Table 1. Relative orientation of two motif occurrences within a dimer.

Orientation o	Short-hand		o 1	o 2
Head-to-Tail	HT	→ →	+1	+1
Head-to-Head	HH	→ ←	+1	−1
Tail-to-Tail	TT	← →	−1	+1
Tail-to-Head	TH	← ←	−1	−1

Exponents o₁ and o₂ give the orientation of the first and the second PPM: for a PPM θ_k, leaves the matrix intact but takes the reverse complement.