What have you tried? Why didn't it work? Please read How do I post a question effectively?. In particular, input and expected output should be wrapped in code tags to maintain formatting. In addition, the mapping from your input to your output is not entirely obvious to me, and so you should explain that. Effort is appreciated around here.

The following code does something like what you need. Read it, consider it, and understand it. Post specific questions following site guidelines if anything is unclear. 

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

my $buffer = "";
my $series = 1;
$_ = <DATA>; # Skip first line
while (<DATA>) {
    if (/>/) {
        my @elements = split /N+/, $buffer;
        for my $i (1 .. @elements) {
            print ">Count$series.$i\n$elements[$i-1]\n";
        }
        $buffer = "";
        $series++;
    } else {
        chomp;
        $buffer .= $_;
    }
}
my @elements = split /N+/, $buffer;
for my $i (1 .. @elements) {
    print "Count$series.$i\n$elements[$i-1]\n";
}

__DATA__
>sequence1 123.3
ATGACGTAGACGATGAGTAGACGATAGCAGTGACAGGTGAGTG
ATGACGATGAGTAGAGACGGGGGTAGAGGGGGATAGATAGAGANNNNNNNN
ATAGACAGATAANNNNNNNNNNNNNNNNNAGATGAGACAGATANNNNNNN
>sequence2 143.5
ATGCGATGCNNNNNNCGTAGCTGANNNNNNCGATGCTGATGCTC
CGTAGTCTGCTAGCTAGTCNNNNNNCGTAGTCGATCGATCGANNNNNNCGTGCATGC
CGATGCTACGGATNNNNNCGATCGATCGATCGACNNNNNCGATCAGCTAG
CCCCGCTAGTCANNNNN
>sequence3 132.3
ATGCTGATCAGCTACGCTAGCNNNNNCGATCGATCGATCGACTAGCNNNNNNCGATCCGAGCT
CGATCGATCGATCGATCGANNNNNCGATCGATCGACTAGCNNNNNCGATCGATCGA
CGATCGATCGA
>C1132423 123.4
ATCGTGCATGCATCGATCGACTACGCTGCTACGATCGACTGCTAGCTACGCTAC
CGTCGATCGATCGACTACGCTGACTGACTAGCTAG
>C1123234 176.4
GCTAGCGATCGCACCGATCGATCGTACGCTACGATCGATCGATCGATCGACTGT
CGATCGATCGATCGATCGATCGA
>C1123546 531.1
CGTAGCTACGATCGATCGATCGACTAGCTACGATCGATCGACTAGCTAGCTAGCTAG

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In reply to Re: Parsing and Modifying a flat file in perl by kennethk
in thread Parsing and Modifying a flat file in perl by ad23

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