I couldn't find any files of the correct format. I tried blastn at NCBI on NC_000009.11, but after waiting 45 minutes it said: "Informational Message: blastsrv4.REAL: Error: CPU usage limit was exceeded, resulting in SIGXCPU (24)." which probably just goes to show I don't know what the .... I'm doing.

So I based this upon your sample:

#! perl -slw
use strict;

my( $ID, $query, $off );
while( <DATA> ) {
    if( m[^>]  ) {
        ( $ID ) = (split '\|', $_)[ 1 ];
        next;
    }
    if( m[^Query] ) {
        ( $query ) = m[^Query\s+(\d+)];
        my $top = substr $_, 15;
        my $pipes = substr <DATA>, 15;
        my $bot = substr <DATA>, 15;
        my $p = 0;
        while( $p = 1+index $pipes, ' ', $p ) {
            printf "%20s :(%d) %1s/%1s\n",
             $ID, $query+$p,
             substr( $top, $p-1, 1 ),
             substr( $bot, $p-1, 1 );
        }
    }
}

__DATA__
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Outputs:

c:\test\blast>..\853819.pl
           14079 ref :(75) A/C
           14080 ref :(15) A/A
           14080 ref :(90) T/T
           14080 ref :(124) G/G
           14080 ref :(129) C/C
           14080 ref :(136) A/A
           14081 ref :(75) A/C
[download]