Table 1.

Control sets used as a basis for comparison with the results obtained from our algorithm

	S1 Braich et al. (20)	S2 Brenner et al. (21)	S3 Faulhammer et al. (22)	S4 Frutos et al. (23)	S5 Penchovsky and Ackermann (16)	S6 Random	S7 Shortreed et al. 1(6)	S8 Shortreed et al. 2(6)
Control set: original constraints
Word length	15	4	15	8	16	16	12	16
No. of words	40	8	20	108	24	24	64	64
C1	✓	✓	✓	✓
	≥4 mismatches	≥3 mismatches	maximize mismatches	≥4 mismatches
C2	✓			✓
	≥4 mismatches			≥4 mismatches
C3	✓
	≤7 matches
C4			✓
			≤7 matches
C5	✓	✓
	35.33%	25.00%
C6	✓				✓		✓	✓
							CCC	CCC
	5H				CCC (5′,3′ ends)		CC (5′,3′ ends)	CC (5′,3′ ends)
C7	✓	✓	✓		✓	✓	✓	✓
	A,C,T	A,C,T	A,C,T		A,C,T	A,C,T	A,C,T	A,C,T
T1					✓
					Implicit		✓	✓
T2					✓		✓	✓
T3				min value: −6.46 ≥ −8.24	min value: −2.62 ≥ −2.79	min value: −4.50 ≥ −5.48	✓	✓
					Implicit	max value: −0.07 ≥ 0.00
T5			✓		✓		✓	✓
			average = 45°C		range of ±1.5°C		1°C range	1°C range
Control sets: extrapolated constraints
T1 range (kcal/mol) $[\Delta G_{min1}^0,\Delta G_{max1}^0]$	[−16.80, −13.57]	[−1.96, −1.01]	[−17.56, −11.63]	[−8.95, −6.50]	[−17.94, −16.84]	[−19.31, −12.74]	[−12.66, −11.78]	[−16.42, −15.45]
T2 range (kcal/mol) $[\Delta G_{min2}^0,\Delta G_{max2}^0]$	[−9.29, −0.22]	[−1.86, 0.00]	[−7.98, −1.29]	[−6.83, 0.00]	[−8.72, −2.26]	[−8.35, −0.86]	[−8.94, −0.93]	[−7.62, −1.10]
T3 range (kcal/mol) $[\Delta G_{min3}^0,\Delta G_{max3}^0]$	[−4.48, 0.00]	[−0.64, 0.00]	[−5.02, 0.00]	[−8.24, 0.00]	[−2.79, 0.00]	[−5.48, −0.00]	[−5.06, 0.00]	[−9.06, 0.00]
T5 range (°C) $[{\text{TM}}_{min5},{\text{TM}}_{max5}]$	[46.64, 55.75]	[−67.19, −48.07]	[40.87, 58.20]	[17.06, 27.34]	[55.15, 58.65]	[43.56, 62.23]	[42.38, 43.50]	[51.81, 52.77]

Each column of the table, other than the leftmost, corresponds to one set. Each column header gives a set ID and, for all but set S6, a reference to the paper in which the set was published. The next two rows report the strand length and the number of strands in each set. Following these, there is one row per type of combinatorial or thermodynamic constraint C1 to T5 (except for T4—see Materials and Methods for details). A check mark in a column indicates that a constraint of the column's type was enforced when designing the set, and further information about the composition of the strands is given where available. The second part of the table describes thermodynamic properties of control sets. For each set, the rows of the table give the free energy ranges corresponding to constraints T1 (desired word–complement interactions), T2 (undesired word–complement interactions) and T3 (undesired complement–complement interactions), respectively and the melting temperature range corresponding to constraint T5. Note that these thermodynamic constraints were not used as design constraints for the control sets, other than those of the accompanying paper of Shortreed et al. (6).