A colinear exon block between an EST and a reference genome. (A) A colinear exon block is found if there are two or more consecutive exon matches (i.e., one or more splice sites) within a gene and if the intron length between two consecutive exons is less than 1.5 Kb. (B) If the intron length between two consecutive exons is larger than 1.5 Kb, the alignment may be split into two smaller colinear exon blocks if possible. (C) A non-unique colinear exon block is found if the same region of an EST sequence has two or more colinear exon blocks found in different locations of the reference genome. The ESTs with non-unique colinear exon blocks are excluded from conserved primer design to avoid amplifying paralogous genes.