Ok, here's breaking into groups of 50 (had to make some changes to HTML-ize it for Perlmonks display, but you should get the idea):

c:\@Work\Perl\monks>perl -wMstrict -le
"my $red  = '<font color=\"red\">';
 my $blue = '<font color=\"blue\">';
 my $post = '</font>';
 my $brk  = qq{<br> \n};
 ;;
 my $base = qr{ [ATCG] }xms;
 ;;
 my $sequence = 'GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCT
+TCCCGAGGCTCCGCACCAGCCGCGCTTCTGCCGCCTGCAGGGCATT';
 ;;
 my $colorized_seq =
   join '',
   map qq{$red$_$post$brk},
   map { s{ ($base{1,10} \z) }{$blue$1$post}xms;  $_; }
   $sequence =~ m{ $base{1,50} }xmsg
   ;
 print qq{[[ $colorized_seq]]};
"
[[ <font color="red">GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCA<font col
+or="blue">GTTCTGCGCA</font></font><br>
<font color="red">GCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGCCGCCT<font color="
+blue">GCAGGGCATT</font></font>
<br>
]]
[download]

Which looks like:
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCA
GCTTCCCGAGGCTCCGCACCAGCCGCGCTTCTGCCGCCTGCAGGGCATT