F-type promoters

Unlike the A-type promoters, F-type promoters haven't been well organized into an evolutionary series. The following are various consensus F-type promoter sequences for use in detecting F-type promoters, and eventually in organizing the evolutionary history:

• FCON: This is the overall consensus of F-type promoters published by Adey et al., 1994. I resolved a few ambiguities. Basically this is a random collection of F-promoters detected by hybridization to a specific F-type probe. The degree of diversity of different types within the collection and the degree of bias against various types by the hybridization is not known, but no TF members were included. This could be taken as generic "old" F-type.

• YFCON: This is Adey et al.'s "young" consensus. It is only slightly different than the overall consensus. These were judged to be "young" because they were less divergent from each other than were the members of the overall collection on average. Note that the acceleration of base substitutions on active lineages makes this assumption hazzardous.

• FCONA: Among the representatives that Adey et al did not consider "young" this represents a subgroup that was clearly more internally similar than the overall collection.

• FCONB: Among the representatives that Adey et al. did not consider "young", this represents a subgroup that was clearly more internally similar than the overall collection.

• FCONC: Among the representatives that Adey et al. did not consider "young", this is a consensus of those that shared a large gap.

• F2406: An F-type promoter with a triplicated region near the 3' end that is found in AC2406a, and several M lineage L1's. This is the copy from AC2406a.

• AFcons: Consensus of mmPG14LH, A12, and 4 AF037352b F monomers.

• TF monomer 1: A consensus of TF family monomer 1 (closest to body) promoter sequences. The left half of the m1 TF monomer is essentiall indistinguishable from the other monomers, but the right half is quite distinctive.

• TF m2-m7 monomer: A consensus of TF promoter monomers other than m1.

• Alignment for F promoters (nexus format)

• Alignment of all TF promoter monomers (nexus format)

• Arrangement of Informative Positions in TF promoter arrays.