#!/usr/bin/perl
#use strict;
use warnings;

my $filename =  "NM_014143.3.fasta";
my @name     = split( /\./, $filename );
my $name     = $name[0];
my ($infile, @temp);
open( $infile, "<", $filename ) || die "Check the $filename $!\n";
while ( my $line = <$infile> ) 
{
    chomp $line;
    if    ( $line =~ /^>/ )    { next; }
    elsif ( $line =~ /^\s*$/ ) { next; }
    elsif ( $line =~ /^\s*#/ ) { next; }
    else                       { $sequence .= $line; }
}
$sequence =~ s/\n//g;
$sequence =~ s/\s+//g;
#print "$sequence\n";
close ($infile);

my @seq = (1 .. 15, 30 .. 40, 50 .. 60); #this is a range array

for (my $pos=1;$pos<=length($sequence);$pos++){
    foreach my $ar(@seq){
	if($pos == $ar){
	    push (@temp, "<b>",$sequence, "</b");
	}
	else{
	    push (@temp, $sequence);
	}
    }
}
my $tmp = join ("", @temp);
print "$tmp\n";

##</code><code>##

Data file:
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACC                                                                   CCTGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGACCATTTGCTGAACGCATT
TACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGC                                                                                           ATGACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGG
AAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTA
CAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTG
AAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTG
TGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACA
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA