Do you mean something like this? If not, try explaining how your problem differs. In particular, show us an example of the input and output you are after:

#! perl -slw
use strict;

my @table;
while( <DATA> ) {
    push @table, [ split ];
}

for my $y ( 0 .. 4 ) {
    for my $x ( $y+1 .. 4 ) {
        my $temp = $table[ $y ][ $x ];
        $table[ $y ][ $x ] = $table[ $x ][ $y ];
        $table[ $x ][ $y ] =  $temp;
    }
}

print join "\t", @$_ for @table;

__DATA__
H1-1    H1-2    H1-3    H1-4    H1-5
H2-1    H2-2    H2-3    H2-4    H2-5
val1    val2    val3    val4    val5
val6    val7    val8    val9    val10
val11   val12   val13   val14   val15
[download]

Output:

C:\test>689907.pl
H1-1    H2-1    val1    val6    val11
H1-2    H2-2    val2    val7    val12
H1-3    H2-3    val3    val8    val13
H1-4    H2-4    val4    val9    val14
H1-5    H2-5    val5    val10   val15
[download]