Table 1

Summary of parameters used in simulations of noncoding sequence evolution.

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]

Pollard et al. BMC Bioinformatics 2004 5:6   doi:10.1186/1471-2105-5-6