>sp|P05100|3MG1_ECOLI DNA-3-methyladenine glycosylase 1

MERCGWVSQDPLYIAYHDNEWGVPETDSKKLFEMICLEGQQAGLSWITVLKKRENYRACF

HQFDPVKVAAMQEEDVERLVQDAGIIRHRGKIQAIIGNARAYLQMEQNGEPFVDFVWSUV

>sp|P30871|3PASE_ECOLI Inorganic triphosphatase

MAQEIELKFIVNHSAVEALRDHLNTLGGEHHDPVQLLNIYYETPDNWLRGHDMGLRI

RGE NGRYEMTMKVAGRVTGGLHQRPEYNVALSEPTLDLAQLPTEVWPNGELPADLASRVQPLF

I hope this little piece of code help. I supposed that the residues are marked with letters A-Z.

#!/usr/bin/perl -w

use strict;

open FILE1, "<e.txt" or die "can't open file for reading: $!\n";

my %Fasta_split;

my $id;
while (<FILE1>) {
  chomp;
  next if(/^\s*$/);

  my $FastaLine = $_;

  if ( $FastaLine =~ /^>sp\|(\w+\S+)\|/ ) {
    $id = $1;
  } else {
    $Fasta_split{$id} .= $FastaLine;
  }
}

# print header
my @header = qw/A B C D E F G H I J K L M N O P Q R S T U V W X Y Z/;
print "ID        " . join('  ', @header) . "\n";
# print data
foreach my $id (sort keys %Fasta_split) {
    my %words;
    # count letters
    $words{$_}++ for split('', $Fasta_split{$id});

    printf "%8s ",  $id;
    # print counts
    foreach my $w (@header) {
      if (defined $words{$w}) {
        printf "%2d ", $words{$w};
      } else {
        print ' - ';
      }
    }
    print "\n";
}
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