use strict;
use warnings;
use Data::Dumper;

local $/ = '>';
my %hash;

while( <DATA> ) {
  if( my($k,$v)
    = /
        ^(\N+)\n    # Capture the key.
        ([CTGA]+)$     # Capture the value.
      /mx
  ) {
    $hash{$k}=$v;
  }
}

print Dumper \%hash;

__DATA__
>sequence_5849
CCTGCGGAAGATCGGCACTAGAATAGCCAGAACCGTTTCTCTGAGGCTTCCGGCCTTCCCTCCCACTAATAATTCTGAGG
>sequence_5959
CCATCGGTAGCGCATCCTTAGTCCAATTAAGTCCCTATCCAGGCGCTCCGCCGAAGGTCTATATCCATTTGTCAGCAGACACGC
>sequence_0808
CCACCCTCGTGGTATGGCTAGGCATTCAGGAACCGGAGAACGCTTCAGACCAGCCCGGACTGGGAACCTGCGGGCAGTAGGTGGAAT