use strict;

my $count=1;
while(<DATA>){
    s/\s//g;
    chomp;
    /^>/ ? print "\n " . $count++ . ": " : print;
}
__DATA__
> Seq 1 (two lines)
AAAAAAAAAAAAA
CCAAAAAAAAAAA
> Seq 2 (two lines)
AAAAAAAAAAAAA
AAAAAAAAAAAAA
> Seq 3 (one line)
TTTTTTTTTTTTAACTGAAGATTCGC