#NEXUS 

[file=ptf.nex
 Alignment showing 2 clones of TF fragments with part of monomer 1
 and the 5' body segment that were recovered from the 
 M. spicilegus strain PANCEVO by PCR.  TFcons is the M. m. domesticus
 TF consensus.  10/6/99]

Begin data;
    Dimensions ntax=3 nchar=577;
    Format datatype=DNA interleave gap=- machchar=.;
    Matrix
[          |-- TF monomer1 ------------------------------------->]
   TFcons  TTAGTCTGCT TAGGTGAGAG TCTGTACCAC CTGGGAACTG CCAAAGCAAC 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  ...a...... .......... .......... .......... .......... 

[          ------------------------------------>|Body     1550   ]
   TFcons  ACAGTGTCTG AGAAAGGTCC TGTTTTGGGC CTTCTTCTTC GGCCAGGAGG 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '    1600       ]
   TFcons  AGGTCCAAAT ACAAGATATC TGCGCACCTT CCCTGTAAGA GAGCTTGCCA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[            '          '          '            '       1650     ]
   TFcons  GCAGAGAGTG CTCTGAGCAC TGAAACTCAG AGGAGAGAAT CTGTCTCCCA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '       1700    ]
   TFcons  GGTCTGCTGA TAGACGGTAA CAGAATCACC AGAAGAACAA TCTCTAAACA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... ......-... .......... .......... .......... 

[               '          '          '          '       1750    ]
   TFcons  GAGTCAACTA TAACTACTAA CTCCAGAGAT TACCAGATGG CGAAAGGTAA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '       1800    ]
   TFcons  ACGGAGGAAT CTTACTAACA GGAACCAAGA CCACTCACCA TCACCAGAAC 
     Ptf5  .......... .......... .........t .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '       1850    ]
   TFcons  CCAGCACACC CACTTCGCCC AGTCCAGGGA ACCCCAACAC ACCTGAGAAC 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '       1900    ]
   TFcons  CTAGACCTAG ATTTAAAAGC ATATCTCATG ATGATGGTAG AGGACATCAA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[               '          '          '          '       1950    ]
   TFcons  GAAGGACTTT AATAAATCAC TTAAAGAAAT ACAGGAGAAC ACTGCTAAAG 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[                                                         a1960  ]
[               '          '          '          '       2000|<--]
   TFcons  AGTTACAAGT CCTTAAAGAA AAACAGGAAA ACACAATCAA ACAGGTAGAA 
     Ptf5  .......... .......... .......... .......... .......... 
     Ptf2  .......... .......... .......... .......... .......... 

[             a1970      a1980          ]
[          -- LPR 42bp block 3 ------->|]
   TFcons  GTCCTTACAG AAAAAGAGGA AAAAACA
     Ptf5  .......... .......... .......
     Ptf2  .......... .......... .......
    ;
End;