If production is your goal, frozenwithjoy's suggestion may be just what you need.

If this is (as it appears) schoolwork (homework?), then you need to understand that this is NOT 'code-a-matic.'

We'll be pleased to help you learn; you need merely show that you've made a good faith effort to solve your problem. In this case, means, post your code and tell us how it fails or post an algorithm (or pseudo-code) where you can't work out the syntax.

You've outlined a fairly ambitious project for a 'complete newbie in perl,' so -- in case you're stuck on which of Perl's capabilities will help you here, consider

• Do you know how to get the data from the "main file" into a script? If not, perldoc -f while will be helpful. Hint: given the size of your data file, you'll probably want to do so, line by line.
• Consider pushing each line into a temporary cache as it's read; then test to see if it satisfies some criterion for being line 2. If not, read the next line, and see if it's line 2. If so, test its first 9 chars with regexen (lottsa' reading here: perldoc perlretut and company) and if those match the characteristics for replicate 1, 2 or 3, stashthe cached line, the line with the match and the next two lines (Hint: set a flag when you find any match for any target replicate and use it and the ++ [perldoc -f increment increment operator to know when you've pushed all four lines of the record) into the approrpiate array, say, @rep1, @rep2 or @rep3.
• wash, rinse, repeat...

My suspicion is that working out an appropriate set of regular expressions (there's a broad hint in the word "set" and a part of one of many possible solutions next) will be your biggest challenge, so...

my (@rep1,@rep2,@rep3);

my $prefix = qr/[ACTG]{3}/;
my $rep1 = qr/TTGT/;
my $rep2 = qr/GGTT/;
my $rep3 = qr/ACCT/;
my $postfix = qr/[ACTG]{2}/;

while (my $line = <DATA>) {
    if ($line =~ /^$prefix
                   $rep1
                   $postfix/x )
    {
     push @rep1, $line;    # ignoring, for regex instruction, 
                           #  the need to push your cached line, etc..
+.
    }
    elsif  ($line =~ /^$prefix
                 $rep2
                 $postfix/x )
    {
                 ....
[download]

There may be a way around this line-by-line approach. If you can absolutely count on "+" as the entire content of the third line of each record, you could use that fact as part of an approach to reading your "main file" record-by-record -- but that would be an additional complexity. Your addendum does, however, suggest an approach.

So, my suggestion is -- try this, if you're working on homework... and come back when you get stuck, with code, and details about the shortcomings of that code

And BTW, welcome to the Monastery.

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