#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:__e
xtension'	[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_c
ells:__fusion'	[14]	'Ray_cell_associations:__ray_1'	[15]
	'Ray_cell_associati
ons:__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

1111111111222222222233333333334444444444555555555566666666667777777777888888
888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAG
CAGATATCACCTTGTTCGGAA-TC
Cvu
GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAG
CAGATATCACCTTGTTCGGAA-TC
Cel
GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAG
CAGATATCACCTTATCCGGGA-TC
Cre
GATTAAGCCATGCA-???????TGC-TTTGATTCATCA-???ATGAA-?ATTG-CGTA-CGG-???CTCATTAGAG
CAGATATCACCTTATTCGGAA-TC
Rbr
GATTAAGCCATGCA-???????TGT-AAAAGTTCAACTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAG
CAGCTATCATTCTCTTCGGAT-AT
Rbl
GACTAAGCCATGCA-???????TGT-CTCAGATCCCCATTTCACGGA-?ATCGGCGAA-CGG-???CTCAATATTA
CAGCTATCACT-TATTCGGTG-AT
Rax
GATTAAGCCATGCA-???????TGT?-ATAGTTCATTTTTTC-TGAA-?ACTG-CGAA-CGG-???CTCATTAGAG
CAGATTTTAC-CTATTCCGAA-AT
Pty
????????????????????????????????????????????GAA-?ACTG-CGAA-CGG-???CTCATTAGAG
CTTATACTAAGCTAG-CACCT-GC
Tpa
GATTAAGCCATGCA-???????TGTATTCGAACGGTCATTTTATGGCCCATCTGCGAA-CGG-???CTCATTACAA
CAGTTAAAATTCGCATGACGA-TT
Pst
GATTAAGCCATGCAAGTAAAAGTGCCAACTTGTTCGTTCTTCGGAACTAAGTTGAACTACGGACTACTCATTGCAA
TGTTTTGAAAAAAGCTGAAAAGAC


    [


1111111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111112

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
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-????????????????????CACCTAGC
TATGGATAAAGAAATCG-???AAG


    [


2222222222222222222222222222222222222222222222222222222222222222222222222222
222222222222222222222223

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCT
TTCAACTA-?GATGGTAGTTTATT
Cvu
ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCGGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCT
TTCAACTA-?GATGGTAGTTCATT
Cel
ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGGAAAGGGTGTCTGCCCT
TTCAACTA-?GATGGTAGTTTATT
Cre
ACGTTGTTTGTTGACTCTGAATAAAGCAGTTTACTGTCAGTTTCGACTGACTCTATCCGAAAAGGGTGTCTGCCCT
ATCAACTA-?GATGGTAGTCTATT
Rbr
ACGTTGTTTGTTGACTCTGAATATCGCAGTTTATCGGCAGGTA-ATCTACCGATAACCGAAAGAAGTGTCTGCCCT
ATCAACCA-?GATGGTAGTCTATT
Rbl
GCGTTGTTTGTTGACTCTGAATAACGTAGTTTATCGGTGGTTT-ATCTGCCGAAGTCCGAAATAGGTGTCTGCCCT
ATCAACT-??GACGGTAGTCTATT
Rax
ACGAAGTTTGTTGACTCTGAATATCGTAGCTGATCGACGGTTT-ACCTGTCGACGATCGGAGAAGGAGTCTGCCCT
ATCAACCA-?GATGGTAGTCTATT
Pty
ATA-?????GTTGACTTTAATTATCGTAGA-AATCGGCAGCGTGAGCT-CCGATGGGTGCAAGTTATGTACGCCCT
ATCACCCA-?GCAGGCTGTTTAAC
Tpa
GCGTTTTGTGTTGACTCTGAATATT-TTGCAGACCG-CATGCGAAAGCGGCGGCGTGTCATGCGATTAACTGCCCT
ATCAACTTTTGATGGTAGTTTAGT
Pst
AGAATGGCCGTCCACTTT-???????TTGCGGATTGACAGCCGGAACC???????????????????-AACACCAT
TTTCTG-???GTTGGTGGTGTA-?


