#!/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 );
    $valid =~ s#(...)#(.*?)\Q$1\E#g;
    my @intron=  $dirty =~ /^$valid(.*?)/;
    for my $intron (  @intron  ) {
        next   if  ! length($intron);
        print "$intron\n";
    }
}
__END__
ATGGAGTCGACGAATTTGAAGAAT
GCACCGATGGAGTAGGTCGACGATCTCAATTTGTCGAAGAAT