Hi Tony1, try like this

use strict;
use warnings;

my $str = 'mASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGS
+PTASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSANSSS';
$str =~ s/(.{10})/$1 /g;
$str =~ s/(S{3,})/<font color=red>$1<\/font>/g;
$str =~ s/<\/font> <font color=red>/ /g;

print $str;
__END__
Output is:
----------
mASVK<font color=red>SSSSS SSSS</font>FISLLL LILLVIVLQS QVIECQPQQS CTA
+SLTGLNV CAPFLVPGSP TASTECCNAV QSINHDCMCN TMRIAAQIPA QCNLPPLSCS AN<fon
+t color=red>SSS</font>
[download]

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chargrill++