What are pseudoknots?
is the pseduoknot the alignment of these base pairs


I'm not exactly sure what is meant by alignment, but if you mean base pairing from the flanking RNA to the loop of the hairpin you have depicted, then you would have an H-type pseudoknot.

Since you are interested in predicting these structures, it's important to note that a nucleic acid sequence capable of forming the necessary base-pairs for a pseudoknot structure does not imply that the sequence indeed forms a pseudoknot. It's likely that the sequence has a minimum free energy (MFE) structure that is not pseudoknotted. So the base-pairing capability is necessary but not sufficient for predicting these structures.

Take a look at the following (full-text) articles on pseudoknot prediction for additional information:


Computational Analysis of Noncoding RNAs
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model
A fast and robust iterative algorithm for prediction of RNA pseudoknotted secondary structures
KnotSeeker: Heuristic pseudoknot detection in long RNA sequences