAAAGAAATCG-???AAG


    [                                                                                                    
     2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222223
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTTATT
Cvu  ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCGGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTCATT
Cel  ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCTTTCAACTA-?GATGGTAGTTTATT
Cre  ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCTATCAACTA-?GATGGTAGTCTATT
Rbr  ACGTTGTTTGTTGACTCTGAATATCGCAGTTTATCGGCAGGTA-ATCTACCGATAACCGAAAGAAGTGTCTGCCCTATCAACCA-?GATGGTAGTCTATT
Rbl  GCGTTGTTTGTTGACTCTGAATAACGTAGTTTATCGGTGGTTT-ATCTGCCGAAGTCCGAAATAGGTGTCTGCCCTATCAACT-??GACGGTAGTCTATT
Rax  ACGAAGTTTGTTGACTCTGAATATCGTAGCTGATCGACGGTTT-ACCTGTCGACGATCGGAGAAGGAGTCTGCCCTATCAACCA-?GATGGTAGTCTATT
Pty  ATA-?????GTTGACTTTAATTATCGTAGA-AATCGGCAGCGTGAGCT-CCGATGGGTGCAAGTTATGTACGCCCTATCACCCA-?GCAGGCTGTTTAAC
Tpa  GCGTTTTGTGTTGACTCTGAATATT-TTGCAGACCG-CATGCGAAAGCGGCGGCGTGTCATGCGATTAACTGCCCTATCAACTTTTGATGGTAGTTTAGT
Pst  AGAATGGCCGTCCACTTT-???????TTGCGGATTGACAGCCGGAACC???????????????????-AACACCATTTTCTG-???GTTGGTGGTGTA-?


    [                                                                                                    
     3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGA
Cvu  GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGA
Cel  GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGA
Cre  GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACGTCCAAGGAAGGCAGCAGGCGCGA
Rbr  AGTCTACCATGGTTATTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGT
Rbl  AGTCTACCGAGGTTATCACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGT
Rax  AGTCTACCATGGTGATCACGGGTAACGGAGAATCAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGT
Pty  CGACAGCCAGGGGTATAACGGGTAACGGAGAACTAG-GTTCGTCTCCGGAGAAGAAGCCTTCGAAA-GGCTACTACATCCAAGGAAGGCAGCAGGCGCGT
Tpa  TGACTACCATGGTGATAACGGGTAACGGAGGATCAGGGTTTGACTCCGGAGAGTATCCT-GAGAGACGGCAAACACATCTAAGGAAGGCAGCAGGCGCGC
Pst  TTGGTGCAAATAGGACAAT-GGTTGCGGATGATAGTTGTCGGGCGTCGGAGAATACGCTTGAGAAACGGCGAATACTTCTAAGGAAGGCAGCAGGCTCGC


    [                                                                                                    
     4444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444445
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATG
Cvu  AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATG
Cel  AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATACAAATG
Cre  AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-TCAATGAGTTGAATATAAATG
Rbr  AACTTATCCA-?CTACTT-CA-???GTGAG-?ATAGTGACTAAAAATAAAAAG-ACCAATCCTCACGGATCGGTTATT-TCAATGAGTTGAGCTTAAATA
Rbl  AACTTATCCA-?CTACCAATA-???GTGAG-?ATAGCGACAGAAAATAAAAAG-ACCAGTCCTCT-GGATTGGTTATT-TCAATGAATTGAGTCTAAACA
Rax  AACTTATCCA-?CTACC-TTA-???GTGAG-?ATAGTGACTAAAAATAAAGAG-ACCAATCCTTT-GGATTGGTTATT-TCAATGAGTTGAGCTTAAATA
Pty  AACTTATCCA-?CTAC-ATCA-???GTGAG-?ATAGTAACTAGTCTTAACTATTAACTGACTTTTCAAGTTAGTTATGGTCCATGAGTTGAGCTTAAATA
Tpa  AAATTACCCA-?CTCTCAATTC-?GAGGAG-?GTAGTGACAACAACTAACGAG-ACTGCTCCTACGGGAACAGTCATCG-AAATGGGTACAATTTAAACC
Pst  AAATTACCCATACTTCTAATTTTGAGCGGGTGGTAGTGACAACAAATACCGAA-ACCTTCCTCATATGAGGAGCTATTGG-AATGATTTTCTTTTAAACC


