Figure 5 shows the model used in performance evaluation. States are included to model splicing patterns in exons at the beginning and end of genes and to account for the three possible reading frames and to allow for the entire sequence to be a coding exon or intron. For example, "Alternative Exon Only" is the signal pair (Beg,END-EXONA) and emits a contiguous coding sequence with no splice sites. Some candidate alternative splicing events are excluded from Figure 5. For example, the interval between the two splice site signals MDN-IR and MA1-IR represents a retained intron between an upstream exon with multiple functional donor sites and a downstream exon with multiple functional acceptor sites. While such an alternative splicing pattern might occur (at least in theory), no examples were found in the training of ExAlt, thus, there is 0 probability of entering the state. There were 15 cases of "rare" alternative splicing types: 8 exons contained more than 2 donor or acceptor sites, 6 exons classified as intron retention cases contained multiple splice sites in one of the exon forms and 1 exon contained both multiple acceptor sites and multiple donor sites. Each exon form was included in the performance analysis. [47] gives a more complete survey of complex alternative splicing patterns.