Table 2. Results of redundancy analysis of the 6,918 DArT marker probe sequences under four different sets of assembly parameters from the most stringent (A1) to the most relaxed (A4) (see Material and Methods for details).

Parameter	A1	A2	A3	A4
Word length	18	14	12	10
Index Word length	13	12	11	10
Mismatches	10%	15%	20%	20%
Ambiguities per read	4	4	16	16
Maximum % gaps per read	10%	15%	20%	20%
Gap size	1bp	2bp	5bp	5bp
Results of redundancy analysis
# Unmatched singletona	3,209	2,607	2,381	2,276
# Redundant sequencesb	3,709	4,311	4,537	4,642
# Unique non-redundantsequencesc	1,374	1,537	1,587	1,588
Total selected sequencesd	4,583	4,144	3,968	3,864
Estimated rate of sequenceredundancy	33.75%	40.0%	42.64%	44.14%

^aUnique sequences not matching any of the other reads.

^bSequences that fall into multi-sequence clusters with more than two sequences per cluster.

^cUnique sequences drawn from the redundant clusters.

^dSum of unmatched singleton and non-redundant sequences.