State q emitting columns X[b, e] from b to e models the downstream signal Sige but excludes the upstream signal Sigb. For example, when q = Multiple Donor 1, q outputs columns between two donor sites, Sigb = MD1 and Sige = MD2. The exon interval is scored from b to e-Wdon - 1 inclusive and the donor columns are scored from e - Wdon to e inclusive. The upstream donor site window MD1 spans the interval b - Wdon - 1 to b - 1 and is scored in the previous state.