Table 1. New reference sets in BAliBASE version 2.0.

A
	Alignment name	No. of sequences	Total no. of repeats	Max. repeats per sequence	Mean repeat length
Reference 6, repeats	SH3	111	174	5	55
	ZF	29	260	36	25
	APO	46	419	14	22
	SUSHI	45	385	37	55
	MYB	141	284	3	50
	ANK	30	214	24	30
	KRINGLE	35	187	38	100
	DEAD	22	31	2	230
	TRK	33	45	2	84
	FAA	37	39	2	200
	LRR	24	339	41	24
	ION_TM	49	153	4	250
Total		602	2316
B
	AlignmentName	No. of sequences	No. of transmembrane helices per sequence
Reference 7, transmembrane	ION	52	6
	ACR	43	12
	DTD	56	12
	PTGA	51	12
	NaT	59	14
	PHOTO	33	7
	MSL	13	2
	7TM	128	7
Total		422
C
	Alignment Name	No. of sequences
Reference 8, circular permutations	PTGA	20
	LECTIN	31
	GSH	18
	SH3/SH2	44
	CELLULASE	5
Total		118