#!/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