Someone

#!/usr/bin/perl
# p e r l
# r u l e
# s b i g
# t i m e
use strict;
use warnings;

my %fields;
my ($base1, $base2);
my $linenr = 0;
my $pos    = 14;
while(<>) {
    chomp;
    my $line = $_;
    $base1 = substr $line,$pos,1;

    if ( $base1 eq "t" ) {
        pos($line) = 14;
        substr($line,pos($line),1,"a");
    }
    if ( $base1 eq "a" ) {
        pos($line) = 14;
        substr($line,pos($line),1,"t");
    }
    pos($line) = 0;
    $linenr++;
    compare_line($line,$linenr);
}

sub compare_line {
    my $line   = shift;
    my $linenr = shift;
    open (DATA, "test_data.dat")
       or die "Kan het bestand niet openen\n";
    while(<DATA>) {
        chomp;
        $base2 = substr $line,$pos,1;
        $base2 = "a" if $base2 eq "t";
        $base2 = "t" if $base2 eq "a";
        if ( $line eq $_ ) {
        $fields{$linenr} = {
                      base1  => $base1,
                      base2  => $base2,
        };
        }
    }

}

print "SPNL\tBASE1\tBASE2\n";
$pos += 1;
foreach my $linenr (sort keys %fields) {
    print "$pos\t$fields{$linenr}{'base1'}\t$fields{$linenr}{'base2'}\n";
}