Also, read $/:

Remember: the value of $/ is a string, not a regex. awk has to be better for something. :-)

$/ = "\n>";
[download]

You'll need to remove the rest of the header from the the block, though.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]

Can you elaborate more on your last sentece please?

What i want to achieve is:

Reading the header, starts with >. Storing Header info in a csv file or something. Loading in memory all the chunk up to the next header in memory. Search for a complex regexp match, store the match and the position on a csv file. Loop.

I think choroba is proposing a solution along these lines:

#! perl
use strict;
use warnings;

my $target = 'kitten';
my $count  =  0;

{
    local $/  = "\n>";
    my $first = 1;

    while (my $string = <DATA>)
    {
        if ($first)
        {
            next unless $string =~ /^>/;
        }

        (my $header, $string) = split /\n/, $string, 2;

        printf "Header: '%s%s'\n", ($first ? '' : '>'), $header;

        $string =~ s/\n//g;
        print "string is '$string'\n";
        $count += () = $string =~ /\Q$target/g;
    }
    continue
    {
        $first = 0;
    }
}

print "The target string '$target' occurs $count times in the file\n";

__DATA__
not a header
kittens
>Header1
sushikitten
ilovethekit
tensushithe
kittenisthe
>Header2
sushikittAn
ilovethekit
tensushithe
kittBnisthe
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Output:

19:57 >perl 1474a_SoPW.pl
Header: '>Header1'
string is 'sushikittenilovethekittensushithekittenisthe>'
Header: '>Header2'
string is 'sushikittAnilovethekittensushithekittBnisthe'
The target string 'kitten' occurs 4 times in the file

19:57 >
[download]

Hope that helps,

Athanasius <°(((>< contra mundum

Iustus alius egestas vitae, eros Piratica,

Oh, sorry, I lost track, I thought you were interested in the data, not the header.

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]