. 2009 May 27;25(12):i365–i373. doi: 10.1093/bioinformatics/btp212

Table 3.

Experimental and predicted melting temperatures for the set of RNA pairs reported in Mathews and Turner (2002)

Pairs	Experiment		piRNA		RNAcofold		UNAFold
	T_l	T_c
G-GC-G/C-C	45.4	46	56.81		37		21.4
G-GC-G/CaC	51.8	52.2	56.84		37		27.15
G-GC-G/Ca₂C	55.9	56	56.86		37		27.12
G-GC-G/Ca₃C	58.4	57.3	56.85		37		25.73
G-GC-G/CauaC	57.3	56.9	56.84		37		24.35
G-GC-G/Ca₄C	56.7	57.1	56.85		37		25.06
GaGC-G/C-C	51.2	49.3	56.94		37.1		21.25
GaGC-G/CaC	55.2	54.7	56.96		41		21.44
GaGC-G/Ca₂C	56.1	55.6	56.98		41		21.46
GaGC-G/Ca₃C	56.1	54.9	56.97		41		21.44
GaGC-G/CauaC	54.8	54.3	56.98		37.06		21.47
GaGC-G/Ca₄C	55.3	54.8	56.98		37		21.39
Ga₂GC-G/C-C	55.1	52.9	57		50.17		36.04
Ga₂GC-G/CaC	57	56.4	57.03		48.01		36.8
Ga₂GC-G/Ca₂C	55.6	55.4	57.05		41.84		36.91
Ga₂GC-G/Ca₃C	55	54.7	57.03		41.84		36.19
Ga₂GC-G/CauaC	55.3	54.5	57.3		52.17		36.74
Ga₂GC-G/Ca₄C	54.1	53.9	57.05		48.01		34.22
Ga₂GCaG/C-C	56.6	56.6	57.18		47.01		36.01
Ga₂GCaG/CaC	58.7	58.9	57.18		44.1		36.81
Ga₂GCaG/Ca₂C	58	58.8	57.2		44.1		36.13
Ga₂GCaG/Ca₃C	56.5	57.5	57.15		44.1		36.96
Ga₂GCaG/CauaC	57.2	56.9	57.48		43		35.92
Ga₂GCaG/Ca₄C	57.9	57.9	57.17		44.1		34.66
Ga₂GCa₂G/C-C	56	56.9	57.19		37.17		36.14
Ga₂GCa₂G/CaC	58.7	59.1	57.2		44.1		36.94
Ga₂GCa₂G/Ca₂C	59.7	59.6	57.19		44.1		36.22
Ga₂GCa₂G/Ca₃C	58.6	58.7	57.16		44.1		35.89
Ga₂GCa₂G/CauaC	57	57.3	57.74		37		35.03
Ga₂GCa₂G/Ca₄C	57.5	58.1	57.18		44.1		34.93
G-UA-G/C-C	50.4	50.8	56.82		46.26		21.53
G-UA-G/CaC	54.3	55.8	57.88		61.42		34.47
G-UA-G/Ca₂C	56.6	57.8	57.89		61.42		41.68
G-UA-G/Ca₃C	57.6	58.5	57.88		61.42		40.84
G-UA-G/CauaC	57.9	58.7	57.87		61.41		40.96
G-UA-G/Ca₄C	58.6	58.5	57.88		61.43		40.64
GaUA-G/C-C	51.6	51.8	56.96		49.18		21.42
GaUA-G/CaC	55.6	55.7	57.01		37.07		30.98
GaUA-G/Ca₂C	56.7	57.4	57.04		50.31		31.46
GaUA-G/Ca₃C	56.8	56.9	57		44.17		29.91
GaUA-G/CauaC	57	57.1	56.99		37.07		29.98
GaUA-G/Ca₄C	56.8	56.8	57.01		50.31		29.29
G-CG-GC-G/C-C	64.8	65.2	57.24		37		21.38
G-CG-GC-G/CaC	58.8	60.4	57.22		37		21.44
G-CG-GC-G/Ca₂C	55.6	56.4	57.35		37		21.38
G-CG-GC-G/Ca₃C	55.4	55.3	57.32		37		21.56
G-CG-GC-G/Ca₄C	53.9	53	57.19		37		21.38
GaCG-GC-G/C-C	57.3	58.7	57.2		37		21.71
GaCG-GC-G/CaC	59.7	61.2	57.21		37		21.76
GaCG-GC-G/Ca₂C	55.4	57.2	57.19		37		21.45
GaCG-GC-G/Ca₃C	55.2	56.5	57.11		37		21.42
GaCG-GC-G/CauaC	55.2	55.8	57.09		37		21.38
GaCG-GC-G/Ca₄C	55	55.3	57.14		37		21.47
GaCG-GCaG/C-C	58.1	58.8	56.9		37		21.54
GaCG-GCaG/CaC	59.3	59.7	56.99		37		21.76
GaCG-GCaG/Ca₂C	57.5	59.4	56.89		37		63.08
GaCG-GCaG/Ca₃C	57.9	58.2	56.95		37		21.44
GaCG-GCaG/CauaC	58.9	58.3	56.93		37		21.53
GaCG-GCaG/Ca₄C	57.3	58.1	56.84		37		21.46
Ga₂CGa₂GCa₂G/C-C	54.4	55.5	57.12		47.17		67.28
Ga₂CGa₂GCa₂G/CaC	55	56.6	57.04		44.01		67.23
Ga₂CGa₂GCa₂G/Ca₂C	55.3	57.2	57.12		51.31		66.09

		T_l	T_l	T_c	T_l	T_c	T_l	T_c
Avg. difference		0.7	1.87	1.95	14.27	14.41	26.5	26.56
Spearman rank corr.		0.92	0.25	0.35	−0.04	−0.04	0.2	0.28

Each pair is referred to by an identifier. Please refer to our Supplementary Material or Mathews and Turner (2002) to see the exact sequences of each pair. All values, except Spearman's rank correlation, are in degree centigrade. Bold entries are the most accurate predictions. In other words, they have the least difference from experimental measurements.