HI Thanks for that! Insted of getting the position in reference to Query, I qould like to have them in reference to Subject. So, the output should be something like this. 14079 ref 487239 A/C. my tweaks other than your suggestions are here 
#!/usr/local/bin/perl -sl
#

use strict;
use Getopt::Long;

my $home = $ENV{'HOME'};


my($ID, $query, $off, $idi, $subject);
print "ID\tposition\tvariation\n";
while(<DATA>) {
  next if $. <20;

  if(m[^>]) {
  
   ($ID) = (split '\|',$_)[1];
   
   #!/usr/local/bin/perl -sl
#

use strict;
use Getopt::Long;

my $home = $ENV{'HOME'};


my($ID, $query, $off, $idi, $subject);
print "ID\tposition\tvariation\n";
while(<DATA>) {
  next if $. <20;

  if(m[^>]) {
  
   ($ID) = (split '\|',$_)[1];
   
   
  }
 if(/^\s+Identities/){
   
   my($identity, undef) = split/,/ ;
   ($idi) = $identity =~ /\sIdentities\s\=\s\d{3}\/\d{3}\s\((\d{2,3}\%
+)\)$/;
 } 
  
 if($idi eq "95%") {
 
  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\t%d\t%1s/%1s\n",$ID,$query+$p, substr( $top, $p-1, 1 
+),substr( $bot, $p-1, 1 );
    
   }
 }
}
   
}
  }
 if(/^\s+Identities/){
   
   my($identity, undef) = split/,/ ;
   ($idi) = $identity =~ /\sIdentities\s\=\s\d{3}\/\d{3}\s\((\d{2,3}\%
+)\)$/;
 } 
  
 if($idi eq "95%") {
 
  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\t%d\t%1s/%1s\n",$ID,$query+$p, substr( $top, $p-1, 1 
+),substr( $bot, $p-1, 1 );
    
   }
 }
}
   
}

[download]
Thanks.

In reply to Re^2: parsing mismatch from blast output by Anonymous Monk
in thread parsing mismatch from blast output by Anonymous Monk

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