    [


3333333333333333333333333333333333333333333333333333333333333333333333333333
333333333333333333333334

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
GTCCAAGGAAGGCAGCAGGCGCGA
Cvu
GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
GTCCAAGGAAGGCAGCAGGCGCGA
Cel
GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
GTCCAAGGAAGGCAGCAGGCGCGA
Cre
GGACTACCATGGTTGTTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
GTCCAAGGAAGGCAGCAGGCGCGA
Rbr
AGTCTACCATGGTTATTACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
ATCCAAGGAAGGCAGCAGGCGCGT
Rbl
AGTCTACCGAGGTTATCACGGGTAACGGAGAATAAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
ATCCAAGGAAGGCAGCAGGCGCGT
Rax
AGTCTACCATGGTGATCACGGGTAACGGAGAATCAGGGTTCGACTCCGGAGAGGGAGCCTTAGAAACGGCTACCAC
ATCCAAGGAAGGCAGCAGGCGCGT
Pty
CGACAGCCAGGGGTATAACGGGTAACGGAGAACTAG-GTTCGTCTCCGGAGAAGAAGCCTTCGAAA-GGCTACTAC
ATCCAAGGAAGGCAGCAGGCGCGT
Tpa
TGACTACCATGGTGATAACGGGTAACGGAGGATCAGGGTTTGACTCCGGAGAGTATCCT-GAGAGACGGCAAACAC
ATCTAAGGAAGGCAGCAGGCGCGC
Pst
TTGGTGCAAATAGGACAAT-GGTTGCGGATGATAGTTGTCGGGCGTCGGAGAATACGCTTGAGAAACGGCGAATAC
TTCTAAGGAAGGCAGCAGGCTCGC


    [


4444444444444444444444444444444444444444444444444444444444444444444444444444
444444444444444444444445

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTA
TT-TCAATGAGTTGAATACAAATG
Cvu
AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTA
TT-TCAATGAGTTGAATACAAATG
Cel
AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTA
TT-TCAATGAGTTGAATACAAATG
Cre
AACTTATCCA-?CTGTTGAGT-???ATGAG-?ATAGTGACTAAAAATATAAAG-ACTCATCCTTTTGGATGAGTTATT-T
CAATGAGTTGAATATAAATG
Rbr
AACTTATCCA-?CTACTT-CA-???GTGAG-?ATAGTGACTAAAAATAAAAAG-ACCAATCCTCACGGATCGGTTA
TT-TCAATGAGTTGAGCTTAAATA
Rbl
AACTTATCCA-?CTACCAATA-???GTGAG-?ATAGCGACAGAAAATAAAAAG-ACCAGTCCTCT-GGATTGGTTA
TT-TCAATGAATTGAGTCTAAACA
Rax
AACTTATCCA-?CTACC-TTA-???GTGAG-?ATAGTGACTAAAAATAAAGAG-ACCAATCCTTT-GGATTGGTTA
TT-TCAATGAGTTGAGCTTAAATA
Pty
AACTTATCCA-?CTAC-ATCA-???GTGAG-?ATAGTAACTAGTCTTAACTATTAACTGACTTTTCAAGTTAGTTA
TGGTCCATGAGTTGAGCTTAAATA
Tpa
AAATTACCCA-?CTCTCAATTC-?GAGGAG-?GTAGTGACAACAACTAACGAG-ACTGCTCCTACGGGAACAGTCA
TCG-AAATGGGTACAATTTAAACC
Pst
AAATTACCCATACTTCTAATTTTGAGCGGGTGGTAGTGACAACAAATACCGAA-ACCTTCCTCATATGAGGAGCTA
TTGG-AATGATTTTCTTTTAAACC


    [


5555555555555555555555555555555555555555555555555555555555555555555555555555
555555555555555555555556

