After getting this line I again need to seperate and have 12..13, 13..14, 14..15 etc..

Try the following. Read in the file one line at a time using the outer while loop. For each line run the inner while loop to extract all of the matches.

The inner while tracks the progress of the pattern along the data because of the g modifier. The pattern itself captures the matched data (using parentheses) which can then be pushed onto an array as $1.

#! /usr/bin/perl -w
use strict;
use warnings;

my @data;

while (<DATA>)
{
    while (/(\d+\.\.\d+)/g)
    {
        push @data, $1;
    }
}

print "@data\n";

__DATA__
This is a file that contains lines like this
12..13 13..14 14..15 15..1 15..2 14..3 13..16 
that we want to extract.
16..4 16..17 17..5 17..18 18..6 18..7 12..19 19..20 20..8 20..10 19..9
+ 12..11
That was another one
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