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Table 1 Accuracy of alignment constraints: Fraction of total number of alignment positions missed in 619941 tRNA pairwise alignments and 180901 5S RNA pairwise alignment in RFAM database.

From: Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

   New constraint M constraint
Fraction of alignment positions missed tRNA 2.2 × 10-4 2.9 × 10-3
  5S RNA 2.0 × 10-4 4.4 × 10-3
  1. For the M constraint a value of M = 7 is chosen is chosen as established in [35]. New constraint refers to the probabilistic alignment constraint proposed in this paper.