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
ATTCTTCGAGTATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCCCTAGTGTATCTCGT
TATTGCTGCGGTTAAAAAACTCGT
Cvu
ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGT
TATTGCTGCGGTTAAAAAGCTCGT
Cel
ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGT
TATTGCTGCGGTTAAAAAGCTCGT
Cre
ATTCTTCGAGTAGCAAGGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCCTAGTGTATCTCGT
TATTGCTGCGGTTAAAAAGCTCGT
Rbr
GCTCTTCGAGGATCTAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTAAATCGT
CATTGCTGCGGTTAAAAAGCTCGT
Rbl
GCTCTTTGAGTAACAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTGTACACCGT
TATTGCTGCGGTTAAAAAGCTCGT
Rax
GCTCTTCGAGGACCCAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGTATAAATCGT
CATTGCTGCGGTTAAAAAGCTCGT
Pty
GCTCTTCGAGGATCAAGTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCACTAGCGTAAATTAT
TACTGCTGCGGTTAAAAAGCTCGT
Tpa
CTTTAACGAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCTCAAAGTGTATGTCAT
TATTGCTGCGGTTAAAAAGCTCGT
Pst
GAGATCGCAGGATCTATGAGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAACTCCAGCTCTTAAAGTTTATACCAT
ATCTGCTATGGTTGGCAAGTCTGT


    [


6666666666666666666666666666666666666666666666666666666666666666666666666666
666666666666666666666667

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
AGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTC
TAATTTGCTGGTTTGAGGTTGGGT
Cvu
AGTTGGATCTAGGTTACGTGCTGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTAGTCGTGACTTC
TAATTTGCTGGTTTGAGGTTGGGT
Cel
AGTTGGATCTAGGTTACGTGCCGCAGT-??????TCGCA-????????ATT-TGCGTCAACTGTGGTCGTGACTTC
TAATTTGCTGGTTTGAGGTTGGGT
Cre
AGTTGGATCTAGGTTACGTGTTGCAGT-??????TCGCC-????????CTCGTGCGTCAACTGTAGCCGTGACTTC
TAATTTGCTGGTTTGAGGTTGGGT
Rbr
AGTTGGATCTGAGTTGCATGCGTTGGT-??????TCCTC-????????TCTG-AGGTTAATCTTCGCTGCAACTAT
TTTGCTGGTTTTCTGCAGATAGCT
Rbl
AGTTGGATTTGAGTCGTTCGTTTGCGT-??????TGCTC-????????TTTG-AGCTTAACGTAGGCAGCGACTAT
TTTGCTGGTTTGCTGTTGTAGCTT
Rax
AGTTGGATTTGAGGCACGTACAGCGGT-??????TCGGC-????????TCTGCCG-TTAATCACTGTTGTGTCTAA
TTTGTTGGTTTTCTGTTGGTAACT
Pty
AGTTGAATCT-AGACGTGTATTGTTGGCATGCTTTTGGCATTCATTTGTCATTGGCTTTAGCCTTCAACCGTCT-?
?TTGCTGGTTTTCTGTTGGTG-?T
Tpa
AGTTGGATCTGAGCTCGTGAATCCAGT-??????CTGCC??????-TCTGTGTGGTACTGGCATTC-TGAGTTTGA
TTCGTCGGC-??????????????
Pst
-GCCAGCAAGCCCGTACACAGCTCTTAAA-?GTTATACCAT-???ATCTGCTATGGTT-GGAATGCATTACTTTGG
ATTCTA-??TTTGCCGGTGCAGCT


    [


7777777777777777777777777777777777777777777777777777777777777777777777777777
777777777777777777777778

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr  CCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-TGTTTGCTTG
AATAGCTCAT-CATGGAATAATGAAACAG
Cvu
CCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-TGTTTGCTTGAATAG
CTCAT-CATGGAATAATGAAACAG
Cel
TCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAATACAAG-CGCTTGCTTGAATAG
CTCAT-CATGGAATAATGAAACAG
Cre
TCG?-CCC-TTCAACTGCCAGCAGGTTTACC-TTGAATAAATCAGAGTGCTCAAAACAAG-GCTTTGCTTGTATAG
CTCAT-CATGGAATAATGAAATAG
Rbr
TCGGCTTC-TGTAGTGGCTAGCGAGATTACT-TTGAATAAAACAGAGTGTTCAAAACAAG-CGATTGCTTGAATGC
TCGAT-CATGGAATAATGGAATAG
Rbl
TCGGGCTC-TTCAGTTGCTAGCGAGTTTACT-TTGAATAAATCAGAGTGTTCATGACAGG-TGTTTGCCTGAATGG
TCTAT-CATGGAATAATAGAATAG
Rax
TCGGTTCC-TTCAGTGGCTAGCAAGTTTACC-TTGATCAAATCAAAGCGCTCAAAGCAGG-CGATTGCTTGCATTT
TGGAT-CATGGAATAATAAAATAG
Pty
TCG-CATC-TTCAGTGGCCAGCGAGT-TACT-TTGACCAAATCAGAGTGCTCAAAACAGG-CGAAAGCTTGTATGA
TTTCT-CGAGGAATAACAGAATAG
Tpa
?????????CTCGCCGGCGAG-?AGT-TACTCTTGAATAAATCGGAGTGCTCAAAACAAC-GTTTCGCTTGAACGT
TTTTG-CATGGAATAATGGAAAAG
Pst
TCGGTTGCGCATGCCGGCGGAA-????TACT-CCGAGTCTCACGGAGTGTTCAAAACAAGACTTTTGCTTGAACGA
TCATTGCATGGGATATTGGAAAAG