    [                                                                                                    
     5555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555556
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  ATTCTTCGAGTATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAACTCGT
Cvu  ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGT
Cel  ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGT
Cre  ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGTTATTGCTGCGGTTAAAAAGCTCGT
Rbr  GCTCTTCGAGGATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTAAATCGTCATTGCTGCGGTTAAAAAGCTCGT
Rbl  GCTCTTTGAGTAACAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTACACCGTTATTGCTGCGGTTAAAAAGCTCGT
Rax  GCTCTTCGAGGACCCAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTATAAATCGTCATTGCTGCGGTTAAAAAGCTCGT
Pty  GCTCTTCGAGGATCAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGCGTAAATTATTACTGCTGCGGTTAAAAAGCTCGT
Tpa  CTTTAACGAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCAAAGTGTATGTCATTATTGCTGCGGTTAAAAAGCTCGT
Pst  GAGATCGCAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAACTCCAGCTCTTAAAGTTTATACCATATCTGCTATGGTTGGCAAGTCTGT


    [                                                                                                    
     6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666667
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  AGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGT
Cvu  AGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGT
Cel  AGTTGGATCTAGGTTACGTGCCGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTGGTCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGT
Cre  AGTTGGATCTAGGTTACGTGTTGCAGT-??????TCGCC-????????CTCGTGCGTCAACTGTAGCCGTGACTTCTAATTTGCTGGTTTGAGGTTGGGT
Rbr  AGTTGGATCTGAGTTGCATGCGTTGGT-??????TCCTC-????????TCTG-AGGTTAATCTTCGCTGCAACTATTTTGCTGGTTTTCTGCAGATAGCT
Rbl  AGTTGGATTTGAGTCGTTCGTTTGCGT-??????TGCTC-????????TTTG-AGCTTAACGTAGGCAGCGACTATTTTGCTGGTTTGCTGTTGTAGCTT
Rax  AGTTGGATTTGAGGCACGTACAGCGGT-??????TCGGC-????????TCTGCCG-TTAATCACTGTTGTGTCTAATTTGTTGGTTTTCTGTTGGTAACT
Pty  AGTTGAATCT-AGACGTGTATTGTTGGCATGCTTTTGGCATTCATTTGTCATTGGCTTTAGCCTTCAACCGTCT-??TTGCTGGTTTTCTGTTGGTG-?T
Tpa  AGTTGGATCTGAGCTCGTGAATCCAGT-??????CTGCC??????-TCTGTGTGGTACTGGCATTC-TGAGTTTGATTCGTCGGC-??????????????
Pst  -GCCAGCAAGCCCGTACACAGCTCTTAAA-?GTTATACCAT-???ATCTGCTATGGTT-GGAATGCATTACTTTGGATTCTA-??TTTGCCGGTGCAGCT


