Filtering set of alignments based on exon length

Question

[iheartplants]

Hi All,

I have a series of multiple sequence alignments of putative LCNGs that I would like to filter based on exon length. Most of the sequences themselves are from transcriptome data so to infer exon/intron boundaries I included CDS data from a model organism in the group during clustering (intronic regions removed) After aligning the sequences, I added the reference CDS with intron data included (as Ns). What I would like to do now is select alignments that only contain exons above a certain length threshold. Ill be using these data to develop hyb-seq probes.

Any help will be greatly appreciated.