Editing Probabilistic context-free grammar (section)

===== Estimate column probabilities for paired and unpaired bases =====
In a structural alignment the probabilities of the unpaired bases columns and the paired bases columns are independent of other columns. By counting bases in single base positions and paired positions one obtains the frequencies of  bases in loops and stems.
For basepair {{mvar|X}} and {{mvar|Y}} an occurrence of <math>XY</math> is also counted as an occurrence of <math>YX</math>. Identical basepairs such as <math>XX</math> are counted twice.