    [                                                                                                    
     7777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777778
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  CCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-TGTTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAG
Cvu  CCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-TGTTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAG
Cel  TCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-CGCTTGCTTGAATAGCTCAT-CATGGAATAATGAAACAG
Cre  TCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-GCTTTGCTTGTATAGCTCAT-CATGGAATAATGAAATAG
Rbr  TCGGCTTC-TGTAGTGGCTAGCGAGATTACT-TTGAATAAAACAGAGTGTTCAAAACAAG-CGATTGCTTGAATGCTCGAT-CATGGAATAATGGAATAG
Rbl  TCGGGCTC-TTCAGTTGCTAGCGAGTTTACT-TTGAATAAATCAGAGTGTTCATGACAGG-TGTTTGCCTGAATGGTCTAT-CATGGAATAATAGAATAG
Rax  TCGGTTCC-TTCAGTGGCTAGCAAGTTTACC-TTGATCAAATCAAAGCGCTCAAAGCAGG-CGATTGCTTGCATTTTGGAT-CATGGAATAATAAAATAG
Pty  TCG-CATC-TTCAGTGGCCAGCGAGT-TACT-TTGACCAAATCAGAGTGCTCAAAACAGG-CGAAAGCTTGTATGATTTCT-CGAGGAATAACAGAATAG
Tpa  ?????????CTCGCCGGCGAG-?AGT-TACTCTTGAATAAATCGGAGTGCTCAAAACAAC-GTTTCGCTTGAACGTTTTTG-CATGGAATAATGGAAAAG
Pst  TCGGTTGCGCATGCCGGCGGAA-????TACT-CCGAGTCTCACGGAGTGTTCAAAACAAGACTTTTGCTTGAACGATCATTGCATGGGATATTGGAAAAG


    [                                                                                                    
     8888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888889
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGA
Cvu  GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGA
Cel  GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGA
Cre  GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCATTACGCGAGAGGTGAAATTCGTGGA
Rbr  GACCTCG-GTTCTAT-TTATTGGTTCAAGAATTGAGGTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCC-TGCGCGAGAGGTGAAATTCGTGGA
Rbl  GACTTCG-GTTCTGT-TTATTGGTTTCTGAACCGATGTAATGATTAACAGGAACAAACCGGGGGCATACGTATTTCTGCGCGAGAGGTGAAATTCGTGGA
Rax  GATTTCG-ATTCTAT-TTATTGGTTTAAGAATTGAATTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCCCTGCGCGAGAGGTGAAATTCGTGGA
Pty  GACTTCG-GTTCT-TGTTGTTGGTTCCAGAATCG-TTTAATGGTTAAGAGGGACAATTCGGGGGCAGCCGTATCCTCGGGCGAGGGGTGAAATCCGTAGA
Tpa  GAATTCG-GTTCCTTACTGTTGGTTTCGGAATTGAATTAATGATTAAGAGGGACCAA-CGGGGGCATGCGTATCGCTGCGCGAGAGGTGAAATTCATGGA
Pst  GACTATGTGCTCTTTATT-TTGGTTTCGGCCTAG??-TAATGGATAGCAGGGTCTG-CCGGGGGCGTACGTATCGTCCCGCGAGGGGTGAAATCCGTAGA


    [                                                                                                   1
     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999990
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Cvu  CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Cel  CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Cre  CCGTAGTGAGACGCCCAATAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Rbr  CCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Rbl  CCGCAGAAGGACGCCTAAAAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCATGAGCGAAAGTTAGAGTTTCGAAGGCGATTAGATACCGCCCTAGT
Rax  CCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Pty  CCCTGAGGAGACGACCAATAGCGAAAGCAGCTGCCAAGAATGTCTCCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCCTAGT
Tpa  CCGCAGCGAGACGGCCTACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATTAGATACCGCCGTAGT
Pst  CCGTGACGAGACGACCAAGAGCGCAAGCATACGCCAAGAAAGAC-CCGCTAACCTCTGGCGAGAGCCTGACGATTAAAGACGATTAGATACCGTCGTAGT


