An embedding and its relationships with the genome and a transcript. The x1,...,x9 are substrings shared by the genome and the transcript corresponding to pairings. Each common substring (pairing) is longer than a fixed threshold ℓ
. Intuitively, when the distance (measured on the genome) between two consecutive pairings is smaller than ℓ
then we assume that those pairings belong to the same exon. When the same distance is larger than ℓ
then those pairings belong to different exons.