Detect 3' end of SSU

[brendanf]

This would be helpful for studies using primers that include enough SSU to be useful.

[brendanf]

To detect SSU: There is not a lot of conserved short-range secondary structure at the 3' end of SSU. Either use a CM including all of V10 and the helix it sits on, or HMMs (the same ones used in ITSx?).