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000001
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGG
Cvu  TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGG
Cel  TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGG
Cre  TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAAACGAAAGTCTTTCGGTTCCGGGGG
Rbr  TCTGACCGTAAACTATGCCATCTAGC-??GATCCGGTGG?-GGTTAT?-TCGCCTCGCCGGGGAGCT-TCCCGGAAACGAAAGTCTTTCGGTTCCGGGGG
Rbl  TCTGACCGTAAACTATGCCATCTAGC-??GATCCAATGG?-GATGTT?-AAGTCTCGTTGGGGAGCT??-????AAACGAAAGTCTTTCGGTTCCGGGGG
Rax  TCTGACCGTAAACTATGCCATCTAGC-??GATCCGATAG?-GGTATT-CATGCCTTG??GGG-AGCT-TCCCGGAAACGAAAGTTTTTCGGTTCCGGGGG
Pty  TCTGACCGTAAACTATACCAGCTCAT-??GACTAGTTGG?-GATGT-?AATGTCCACAACGG-GTCTGATCCGGAAACGAAAG-CTTTCGGTTCCGGGGG
Tpa  TCTGACCGTAAACGATACCATCTAGC-??GATCCGGCGG-CGGTATT-TTCGCCTCGCCGGGGAGCT-TTCCGGAAACGAAAGACTTCAGGTTCCGGGGG
Pst  TTTATCTGTGAACGATGGGAACTGACTGAAGTTTTATGCGAAGTACTACAAGAGTTGTT-?TGAATT?-CCTGGAAACGTCGAGTGTCC-?CTCCAGGGG


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111112
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Cvu  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Cel  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Cre  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Rbr  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Rbl  TAGTATGGTTGCAAAACTGAAACTTAAAGAAATTGACGGAATGGCACCACCA???GTGGATTTTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Rax  TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Pty  GAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTAGACTCAACACTGGGAAGCTCACCC
Tpa  TAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAATCGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAACTCACCC
Pst  TAGTATTGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGCGCACCACCAGGAGTGGAGCCTGTGGCTTAATTTGACTCAACACGGAGAAACTTACCC


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     2222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222223
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCT
Cvu  GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCT
Cel  GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCT
Cre  GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCT
Rbr  GGCCCGGACACCGTTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCT
Rbl  GGCCCGGACACTGTTAGGATTGACAGA-TT-GATA-GCTCTTTCTTGATTC-GGTGGTTGGTGGTGCATGGCCGTTCTTGGTTGGTGGAGTGATTTGTCT
Rax  GGCCCGGACACCAGTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCT
Pty  GGTCTGGACACTATGAGGATTGACGGAACT-CGAA-GCTCCTTCTCGATTT-AGTGGCTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATCTGTCT
Tpa  GGCCCGGACACTGAAAGGACTGTCAGA-CT-GAAA-GCTCTTACTTGATTC-AGTGGTTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCT
Pst  AGCCATCACGTTTAGTGGATGGACCTGCGA-AAGT-GAGCGTTCTTGATTT-TACGAATAGTGGTGCATGGTCGATTTTAGTTCGTGGGTTGATCTCTCA


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     3333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333333334
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-
Cvu  GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-
Cel  GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-
Cre  GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTCGGCGAAT-?CTTCGG-??GTTCGTATAACTTC-TTAGAGGGATAAGCGGTGTTT-
Rbr  GGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCACGAT-?TTTCGG-??GTCGTGTGAACTTC-TTAGAGGGATAAGCGGTGTTT-
Rbl  GGTTGATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCTGAAT-?CTTCTA-??GTTCAGTAAACCTC-TTAGAGGCATAAGCGGTGTGA-
Rax  GGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTACAGAAT-?TATTAA-??GTTCTGTTAACTTC-TTAGAGGGATAAGCGGTGTTT-
Pty  GGTTTATTCCGGT-AACGATCGAGACTCTAGCCAACTCAATAGTTACTGGATC-GCAAGG-??ATCCAGGTAACTTC-TTAGAGGGATTAGTGGCGTTT-
Tpa  GGTTTATTCCGAT-AACGAGCGAGACGCACGCCTACTCAATACGACTCGAGT-?TCTTTC-??GCTCGATGCCGTTC-TTAGAGGAATGGGCGGTATAG-
Pst  GCTTAATTGCGTT-AACGAACAAGATACAAAAACCCCAAAAGGATT-????????????????ATCCAAGTGGGTTC???????-AACGGTTACTTCCAA


