In order for a read to qualify for assignment in ArrayStar, a threshold must first be met. This threshold is controlled via the Read Handling tab of the QSeq Advanced Options dialog . The default threshold for QSeq is that 20 bases or 50% of the read (whichever is greater) must match the target.
Since QSeq does not do alignment, and relies only on exact mer matches, the smallest exact sequence match that can be considered for read assignment is that of the length of a single mer. If a mer length of 25 is specified, then, by default, the minimum criteria for assignment consideration would be 25 bases.
Reads that are scored as ties during the read assignment phase have their assignment deferred until all the unique read assignments have been completed. A second pass is then made through all the assignment data and the repeated reads have their value divided proportionately amongst their targets, based upon the amount of unique signal value already assigned to their targets.