FASTA cannot remove low complexity regions before aligning the sequences as it is possible with BLAST. This might be problematic as when the query sequence contains such regions, e.g. mini- or microsatellites repeating the same short sequence frequent times, this increases the score of not familiar sequences in the database which only match in this repeats, which occur quite frequently. Therefore, the program PRSS is added in the FASTA distribution package. PRSS shuffles the matching sequences in the database either on the one-letter level or it shuffles short segments which length the user can determine. The shuffled sequences are now aligned again and if the score is still higher than expected this is caused by the low complexity regions being mixed up still mapping to the query. By the amount of the score the shuffled sequences still attain PRSS now can predict the significance of the score of the original sequences. The higher the score of the shuffled sequences the less significant the matches found between original database and query sequence.