To add highlight to HTML given start $index and $length:

substr($str, $start_idx, $length) =
   '<b>' . substr($str, $start_idx, $length) . '</b>';
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Once you add searching, it looks like:

my $index = 0;
my $replace = "<b>$seq</b>";
while (($index = rindex($str, $seq, $index)) >= 0) {
   substr($str, $index, length($seq)) = $replace;
}
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Update: Optimized