#!/usr/bin/perl
print "type the sequence to search:";
$masked_sequence = <>;
chomp($masked_sequence);
print "now type the fasta sequence:\n" ;
$fasta_header = <>;
chomp($fasta_header);
while ($line = <>){
    #chomp($line);
    $main_sequence = $main_sequence . $line;
}
$main_sequence =~ s/$masked_sequence/XXXX/g;
print "new sequence:\n";
print "$fasta_header\n";
print "$main_sequence \n";
