mRNA polyadenylation is an essential mechanism in human genes and is direct linked to the termination of transcription. Alternative polyadenylation changes the length of the mature mRNA's 3′UTR. Since 3′UTRs have been shown to contain regulatory elements that control mRNA functioning, alternative polyadenylation plays an important role in controlling the expression of human genes. Prediction of polyadenylation sites can help with the identification of genes and aid our understanding of the mechanisms of alternative polyadenylation. In this study, we constructed a system for mRNA polyadenylation site prediction in human genes using SVM and based on an analysis of the sequence alignment between pair-end diTags (PET) and genome sequences. The PET sequences were mapped to the reference genome more accurate compared to earlier methods. We also analyzed single-site type and multiple-site type sequences PET sequence datasets and found that the frequencies of each nucleotide were different when the single-site type and multiple-site type PET sequences were compared.