A portion of the sequence that I entered was replaced with [N](X)! What happened?

Last updated:2015.6.3.

The sequence that you entered was filtered by the BLAST program.
The filtering has the effect of replacing regions of your input sequence of low structural complexity with “N” (or “X” for amino-acid sequences).
For details on filtering, see the section “Filtering” in the BLAST HELP. To disable filtering, select the OFF radio button in the “Filter” option in the lower portion of the Settings screen.
Note with caution that setting this option to “OFF” may result in search times that are longer than normal.