File 1 looks ilke this:-
12345   11
67890   21

File 2 looks like this:-
12345
ABCDEFANABCDEFGHIJKLMNOPQRSTVVWXWZ
67890
ABACFHAYJAYAFANJAKALAHUSSGSJISUSSKSOWUWSLSS

--------------------END----------------

##</code><code>##

#!/usr/bin/perl -w

  my %href;
      my $fn = "key.txt";
      open(FH, "$fn") || die "Cannot open file";

      while (<FH>) {
              chomp($_);
              $href{$1} = $2 if $_ =~ /(\S+)\s+(\S+)/;
      }

      while (my ($key, $value) = each(%href)) {
              #print $key. ", ". $value."\n";
      }

open(FD,"<check.txt") || die("Can't open: $!");

$/ = '>';
while ( <FD> ) {
    chomp;
    next unless ( s{ \A (\S+) \s+ (?= \d ) }{}xms and exists( $href{$1} ));

    my $name = $1;
    my $position = $2;
    my @numbers = split /\w+/;
    my $one_number = $numbers[$href{$name} - 1];
    #if ( $one_number >= $quality ) {
        print "$name\t\t$href{$name}\t$one_number\n";
        #print F1 "$name\t\t$href{$name}\t$one_number\n";
  #  }
}
close FD;
#close F1;