Could you provide perhaps a single line or maybe even 2 or 3 of the input file?

I modified your code a bit for brevity(untested). I am not all that familiar with microbiology(been 35 years since high school biology). I suspect there are CPAN modules that will handle problems like this. Do a search for like this one at bio:: and see if there might be something you can use if that is an option for you.

Hope that is in some way helpful...

#!/usr/bin/perl
use strict;
use warnings;
print "Select the region where you want to find CpG Island\n";
my ($a,$t,$c,$g,$cg,$total);
print  "1. Region 1-200\n";
print  "2. Region 2-202\n";
print  "3. Region 3-203\n";
my $choice =<STDIN>;
chomp($choice);
my $file = 'd:\perl\1.txt';

if ( $choice == 1 ) {
   region(0);
} elsif ( $choice == 2 ) {
   region(1);
} elsif ( $choice == 3) {
   region(2);
}

sub region {
    my $start = shift;
    open(INPUT, $file) or die ("File not found");
    foreach(my $line = <INPUT>) {
        my $a = substr($line,$start,200) =~ tr/A//;
        my $t = substr($line,$start,200) =~ tr/T//;
        my $g = substr($line,$start,200) =~ tr/G//;
        my $c = substr($line,$start,200) =~ tr/C//;
        my $cg = substr($line,$start,200) =~ tr/ CG //;
        my $total = substr($line,$start,200) =~ tr/ATGC//;
    }
}

my $CpG = ($cg)/$total*100;
print"Count of A = $a\n";
print"Count of T = $t\n";
print"Count of G = $g\n";
print"Count of C = $c\n";
print"CG = $cg\n";
print"total count of ATGC = $total\n";
print"CpG percentage = $CpG\n";

if ($CpG>=60) {
    print"CpG present";
} else {
    print"CpG absent";
}
[download]

Update: moved printing back outside the sub. What I get for messing with code at this hour of the morning...