    [


8888888888888888888888888888888888888888888888888888888888888888888888888888
888888888888888888888889

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCAT
TACGCGAGAGGTGAAATTCGTGGA
Cvu
GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCAT
TACGCGAGAGGTGAAATTCGTGGA
Cel
GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCAT
TACGCGAGAGGTGAAATTCGTGGA
Cre
GACTTCG-GTTCTTT-TTGTTGGTTCTAGAACTGATTTAATGGTTAAGAGGGACAAACCGGGGGCATTCGTATCAT
TACGCGAGAGGTGAAATTCGTGGA
Rbr
GACCTCG-GTTCTAT-TTATTGGTTCAAGAATTGAGGTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCC-
TGCGCGAGAGGTGAAATTCGTGGA
Rbl
GACTTCG-GTTCTGT-TTATTGGTTTCTGAACCGATGTAATGATTAACAGGAACAAACCGGGGGCATACGTATTTC
TGCGCGAGAGGTGAAATTCGTGGA
Rax
GATTTCG-ATTCTAT-TTATTGGTTTAAGAATTGAATTAATGATTAAGAGAGACAATTCGGGGGCATTCGTATCCC
TGCGCGAGAGGTGAAATTCGTGGA
Pty
GACTTCG-GTTCT-TGTTGTTGGTTCCAGAATCG-TTTAATGGTTAAGAGGGACAATTCGGGGGCAGCCGTATCCT
CGGGCGAGGGGTGAAATCCGTAGA
Tpa
GAATTCG-GTTCCTTACTGTTGGTTTCGGAATTGAATTAATGATTAAGAGGGACCAA-CGGGGGCATGCGTATCGC
TGCGCGAGAGGTGAAATTCATGGA
Pst
GACTATGTGCTCTTTATT-TTGGTTTCGGCCTAG??-TAATGGATAGCAGGGTCTG-CCGGGGGCGTACGTATCGT
CCCGCGAGGGGTGAAATCCGTAGA


    [
                            1

9999999999999999999999999999999999999999999999999999999999999999999999999999
999999999999999999999990

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Cvu
CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Cel
CCGTAGTGAGACGCCCAACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Cre
CCGTAGTGAGACGCCCAATAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Rbr
CCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Rbl
CCGCAGAAGGACGCCTAAAAGCGAAAGCATTTGCCAAGAATGTTTTCATTAATCATGAGCGAAAGTTAGAGTTTCG
AAGGCGATTAGATACCGCCCTAGT
Rax
CCGCAGGGGGACGCCCAAAAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Pty
CCCTGAGGAGACGACCAATAGCGAAAGCAGCTGCCAAGAATGTCTCCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCCTAGT
Tpa
CCGCAGCGAGACGGCCTACAGCGAAAGCATTTGCCAAGAATGTCTTCATTAATCAAGAACGAAAGTCAGAGGTTCG
AAGGCGATTAGATACCGCCGTAGT
Pst
CCGTGACGAGACGACCAAGAGCGCAAGCATACGCCAAGAAAGAC-CCGCTAACCTCTGGCGAGAGCCTGACGATTA
AAGACGATTAGATACCGTCGTAGT



[1111111111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111

0000000000000000000000000000000000000000000000000000000000000000000000000000
000000000000000000000001

