I changed this code

for my $href ( @AoH ) {
  for my $role ( sort keys %$href ) {
                     my $key;
    if ( ! exists $sequences{$key} ) {
        warn "KEY $key in File1 not found in File2\n";
        next;
    }
    if ( length( $sequences{$key} ) < $href->{$role} ) {
        warn "KEY $key: File2 string length too short for File1 positi
+on value\n";
        next;
    }
    my $index = rindex( $sequences{$key}, "TTT", $href->{$role} );
    if ( $index < 0 ) {
        warn sprintf( "KEY %s: No TTT in File2 string prior to positio
+n %d\n",
                      $key, $href->{$role} );
        next;
    }
    $index += 3 while ( ($index + 3) < $href->{$role} );
    print "$key $href->{$role} " . substr($sequences{$key}, $index, 3)
+ . "\n";
}
[download]

with this code

for my $href ( @AoH ) {
  for my $key ( sort keys %$href ){
    if ( ! exists $sequences{$key} ) {
        warn "KEY $key in File1 not found in File2\n";
        next;
    }
    if ( length( $sequences{$key} ) < $href->{$key} ) {
        warn "KEY $key: File2 string length too short for File1 positi
+on value\n";
        next;
    }
    my $index = rindex( $sequences{$key}, "TTT", $href->{$key} );
    if ( $index < 0 ) {
        warn sprintf( "KEY %s: No TTT in File2 string prior to positio
+n %d\n",
                      $key, $href->{$key} );
        next;
    }
    $index += 3 while ( ($index + 3) < $href->{$key} );
    print "$key $href->{$key} " . substr($sequences{$key}, $index, 3) 
+. "\n";
}
[download]

I am getting exact outputs now ;)