By "Alanine repeat", I am referring to the suppression of the formation of extra insect legs due to Ubx gene suppression through Distal-less repression.
The new work involved misexpression of the Drosophila Ubx protein in the presumptive thorax of transgenic fruitfly embryos. Limb development was suppressed because of repression of Dll. By contrast, the misexpression of onychophoran and crustacean Ubx proteins did not interfere with Dll expression and the formation of thoracic limbs. These results raised the possibility that the Drosophila Ubx protein is functionally distinct from Ubx in onychophorans and crustaceans. One study suggests that Drosophila Ubx has acquired an alanine-rich peptide that mediates the repression of gene transcription; this peptide is lacking in onychophorans. The other study provides evidence that the crustacean Ubx contains an additional peptide that modulates the activity of the alanine-rich peptide, and possibly other repression domains, in crustacean Ubx.
Insect-restricted sequences include four regions N-terminal to the homeodomain (I1–I4), a peptide motif (QAQAQK), and an extended run of alanine residues C-terminal to the homeodomain
The onychophoran Ubx protein might function as an activator of appendage development. When the onychophorans and arthropods diverged, Ubx acquired an alanine-rich repression domain near its carboxy terminus. This domain mediates constitutive repression in insects. But in crustaceans the addition of the regulatory peptide causes it to function in a conditional fashion. As a result, Ubx does not suppress limb development in crustaceans. But it eliminates abdominal limbs in insects, greatly reducing the overall number of appendages compared with crustaceans.
You can read about it here:
Levine, Mike. "Evolutionary biology: how insects lose their limbs." Nature 415.6874 (2002): 848-849.
Galant, Ron, and Sean B. Carroll. "Evolution of a transcriptional repression domain in an insect Hox protein." Nature 415.6874 (2002): 910-913.