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAA
ACGAAAGTCTTTCGGTTCCGGGGG
Cvu
TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAA
ACGAAAGTCTTTCGGTTCCGGGGG
Cel
TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAA
ACGAAAGTCTTTCGGTTCCGGGGG
Cre
TCTGACCGTAAACGATGCCATCTCGC-??GATTCGGAG-??GGTTTT??-TGCCCTGCCGAGGAGCT-ATCCGGAA
ACGAAAGTCTTTCGGTTCCGGGGG
Rbr
TCTGACCGTAAACTATGCCATCTAGC-??GATCCGGTGG?-GGTTAT?-TCGCCTCGCCGGGGAGCT-TCCCGGAA
ACGAAAGTCTTTCGGTTCCGGGGG
Rbl
TCTGACCGTAAACTATGCCATCTAGC-??GATCCAATGG?-GATGTT?-AAGTCTCGTTGGGGAGCT??-????AA
ACGAAAGTCTTTCGGTTCCGGGGG
Rax
TCTGACCGTAAACTATGCCATCTAGC-??GATCCGATAG?-GGTATT-CATGCCTTG??GGG-AGCT-TCCCGGAA
ACGAAAGTTTTTCGGTTCCGGGGG
Pty
TCTGACCGTAAACTATACCAGCTCAT-??GACTAGTTGG?-GATGT-?AATGTCCACAACGG-GTCTGATCCGGAA
ACGAAAG-CTTTCGGTTCCGGGGG
Tpa
TCTGACCGTAAACGATACCATCTAGC-??GATCCGGCGG-CGGTATT-TTCGCCTCGCCGGGGAGCT-TTCCGGAA
ACGAAAGACTTCAGGTTCCGGGGG
Pst
TTTATCTGTGAACGATGGGAACTGACTGAAGTTTTATGCGAAGTACTACAAGAGTTGTT-?TGAATT?-CCTGGAA
ACGTCGAGTGTCC-?CTCCAGGGG



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111111111111
111111111111111111111112

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Cvu
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Cel
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Cre
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACAAGGCGTGGAGCTTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Rbr
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Rbl
TAGTATGGTTGCAAAACTGAAACTTAAAGAAATTGACGGAATGGCACCACCA???GTGGATTTTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Rax
TAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Pty
GAGTATGGTTGCAAAGCTGAAACTTAAAGAAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTA
GACTCAACACTGGGAAGCTCACCC
Tpa
TAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAATCGCACCACCAGGAGTGGAGCCTGCGGCTTAATTT
GACTCAACACGGGAAAACTCACCC
Pst
TAGTATTGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGCGCACCACCAGGAGTGGAGCCTGTGGCTTAATTT
GACTCAACACGGAGAAACTTACCC



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

2222222222222222222222222222222222222222222222222222222222222222222222222222
222222222222222222222223

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGTGATTTGTCT
Cvu
GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGTGATTTGTCT
Cel
GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGTGATTTGTCT
Cre
GGTCCGGACACCATTAGGACTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGTGATTTGTCT
Rbr
GGCCCGGACACCGTTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGCGATTTGTCT
Rbl
GGCCCGGACACTGTTAGGATTGACAGA-TT-GATA-GCTCTTTCTTGATTC-GGTGGTTGGTGGTGCATGGCCGTT
CTTGGTTGGTGGAGTGATTTGTCT
Rax
GGCCCGGACACCAGTAGGATTGACAGA-TT-GAAA-GCTCTTTCTCGATTT-GGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGCGATTTGTCT
Pty
GGTCTGGACACTATGAGGATTGACGGAACT-CGAA-GCTCCTTCTCGATTT-AGTGGCTGGTGGTGCATGGCCGTTCTTA
GTTGGTGGAGTGATCTGTCT
Tpa
GGCCCGGACACTGAAAGGACTGTCAGA-CT-GAAA-GCTCTTACTTGATTC-AGTGGTTGGTGGTGCATGGCCGTT
CTTAGTTGGTGGAGCGATTTGTCT
Pst
AGCCATCACGTTTAGTGGATGGACCTGCGA-AAGT-GAGCGTTCTTGATTT-TACGAATAGTGGTGCATGGTCGAT
TTTAGTTCGTGGGTTGATCTCTCA



