The key is to extract the column number from the column data then use that to place it in the table. Extracting stuff is what regexes do. Formatting the table is nicely done with printf. Consider:

use warnings;
use strict;
use constant kMaxCol => 7;

# print header
printf "%5s   ", $_ for 1 .. kMaxCol;
print "\n";

# Process data
while (<DATA>) {
    chomp;
    next unless length;

    my @cols = split (/\s+/, $_);
    my @sorted;

    @cols = map {[(m/(\d+)p/i ? $1 - 1 : kMaxCol), $_]} @cols; # Gener
+ate indexes
    $sorted[$_->[0]] = $_->[1] for grep {$_->[0]  >= 0 && $_->[0] < kM
+axCol} @cols;

    $sorted[$_] ||= '' for 0 .. kMaxCol - 1;
    printf " %7s", $_ for @sorted;
    print "\n";
}

__DATA__
c1p110    c2p452    9p235    8p226    5p100    6p218
c1p278    2p397    c6p280    7p273    3p409
[download]

Prints:

    1       2       3       4       5       6       7   
  c1p110  c2p452                   5p100   6p218        
  c1p278   2p397   3p409                  c6p280   7p273
[download]