For each of the speed options (Fast, Medium and Slow), speed may be further enhanced by selecting for "STOP AT FIRST MATCH (SFM)" as opposed to "ALL AGAINST ALL COMPARISONS". SFM option stops further comparisons as soon as the first match conforming to any of the RISCI alignment signatures is found. To avoid orientation bias, the control shifts between plus and minus hits every 15 hits. The scoring scheme becomes redundant since only one match is allowed, and hence duplications cannot be identified with SFM option.
Medium speed option with SFM off and merger on is recommended.