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     4444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444444445
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGACTCAGCGGGTTTTTC-?CTATGC
Cvu  AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGACTCAGCGGGTTTTTC-?CTATGC
Cel  AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGAGTCAGCGGGTTTTTC-?CTATGC
Cre  AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGGAGTCAGCGGGTTTTTC-?CTATGC
Rbr  AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAGGATCAGCTGGTCGCC-??AATTGC
Rbl  AACCGCATGAGAGAGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTAATACACTGGGAGAATCAGCTGGCCATC-??CATTGC
Rax  AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAGAATCAGCTGGTTTTT-??CATTAT
Pty  AGTCACACGAGAAGGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCCACACTGGGAGAATCATTAGGTGTC-???CATGGC
Tpa  AACCGCATGAAAGTGCGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGGGTCTGCAGCG?GTTC-????CATAGC
Pst  ATTTCTATGAAATTGTGCTATATCAGGTCTGT-ACGCTCTACGATGGCTGGGGCCGCACGCGTGCTACACTTAGGTCCGCAGCGAGTTCTTAATCACAGC


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     5555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555555556
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGC
Cvu  CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGC
Cel  CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGC
Cre  CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTATTGC-???CCTTAAACGAGGAATGC
Rbr  CGAAAGGTA-TTGGT-??AAACCGTT?-GAAACCCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTC
Rbl  CGAAAGGTA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGT-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATCG
Rax  CGAAAGATA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTC
Pty  CGAAAGGCT-TTGGT-??AATCCTTT-TGAACCTCTCCCGTGG-CCGGGATAGGGATTTGTA-????????ATTATTTC-???CCTTGAACGAGGAATTC
Tpa  CGAAAGGTCATTGGT-??AAACCGTT?-GAAAGGACTCCGTGA-TCGGGATCGGGAATTGCA-????????ACTATTTC-???CCTTGAACGAGGAATTC
Pst  GGGTAAACCCACTGT??CGAACCAATGCAATGGACCTTCGTGGATTGGGATTGTAATTTGCACGTTTGTCGGCTAATTCGATATCGTGAACAAGGAATTC


    [1111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     6666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666666667
     0000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990
     1234567890123456789012345678901234567890123456789012345678901234567890123456789012345678901234567890]
Cbr  CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTG
Cvu  CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTG
Cel  CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTG
Cre  CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGACT-?GAACTGATTCGAGAAGAGTG
Rbr  CTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGATTCGAGAAGAGTG
Rbl  CTAGTAAGTGTG-AGTCATCAGCTCATATTGATTACGTCCCTGCCATTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGTTTCGAGAAGTGTG
Rax  CTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGACT-?GAGCTGTTTCGAGAAGACTG
Pty  CTAGTAAGTGTG-AGTCATCAACTCACGTTGATTGCGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGAACT-?GAACTGTTTCGAGAAGGCTG
Tpa  CTAGTAAGTGTG-AATCATCATCTCGCTTTTAATACGTCCCTGCGATTTGTACACACCGCCCGTCGCTACCCGGGACT-?GAACCGTTTCGAGAAATCCA
Pst  CTAGTAAGCGTTCAGTCATCATCTCACACTGAATGCGTCCCTGCGCTTTGTACACACCGCCCGTCGCTACCGGGGACTCTGAGCTGCGGCGAGAAGT???


    [11111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111
     77777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777777
     00000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999
     12345678901234567890123456789012345678901234567890123456789012345678901234567890123456789012345]
Cbr  GGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT
Cvu  GGGACTGTGGCTCCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT
Cel  GGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAGCT
Cre  GGGACTGTCGCTTCGAGGTTTTCGGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAAAAGTCGTAACAAGGTAG??
Rbr  AGGACTGACGCAGAGGGGCTT-?CGGC-TCTACTGTGATGGGAATCACTTTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTACCT
Rbl  AGGACTTTTGTTGCGGGGCTT-?CGGC-TCTTCTTCGAGAGAAATCATCCTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTA???
Rax  AGGACTGCTGCAGCGAGGCTC-?ACGC-TTTTCTGTTGCGGAAATCATTTTAATCGCAATGGCTTGAACCGGGCAAAAGTCGTAACAAGGTAGCT
Pty  AGGACTGACTTT-????GTTCACTTGTGTTCATTGTT-?GGGAATCAGTTGGATCGAATTGGTTTGAACCGGGCACAAGTCGTAACAAGGTAG??
Tpa  GGGAATCGCTCGCCGGGGTTCGC????????????????????????????????????????????????????????????????????????
Pst  ???????????????????????????????????????????????????????????????????????????????????????????????

