See below for largescale tab-out example. I did recently improve the untranslated nucleotide sensitivity substantially. Maybe this is being good enough for your purposes. I wonder if cows are more or less divergent than mice. Half of all mammalian are rodents, large effective population size, rapid speciation, lots of chr inversions and translocations, lab inbreeding weirdnesses.
Bovines are bad, like lab mice, as inbred.
I should really do this systematically on vertebrates, overlay average protein divergences from human on tree. Might give basis to software design goals. There is a lot of special purpose control of parameters already there. No need for Blat to reinvent the wheel. The per-search limit is built into the server as well as the cgi script.