The structure of plant mRNA polyadenylation signals, the order of the GHMM, and a flowchart of PASS. A. A working model based on . B. The order of GHMM. The arrowheads indicate the probability of changing of states (all probabilities were set to be 1). The rectangles represent regions with fixed length while the braces indicate regions with variable length. 3'-UTR, 3' untranslated region; CD, coding region; FUE, Far Upstream Element; NUE, Near Upstream Element; CE, cleavage element; CE-L, CE-R, Cleavage element left or right to the poly(A) site; CS, cleavage site, also known as poly(A) site; YA, represents TA or CA – predominant dinucleotides right before CS; B, beginning of the scan; Bg, background sequences between cis-elements; E, end of scan. Note that because YA is not found in all sequences, other dinucleotide combinations are also considered in GHMM. C. Flow chart of the PASS algorithm.