#!/usr/bin/perl
use strict;

while(  1  ) {
    my $valid= <DATA>  or  exit( 0 );
    chomp( $valid );
    my $dirty= <DATA>  or  die "Missing second sequence";
    chomp( $dirty );
    print "Comparing $valid\nto $dirty\n";
    my $pos= 0;
    while(  "" ne $valid  ) {
        my $codon= substr( $valid, 0, 3, "" );
        my $next= index( $dirty, $codon, $pos );
        if(  $next < 0  ) {
            print "Match was not complete.\n";
            last;
        }
        if(  $pos < $next  ) {
            print substr( $dirty, $pos, $next-$pos ), $/;
        }
        $pos= $next + 3;
        if(  "" eq $valid  &&  $pos < length($dirty)  ) {
            print substr( $dirty, $pos ), $/;
        }
    }
}
__END__
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGAATTGG
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGACTTGG