Performance of CapR. (A) Computational run-times for different values of maximal span W and sequence length N. The x-axis represents the sequence length N. The y-axis represents the computational run-time. (B) The receiver operating characteristic curve for each loop context. The x-axis represents 1-specificity and the y-axis represents the sensitivity. The specificity and sensitivity are defined as true positive/(true positive + false negative) and true negative/(true negative + false positive), respectively. (C) The structural profiles of tRNAs. The x-axis represents the nucleotide positions from 5′ to 3′. The y-axis represents averaged probabilities that each base belongs to each structural context across all tRNA genes in the Rfam dataset . The black boxes represent the nucleotides annotated as stem in Rfam. (D) tRNA cloverleaf structure annotated in Rfam. B, bulge loop; E, exterior loop; H, hairpin loop; I, internal loop; M, multibranch loop; S, stem.