#!/usr/bin/perl

use strict;

if ( @ARGV != 2 ) {
    die "Usage:  $0  pattern  file.name\n";
}
my ( $find, $filename ) = @ARGV;
open( my $fh, "<", $filename ) or die "Cannot open $filename: $!\n";

$/ = undef;   # set  INPUT_RECORD_SEPARATOR to "slurp-mode"

my $seq = <$fh>;   # entire file is now in $seq;
$seq =~ tr/\n//d;  # remove all newlines (I think you don't want spaces)
open( my $out, ">", "write.txt" ) or die "Cannot create write.txt: $!\n";
while ( $seq =~ /(..)$find(..)/g ) {
    print "before = $1 ; after = $2\n";
    print $out "$1\n$2\n";
}

##</code><code>##

your_script_name  agt  input_file.name

# or:

perl your_script_name  agt  input_file.name