Gaps in FASTA formatted genome?
Your question is based on a misunderstanding. You have a single strand, lets assume it's the red sequence in the image. The linear sequence along this strand is not limited by base-pairing rules. 

The base-pairing rules (A-T, G-C) apply to the complimentary strand, given in blue in the image. 


It's convention to only give the sequence for one strand because the base-pairing rules allow us to infer the complimentary sequence.