c:\@Work\Perl\monks>perl -wMstrict -le
"my $red  = '<span style=\"color:red\">';
 my $blue = '<span style=\"color:blue\">';
 my $post = '</span>';
 ;;
 my $bases = qr{ [ATCG] }xms;
 ;;
 for my $s (qw(
   GGCGCAACGCTGAGGCCCCAGTTCTGCGCAGCTGCAGGGCATT
   ATCGATCGATC
   ATCGATCGAT
   A
   )) {
   my $seq = $s;
   $seq =~ s{ ($bases{1,10} \z) }{$blue$1$post}xms;
   $seq = qq{$red$seq$post};
   print $seq;
   }
"
<span style="color:red">GGCGCAACGCTGAGGCCCCAGTTCTGCGCAGCT<span style="color:blue">GCAGGGCATT</span></span>
<span style="color:red">A<span style="color:blue">TCGATCGATC</span></span>
<span style="color:red"><span style="color:blue">ATCGATCGAT</span></span>
<span style="color:red"><span style="color:blue">A</span></span>