Dear Roboticus and Anonymous Monk

Thank you for your suggestions and directions and I am extremely sorry for any confusion if any.

As you mentioned in your earlier post, that this will not work if the sequences are overlapping and I have found that some of my regions would be overlapping.

I was also thinking if this could be done by an array of range operator and for each array element the sequence will be either bold or colored.

Below is my code which I was trying:

#!/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";
[download]

Data file:
GGCGCAACGCTGAGCAGCTGGCGCGTCCCGCGCGGCCCCAGTTCTGCGCAGCTTCCCGAGGCTCCGCACC
+                                                                   CC
+TGCAGGGCATTCCAGAAAGATGAGGATATTTGCTGTCTTTATATTCATGACCATTTGCTGAACGCATT
TACTGTCACGGTTCCCAAGGACCTATATGTGGTAGAGTATGGTAGC                        
+                                                                   AT
+GACAATTGAATGCAAATTCCCAGTAGAAAAACAATTAGACCTGGCTGCACTAATTGTCTATTGGG
AAATGGAGGATAAGAACATTATTCAATTTGTGCATGGAGAGGAAGACCTGAAGGTTCAGCATAGTAGCTA
CAGACAGAGGGCCCGGCTGTTGAAGGACCAGCTCTCCCTGGGAAATGCTGCACTTCAGATCACAGATGTG
AAATTGCAGGATGCAGGGGTGTACCGCTGCATGATCAGCTATGGTGGTGCCGACTACAAGCGAATTACTG
TGAAAGTCAATGCCCCATACAACAAAATCAACCAAAGAATTTTGGTTGTGGATCCAGTCACCTCTGAACA
TGAACTGACATGTCAGGCTGAGGGCTACCCCAAGGCCGAAGTCATCTGGACAAGCAGTGACCATCAAGTC
CTGAGTGGTAAGACCACCACCACCAATTCCAAGAGAGAGGAGAAGCTTTTCAATGTGACCAGCACACTGA
[download]