#! /usr/local/bin/perl -w

use strict;

open (INPUT, "<positions.input") or die "unable to open file";

open (INPUT2, "<dna.file") or die "unable to open file";

open (OUTFILE, ">$$.output");

@dna = <INPUT2>;

$dna = join ('', @dna);

$dna =~ s/\s//g;

@dna = split ('', $dna);

$count = 0;

$base = ("A"| "C"| "G" | "T");

foreach $base (@dna)
{
++$count;
}


while (<INPUT>)
{
	$line = $_;
	chomp ($line);
	@orfs = ();
	@orfs = split (/\s+/, $line);

my @start = $orfs[0];
my @finish = $orfs[1];

}

foreach $start (@orfs)
{
$start = substr ($dna, 0, $start);

substr ($dna, $start +1, $finish - $start) =~ s/A-Z/X/g;
$dna =~ s/(.{60})/$1\n/g;

print "$dna\n";
print OUTFILE "$dna\n";
}

close INPUT;
close INPUT2;
close OUTFILE;
exit;