    [Male tail character numbers:
              111111111122222222223333333
	 123456789012345678901234567890123456
	 Alignment character positions:
	 111111111111111111111111111111111111
	 777788888888888888888888888888888888
	 999900000000001111111111222222222233
	 678901234567890123456789012345678901]
Cbr  221111122211222321211222211123332444
Cvu  221111122111222321211222211123332444
Cel  221111122111222321211222211123332444
Cre  221111122111222321211222211123332444
Rbr  111121111112111112112111111111111144
Rbl  111121211112111112113111111111111144
Rax  1122211111221122412111111111144435{34}4
Pty  111111111111112232121111111214443242
Tpa  111112111111144441231111122212221323
Pst  111112111111133443211111111114443242

;
ENDBLOCK;

BEGIN ASSUMPTIONS;
 [Transversion Parsimony Stepmatrix]
   usertype TvPars stepmatrix = 5 ACGT-
     0 1 0 1 1
	 1 0 1 0 1
	 0 1 0 1 1
	 1 0 1 0 1
	 1 1 1 1 0
	 ;
  [Transversions weighted twice transitions]
   usertype Tv2Ts stepmatrix = 5 ACGT-
     0 2 1 2 1
	 2 0 2 1 1
	 1 2 0 2 1
	 2 1 2 0 1
	 1 1 1 1 0
	 ;
  [Only indels counted]
   usertype GapsOnly stepmatrix = 5 ACGT-
     0 0 0 0 1
	 0 0 0 0 1
	 0 0 0 0 1
	 0 0 0 0 1
	 1 1 1 1 0
	 ;
  [Conserved regions]
   charset GoodAligns = 301-410 483-600 733-1026 1075-1697;
  [Variable regions]
   charset AmbigAlign = 1-300 411-482 601-732 1027-1074 1698-1795;
  [Characters involved in "loop" secondary structures, C. elegans model, Ellis et al. 1986]
   charset Loops = 1-6 26 27 32-35 44-52 58-66 70-75 97-104 120-124 141 146 147
     153-162 169-171 195-200 225-227 242-245 274-277 297-301 323-325 334-337 352 360-367
	 375 380-383 388-390 397-403 417-425 437-449 463-466 481-483 494-500 509-515 
	 538-546 576-596 607-610 640-652 676 677 700-705 737-741 750-753 763-766 775-777 
	 786-788 796-804 814-827 836-843 887-892 963 964 983-991 1007-1031 1045-1051
	 1063-1069 1083-1085 1099-1101 1111-1114 1125-1127 1132 1133 1147 1148 1158 1159
	 1170-1173 1178-1185 1190-1197 1203-1208 1228-1238 1257 1280 1290-1293 1303-1308
	 1312-1318 1322-1325 1329-1331 1356-1359 1386-1390 1396-1401 1407-1414 1418
	 1444-1447 1453-1455 1467-1470 1502-1505 1541-1551 1558-1576 1587-1596 1606
	 1617-1621 1631-1641 1655-1667 1721-1724 1776-1790;
  [Characters involved in "stem" secondary structures, but that are not paired in this dataset]
   charset OddStems = 565-575 1128-1131 1791-1795;
  [Characters involved in the 3'-side of the "stem" structures]
   charset RStems = 7-13 14-25 28-31 67-69 76-96 105-119 142-145 148-152 172-194
     232-241 278-296 326-333 353-359 376-379 404-416 450-462 484-493 516-537 597-606
	 611-639 678-699 728-736 754-762 778-785 805-813 844-886 965-982 1032-1044
	 1070-1082 1102-1110 1134-1146 1149-1157 1160-1169 1174-1177 1198-1202 1209-1227
	 1258-1279 1281-1283 1284-1289 1300-1302 1326-1328 1332-1355 1391-1395 1471-1501
	 1552-1557 1607-1616 1668-1720;
  [Characters involved in the 5'-side of the "stem structures]
   charset LStems = 36-43 53-57 125-140 163-168 201-224 228-231 246-255 256-273
     302-322 338-348 349-351 368-374 384-387 391-396 426-436 467-480 501-508 547-564
	 653-675 706-727 742-749 767-774 789-795 828-835 893-952 953-962 992-1006
	 1052-1062 1086-1098 1115-1124 1186-1189 1239-1256 1294-1299 1309-1311 1319-1321
	 1360-1385 1402-1406 1415-1417 1419-1443 1448-1452 1456-1466 1506-1540 1577-1586
	 1597-1605 1622-1630 1642-1654 1725-1775;
  [All rDNA characters]
   charset rDNA = 1-1795;
  [All Male Tail characters]
   charset MaleTail = 1796-1831;
  [Multistate male tail characters]
   charset MaleMulti = 1809-1813 1825-1831;
  [Independent male tail characters]
   charset MaleIndep = 1796 1801 1804-1831;
  [Dependent adult male tail characters]
   charset MaleNonind = 1797-1800 1802-1803;
  [Interdependent Rn.p fusion characters]
   charset Fusions = 1826-1829;
   
