| Group | Alignment | Sequence |
| Metazoa | metazoans.U3.stk | metazoans.U3.fa |
| Plants | plants.U3.stk | plants.U3.fa |
| Fungi | fungi.U3.stk | fungi.U3.fa |
| Other Eukayots | others.U3.stk | others.U3.fa |
| Questionable Candidates | add-ons.stk | add-ons.fa |
| Organism | Alignment | PSE | TATA |
| Anopheles gambiae | aga.all.100up.aln | Y | N |
| Apis mellifera | ame.all.100up.aln | Y | Y |
| Bombyx mori | bmo.all.100up.aln | Y | N |
| Drosophila melanogaster | dme.all.100up.aln | Y | weak YES |
| Caenorhabditis elegans | cel.all.100up.aln | Y | N (for all pol III) |
| Caenorhabditis japonica | cja.all.100up.aln | Y | N |
| Saccoglossus kowalevskii | sko.all.100up.aln | Y | Y |
| Arabidopsis thaliana | path.all.100up.aln | Y | Y |
| Oryzia sativa | posa.all.100up.aln | Y | Y |
| Chlamydomonas reinhardii | acre.all.100up.aln | N | N |
| Saccharomyces cerevisae | fsce.all.100up.aln | N | N |
| Schizosaccharomyces pombe | fspo.all.100up.aln | ? | Y |