Table 1.

HMM emission probability distribution of each feature given the state

State (s)	Description	Pr(d|s)a	Pr(c|s), Pr(a|s)a
S+	Site in an RBP-bound motif cluster initiating an input sequence	Pr(0) = 1	+
S−	Site in a background region initiating an input sequence	Pr(0) = 1	−
+	Succeeding site in an RBP-bound motif cluster	+	+
−	Succeeding site in background sequences	−	−
I+	Site initiating an internal RBP-bound motif cluster	−	+
I−	Site initiating an internal background region	−	−

^a‘+’ represents the distribution estimated from motif sites CLIP tag clusters (blue curves in Figure 1B); ‘−’ represents the distribution estimated from motif sites in background sequences (gray curves in Figure 1B).