Table 2.

Run time statistics of five methods over 100 random tRNA pairs, 100 random 5S rRNA pairs and 40 RNase P pairs

	tRNA			5S rRNA			RNase P
	Min	Max	Avg	Min	Max	Avg	Min	Max	Avg
PARTS	1	88	15	3	41	9.91	155	69707	8813.7
Dynalign	1	39	6.48	2	34	5.89	81	52278	6603.3
FOLDALIGN	1	5	1.81	2	15	5.22	221	26226	6800.6
Consan	27	911	187.98	130	1381	303.07	N/A	N/A	N/A
StemLoc	2	533	34.14	3	75	16.7	N/A	N/A	N/A
LocARNA	<0.5	<0.5	<0.5	<0.5	1	0.52	12	53	25.75

‘Min’ corresponds to minimum running time, ‘Max’ corresponds to maximum running time and ‘Avg’ corresponds to average running time in seconds.