open (my $fhConditions, "<1.txt"); 
my $l=6;
open (my $read, "<2.txt");
my @e = <$read>;
my $d = join('', @e );
$d =~ s/\s+//g;
while (<$fhConditions>) {
    push (my @line, $_);
my $count++;
}
for (my $i = 0; $i <$count; $i++)
{
my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g;
if($pos[0] =~/[0-9]/)
{
my $match = substr($d,$pos[0],$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
if($pos[1] =~/[0-9]/)
{
my $a = $pos[0]-$l;
my $match = substr($d,$a,$l);
print "$line[$i]" if $match =~m/AAGCTT/;
}
}
[download]

i am not getting errors as well as output

That’s because you’ve removed

use strict;
use warnings;
[download]

from the head of your script, although they were there in the original. With use strict restored, the errors return:

Global symbol "$count" requires explicit package name at test.pl line 
+13.
Global symbol "@line" requires explicit package name at test.pl line 1
+5.
Global symbol "@line" requires explicit package name at test.pl line 1
+9.
Global symbol "@line" requires explicit package name at test.pl line 2
+5.
test.pl had compilation errors.
[download]

You need to declare my $count and my @line before the while loop, so that they will still be visible in the following for loop:

...
my (@line, $count);

while (<$fhConditions>)
{
    push @line, $_;
    $count++;
}

for (my $i = 0; $i < $count; $i++)
{
    my @pos = $line[$i] =~ /chr[0-9]\s+(.+?)\s/g;
    ...
[download]

See the section “Scope” in the “Functions” chapter of chromatic’s Modern Perl, available free online at http://modernperlbooks.com/books/modern_perl/.

Note: In your original question, you gave a sample of the contents of your first input file (1.txt), but not of the second (2.txt), so it’s difficult to see what your script is trying to do.

Athanasius <°(((>< contra mundum