If you perform a BLAST search using the Standard Nucleotide BLAST® (blastn) suite, your search will run against the Nucleotide collection (nr/nt) database that is set as the default database to search. The database does not contain all types of nucleotide sequences that we archive at NCBI. It excludes Whole Genomes Shotgun (WGS) sequences, Transcriptome (TSA) sequences, and unfinished High-Throughput Genomic (HTG) sequences. The database also excludes sequence tagged sites (STS) and sequences from the GenBank patent (PAT) division. Expressed Sequence Tags (EST) and Genome Survey Sequences (GSS), and unassembled sequence reads (SRA) from next generation sequencing are also not a part of the nr/nt database.
Use the pull-down menu in the Database section of the blastn page to select the appropriate database for your sequence.
Note also that unverified records are not included in any of the BLAST databases.