Table 1. The 14 substitution types that best explain rate differences in untranscribed sequences across clades.

Type	Substitutions
1	CTT→C
2	TTY→C, GTT→C
3	TTR→C, STM→C, ATY→C
4	ATA→C, VTG→C
5	TTD→A, CTA→A, ATN→A
6	TTC→A, CTB→A, GTN→A
7	TTH→G, GTC→G
8	TTG→G, MTN→G, GTD→G
9	ACA→T
10	BCH→T, ACY→T
11	NCG→T
12	NCN→A
13	TCH→G, CCY→G, GCW→G
14	TCG→G, CCR→G, ACN→G, GCS→G

Each substitution type consists of a set of context-dependent substitutions (M = A or C; R = A or G; W = A or T; S = C or G; Y = C or T; V = A, C, or G; H = A, C, or T; D = A, G, or T; B = C, G, or T; and N = A, C, G, or T). For untranscribed regions, each type is also assumed to include the complementary substitutions to those listed, whereas for transcribed regions, the complementary substitutions are considered a separate type (resulting in a total of 28 types in transcribed regions). Although the overall division into substitution types has strong statistical support, support for this particular partitioning over other similar ones is relatively weak in some cases, so the assignment of particular contexts to types may be somewhat arbitrary. See Supporting Text for analysis method.