My apologies; I did misunderstand. The following should work:

use strict;
use warnings;

my %sequences;

while (<>) {
    my $i = 1;

    for my $char ( split '', (split)[1] ) {
        $sequences{ $i++ }{$char}++;
    }
}

for my $pos ( sort { $a <=> $b } keys %sequences ) {
    my @charCount;

    while ( my ( $char, $count ) = each %{ $sequences{$pos} } ) {
        push @charCount, "$char:$count";
    }

    print "POS #$pos " . ( join ' | ', @charCount ) . "\n";
}

[download]

This is the output:

POS #1 a:4
POS #2 q:1 | b:3
POS #3 c:4
POS #4 x:1 | d:2 | z:1
POS #5 e:4
POS #6 f:4
POS #7 c:1 | a:1 | b:1 | d:1
POS #8 h:4
POS #9 i:4
POS #10 j:4

[download]

Run on this data:

12 abcdefahij
12 abcdefbhij
12 aqcxefchij
12 abczefdhij

[download]

In reply to Re^3: What is wrong in this code??? by Kenosis
in thread What is wrong in this code??? by Anonymous Monk

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