#!/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 $dlen= length( $dirty );
    $dirty .= $valid;
    $valid =~ s#(...)#(.*?)\Q$1\E#g;
    my @intron=  $dirty =~ /^$valid(.*?)/
        or  die "Ouch!  We backtracked";
    if(  $dlen < $+[0]  ) {
        print "No match.\n";
    } else {
        for my $intron (  @intron  ) {
            next   if  ! length($intron);
            print "$intron\n";
        }
    }
}
__END__
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGAAT
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGACT