Specifies the gap-open score of affine gap as negative real value.

Specifies the gap-extend score of affine gap as negative real value less than or equal to gap-open penalty.

Enables to insert any base pairs which are not in the folded sequence.
(It is not recommendable, because the scores for inserting base pairs are not defined.)

Proposed by Gorodkin [1] or by Klein [2] is available.

[1] J. Gorodkin, L. J. Heyer, and G. D. Storomo. Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Research, 25 (18) : 3724--3732, Sept. 1997.

[2] R. J. Klein and S. R. Eddy. RSEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics, 4 (1) : 44, Sept. 2003.