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

3333333333333333333333333333333333333333333333333333333333333333333333333333
333333333333333333333334

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Cvu
GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Cel
GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTTGGCGAAT-?CTTCGG-??GTTCGTATAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Cre
GGTTTATTCCGAT-AACGAGCGAGACTCTAGCCTGCTAAATAGTCGGCGAAT-?CTTCGG-??GTTCGTATAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Rbr
GGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCACGAT-?TTTCGG-??GTCGTGTGAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Rbl
GGTTGATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTTCTGAAT-?CTTCTA-??GTTCAGTAAACCT
C-TTAGAGGCATAAGCGGTGTGA-
Rax
GGTTTATTCCGAT-AACGAGCGAGACTCTAACCTACTAAATAGTTACAGAAT-?TATTAA-??GTTCTGTTAACTT
C-TTAGAGGGATAAGCGGTGTTT-
Pty
GGTTTATTCCGGT-AACGATCGAGACTCTAGCCAACTCAATAGTTACTGGATC-GCAAGG-??ATCCAGGTAACTT
C-TTAGAGGGATTAGTGGCGTTT-
Tpa
GGTTTATTCCGAT-AACGAGCGAGACGCACGCCTACTCAATACGACTCGAGT-?TCTTTC-??GCTCGATGCCGTT
C-TTAGAGGAATGGGCGGTATAG-
Pst
GCTTAATTGCGTT-AACGAACAAGATACAAAAACCCCAAAAGGATT-????????????????ATCCAAGTGGGTT
C???????-AACGGTTACTTCCAA



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

4444444444444444444444444444444444444444444444444444444444444444444444444444
444444444444444444444445

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGG
ACTCAGCGGGTTTTTC-?CTATGC
Cvu
AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGG
ACTCAGCGGGTTTTTC-?CTATGC
Cel
AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGG
AGTCAGCGGGTTTTTC-?CTATGC
Cre
AGCCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGTGG
AGTCAGCGGGTTTTTC-?CTATGC
Rbr
AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAG
GATCAGCTGGTCGCC-??AATTGC
Rbl
AACCGCATGAGAGAGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTAATACACTGGGAG
AATCAGCTGGCCATC-??CATTGC
Rax
AACCGCACGAGATTGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCTACACTGGAAG
AATCAGCTGGTTTTT-??CATTAT
Pty
AGTCACACGAGAAGGAGCGATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGCGCCACACTGGGAG
AATCATTAGGTGTC-???CATGGC
Tpa
AACCGCATGAAAGTGCGCAATAACAGGTCTGTGATGCCCTTAGATGTCCGGGGCTGCACGCGTGCTACACTGGGGT
CTGCAGCG?GTTC-????CATAGC
Pst
ATTTCTATGAAATTGTGCTATATCAGGTCTGT-ACGCTCTACGATGGCTGGGGCCGCACGCGTGCTACACTTAGGT
CCGCAGCGAGTTCTTAATCACAGC



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

5555555555555555555555555555555555555555555555555555555555555555555555555555
555555555555555555555556

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTAT
TGC-???CCTTAAACGAGGAATGC
Cvu
CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTAT
TGC-???CCTTAAACGAGGAATGC
Cel
CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTAT
TGC-???CCTTAAACGAGGAATGC
Cre
CGAAAGGTA-TCGGT-??AAACCGTT?-GAAATTCTTCCATGT-CCGGGATAGGGTATTGTA-????????ATTAT
TGC-???CCTTAAACGAGGAATGC
Rbr
CGAAAGGTA-TTGGT-??AAACCGTT?-GAAACCCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTAT
TTC-???CCTTGAACGAGGAATTC
Rbl
CGAAAGGTA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGT-CCGGGATAGGGAATTGTA-????????ATTAT
TTC-???CCTTGAACGAGGAATCG
Rax
CGAAAGATA-TTGGT-??AAACCGTT?-GAAACTCTTCCGTGA-CCGGGATAGGGAATTGTA-????????ATTAT
TTC-???CCTTGAACGAGGAATTC
Pty
CGAAAGGCT-TTGGT-??AATCCTTT-TGAACCTCTCCCGTGG-CCGGGATAGGGATTTGTA-????????ATTAT
TTC-???CCTTGAACGAGGAATTC
Tpa
CGAAAGGTCATTGGT-??AAACCGTT?-GAAAGGACTCCGTGA-TCGGGATCGGGAATTGCA-????????ACTAT
TTC-???CCTTGAACGAGGAATTC
Pst
GGGTAAACCCACTGT??CGAACCAATGCAATGGACCTTCGTGGATTGGGATTGTAATTTGCACGTTTGTCGGCTAA
TTCGATATCGTGAACAAGGAATTC