   typeset *MUnDUn = unord:MaleTail, unord:rDNA;
   typeset MOrdDUn = ord:MaleMulti, unord:rDNA;
   typeset MUnDTv2Ts = unord:MaleTail, Tv2Ts:rDNA;
   typeset MOrdDTv2Ts = ord:MaleMulti, Tv2Ts:rDNA;
   typeset MUnDTvPar = unord:MaleTail, TvPars:rDNA;
   typeset MOrdDTvPar = ord:MaleMulti, TvPars:rDNA;
   typeset MUnDgaps = unord:MaleTail, GapsOnly:rDNA;
   typeset MOrdDgaps = ord:MaleMulti, GapsOnly:rDNA;
   
   wtset *AllEqual = 1:all;
   wtset Lps5Stms4 = 5:Loops OddStems MaleTail, 4:RStems LStems;
   wtset Lps2Stms1 = 2:Loops OddStems MaleTail, 1:RStems LStems;
   
   exset NoAmbNonin = AmbigAlign MaleNonind;
   exset NorDNA = rDNA;
   exset NoMaleTail = MaleTail;
   exset NoStems = OddStems LStems RStems;
   exset LOdStmOnly = Loops RStems;
   exset ROdStmOnly = Loops LStems;

ENDBLOCK;

BEGIN TREES;

   utree I = ((((((Cbr,Cvu),Cel),Cre),((Rbr,Rax),Rbl)),Pty),(Tpa,Pst));
   utree II = ((((((Cbr,Cvu),Cel),Cre),((Rbr,Rbl),Rax)),Pty),(Tpa,Pst));
   utree III = (((((Cbr,Cvu),Cel),Cre),(((Rbr,Rax),Rbl),Pty)),(Tpa,Pst));
   utree IV = (((((Cbr,Cvu),Cel),Cre),(((Rbr,Rbl),Rax),Pty)),(Tpa,Pst));
   utree V = (((((((Cbr,Cvu),Cel),Cre),Pty),Pst),((Rbr,Rbl),Rax)),Tpa);
   utree Polytomy = (((Cbr,Cel),(Rbr,Rbl,Rax),Pty),(Tpa,Pst));
   
ENDBLOCK;

BEGIN PAUP;

   OUTGROUP Tpa Pst;
   DELETE Cvu Cre /PRUNE;
   EXCLUDE MaleNonind;
   
ENDBLOCK;