Skip to main content

Table 1 Summary of parameters used in simulations of noncoding sequence evolution.

From: Benchmarking tools for the alignment of functional noncoding DNA

Parameter Value Source Refs.
Sequence length 10 Kb D. mel this work (Fig. 1)
AT : GC 60 : 40 Drosophila spp. this work, [31, 55]
Transition / Transversion Bias 2 Drosophila spp. [25, 56]
Substitution model HKY85 - [54]
Point substitutions : Indels 10 : 1 Drosophila spp. [22, 23, 25]
Indel spectrum - D. mel [57]
Median constrained block length 18 bp D. mel vs. D. vir [25]
Mean density of constrained blocks 0.2 D. mel vs. D. vir [25]