[111111111111111111111111111111111111111111111111111111111111111111111111111
1111111111111111111111111

6666666666666666666666666666666666666666666666666666666666666666666666666666
666666666666666666666667

0000000001111111111222222222233333333334444444444555555555566666666667777777
777888888888899999999990

1234567890123456789012345678901234567890123456789012345678901234567890123456
789012345678901234567890]
Cbr
CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGA
CT-?GAACTGATTCGAGAAGAGTG
Cvu
CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGA
CT-?GAACTGATTCGAGAAGAGTG
Cel
CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGA
CT-?GAACTGATTCGAGAAGAGTG
Cre
CTAGTAAGTGTG-AGTCATCAGCTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTATCCGGGA
CT-?GAACTGATTCGAGAAGAGTG
Rbr
CTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGA
CT-?GAGCTGATTCGAGAAGAGTG
Rbl
CTAGTAAGTGTG-AGTCATCAGCTCATATTGATTACGTCCCTGCCATTTGTACACACCGCCCGTCGCTGTCCGGGA
CT-?GAGCTGTTTCGAGAAGTGTG
Rax
CTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGGA
CT-?GAGCTGTTTCGAGAAGACTG
Pty
CTAGTAAGTGTG-AGTCATCAACTCACGTTGATTGCGTCCCTGCCCTTTGTACACACCGCCCGTCGCTGTCCGGAA
CT-?GAACTGTTTCGAGAAGGCTG
Tpa
CTAGTAAGTGTG-AATCATCATCTCGCTTTTAATACGTCCCTGCGATTTGTACACACCGCCCGTCGCTACCCGGGA
CT-?GAACCGTTTCGAGAAATCCA
Pst
CTAGTAAGCGTTCAGTCATCATCTCACACTGAATGCGTCCCTGCGCTTTGTACACACCGCCCGTCGCTACCGGGGA
CTCTGAGCTGCGGCGAGAAGT???



[111111111111111111111111111111111111111111111111111111111111111111111111111
11111111111111111111

7777777777777777777777777777777777777777777777777777777777777777777777777777
7777777777777777777

0000000001111111111222222222233333333334444444444555555555566666666667777777
7778888888888999999

1234567890123456789012345678901234567890123456789012345678901234567890123456
7890123456789012345]
Cbr
GGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAA
AAGTCGTAACAAGGTAGCT
Cvu
GGGACTGTGGCTCCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAA
AAGTCGTAACAAGGTAGCT
Cel
GGGACTGTCGCTTCGAGGTTTAACGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAA
AAGTCGTAACAAGGTAGCT
Cre
GGGACTGTCGCTTCGAGGTTTTCGGAC-TTCGTTGTTGCGGAAACCATTTTTATCGCATTGGTTTGAACCGGGTAA
AAGTCGTAACAAGGTAG??
Rbr
AGGACTGACGCAGAGGGGCTT-?CGGC-TCTACTGTGATGGGAATCACTTTAATCGCAATGGCTTGAACCGGGCAA
AAGTCGTAACAAGGTACCT
Rbl
AGGACTTTTGTTGCGGGGCTT-?CGGC-TCTTCTTCGAGAGAAATCATCCTAATCGCAATGGCTTGAACCGGGCAA
AAGTCGTAACAAGGTA???
Rax
AGGACTGCTGCAGCGAGGCTC-?ACGC-TTTTCTGTTGCGGAAATCATTTTAATCGCAATGGCTTGAACCGGGCAA
AAGTCGTAACAAGGTAGCT
Pty
AGGACTGACTTT-????GTTCACTTGTGTTCATTGTT-?GGGAATCAGTTGGATCGAATTGGTTTGAACCGGGCAC
AAGTCGTAACAAGGTAG??
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;