#!/usr/bin/perl
use strict;

my $maxCodons= 2;

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 $dlen= length( $dirty );
    $dirty .= $valid;
    my $pos= 0;
    while(  "" ne $valid  ) {
        my $part= substr( $valid, 0, 3*$maxCodons, "" );
        $part =~ s#(...)#(.*?)\Q$1\E#g;
        pos($dirty)= $pos;
        my @intron=  $dirty =~ /\G$part/
            or  die "Ouch!  We backtracked";
        $pos= $+[0];
        if(  $dlen < $pos  ) {
            print "Match was not complete.\n";
            $valid= "";
        } else {
            for my $intron (  @intron  ) {
                next   if  ! length($intron);
                print "$intron\n";
            }
        }
        if(  "" eq $valid  &&  $pos < $dlen  ) {
            print substr( $dirty, $pos, $dlen-$pos ), $/;
        }
    }
}
__END__
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGAATTGG
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGACTTGG