The number of alignments returned for BLAST searches is search dependent. It is determined by the combination of settings in the ALIGNMENTS, HITLIST_SIZE, MAX_NUM_SEQ, and EXPECT parameters. Some representative situations are described below.
The most important cutoff is EXPECT. If the number of hits satisfying the EXPECT cutoff is fewer than that specified by ALIGNMENTS, all of the hits will be displayed in the results. If the number of hits satisfying the EXPECT cutoff is greater than the value of ALIGNMENTS, only the ALIGNMENTS hits will be displayed. The the EXPECT value of the last alignment is a good indicator of the situation.
Simply specifying a greater value for ALIGNMENTS during the 'Get' step may not necessarily display additional alignments, since the ALIGNMENTS settings during the 'Put' step is the limiting factor. The exception is when a greater value for the HITLIST_SIZE parameter was specified during the 'Put' step, which allows BLAST server to save maximal HITLIST_SIZE number of alignments while displaying only the ALIGNMENTS number of alignments. The function of MAX_NUM_SEQ is similar to ALIGNMENTS. It also set the DESCRIPTIONS to the same value.
Note that the number of alignments specified by ALIGNMENTS is not the total number of HSPs, or alignment fragments, since a given database sequence matching the query may have mulitple HSPs. In Tabular output format, the number of HSPs reported will be greater or equal to max(DESCRIPTIONS, ALIGNMENTS, HITLIST_SIZE).