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CLUSTAL O(1.2.1) multiple sequence alignment

...
gnl|hbvcds|AB194947_PreS2_P-E      -----------------------------------
+-------------------------
gnl|hbvcds|AB194948_PreS2_P-E      -----------------------------------
+-------------------------

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#!/usr/bin/perl
use strict;
...
    print "\n";
}
close (X);

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1       A       20.0    C       0       G       0       T       0
2       A       0       C       0       G       0       T       20.0
...
59      A       20.0    C       0       G       0       T       0
60      A       0       C       0       G       0       T       20.0

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CLUSTAL O(1.2.1) multiple sequence alignment

...
gnl|hbvcds|AB194948_PreS2_P-E      gggtttttcttgttgacaaaaatcctcacaatacc
+gcagagtctagactcgtggtggact
                                     *  * **  *   *       ****** **** 
+***        *    *  *    *