Table 3.

Results of the similarity analyses between clustered miRNAs and other sequences.

Genome		T-COFFEE sequence alignment score				RNAdistance structure alignment score
Human	Category	Maximum	Average	Minimum	Std Dev	Maximum	Average	Minimum	Std Dev
	(i)	79	45.20	17	15.70	71	28.86	0	9.73
	(ii)	73	46.30	15	12.96	94	37.21	15	11.29
	(iii)	74	45.47	17	14.13	203	140.89	104	18.78
	(iv)	77	44.81	15	12.60	134	75.55	28	22.19
Mouse	(i)	79	43.63	0	14.40	72	30.41	0	9.33
	(ii)	78	45.28	16	13.03	69	35.19	10	9.67
	(iii)	75	43.72	16	14.40	239	139.93	103	17.31
	(iv)	72	45.37	15	13.33	128	69.55	26	19.31
Rat	(i)	75	44.28	17	12.83	113	31.41	11	12.60
	(ii)	72	45.18	16	13.12	116	35.68	13	11.73
	(iii)	69	45.03	16	12.48	198	143.12	110	18.43
	(iv)	73	47.90	15	13.26	114	74.69	32	18.74

Sequence and secondary structural alignments are performed for each clustered miRNA with sequences from the following categories: (i) clustered miRNAs, (ii) non-clustered miRNAs, (iii) random and (iv) neighboring sequences. A higher score implies a greater distance and hence a higher degree of dissimilarity. Std Dev, standard deviation.