Sort data by id

use strict;
use warnings;
use autodie qw(open close);

# Replace data.txt with your file name.
my $file = 'data.txt';

open my $FH, '<', $file;

my $index = 0;
my @data; # Array to store data
my @indices; # Array to store indices
while (my $row = <$FH>) {
    chomp $row;
    if ($row =~ /(\d+\s*:\s*\d+\s*:\s*\d+\.\d+)\.(\d+)/) {
        # Put data into the two arrays
        push @data, $row;
        push @indices, [$2, $index];
    }
    $index++;
}
close $FH;

# Sort indices by id
my @indices_sorted = map { $_->[1] } sort { $a->[0] <=> $b->[0] } @indices;
while (@indices_sorted) {
    # Here we assume the data are always paired.
    # You may need to deal with the issue.
    my $i = shift @indices_sorted;
    my $j = shift @indices_sorted;

    # You may use the two indices to access @data
    # and do more.
    print $i, ", ", $j, "\n";
}