Table 2. Statistics of phylogenetic analysis from different alignments.

Statistic	Sequence alignment 1 (guiding without structure)	Sequence alignment 2 (guiding with structure)	Secondary structure	Sequence 2+structure
Aligned length	321	314	315	629
Indel character	37	140	0	140
Total length	358	454	315	769
No. of variable characters	262	325	234	559
No. of parsimony information character	207	222	134	355
No. of shortest trees	128	8	90	61
Tree length	474	536	403	941
CI	0.8143	0.8190	0.8362	0.8236
RI	0.9364	0.9222	0.9241	0.9241