clustering is best left to a module, imho.

use Graph;
use strict;
use warnings;

my %v;
while (<DATA>)
{
    for my $id ( /(\.C\S+)/g )
    {
        push @{ $v{$id} }, $_;
    }
}

my $g = new Graph::Undirected;

for my $id ( keys %v )
{
    my @v = @{ $v{$id} };
    $g->add_vertex( $v[0] ) if @v == 1;
    while ( @v > 1 )
    {
        $g->add_edge( $v[0], $v[1] );
        shift @v;
    }
}

my @clusters = $g->connected_components;
for my $i ( 0 .. $#clusters )
{
    print "\ncluster".($i+1)."\n";
    print for @{$clusters[$i]};
}

__DATA__
ID5141.C1665 ID5141.C2448
ID5141.C1253 ID5144.C2039
ID5141.C1596 ID5144.C1956
ID5141.C1906 ID5144.C2149
ID5141.C1221 ID5144.C1956
ID5141.C2149 ID5141.C2386
ID5141.C2039 ID5142.C1221
ID5141.C5887 ID5141.C7685
ID5141.C1005 ID5142.C2808
ID5141.C1046 ID5141.C1596
ID5141.C2386 ID5141.C4990
ID5141.C7685 ID5141.C4888
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