“…Even allowing up to a 3-bp degeneracy in the established 13-bp TRA-F consensus binding site, we found only two overlapping candidate sites in S. cynipsea tra, neither of which seemed likely to be functional: gaATCAATCAACA and TCAA CAATCgcCA (degenerate sites lower case and overlap underlined). TRA-F from D. melanogaster had been shown to not utilize the first sequence (Inoue et al 1992), and the second sequence lacks the TCAAxx 39 sequence common to every predicted TRA-F binding site for tra, dsx, and fru orthologs all the way to mosquitos (Pane et al 2002;Scali et al 2005;Lagos et al 2007). Moreover, we sequenced a 722-bp fragment of tra from the sister species S. neocynipsea (EU636098) centered on homology to the S. cynipsea degenerate TRA-F sites and found that neither site was conserved, despite 85% overall sequence identity for the two corresponding regions.…”