use strict;
use warnings;

my $str = 'mASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSPTASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSANSSS';
$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 CTASLTGLNV CAPFLVPGSP TASTECCNAV QSINHDCMCN TMRIAAQIPA QCNLPPLSCS AN<font color=red>SSS</font>