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I would strongly recommend looking at the data by hand, aligning the sequences, and then counting substitutions before drawing conclusions from BLAST; if you get about the same number it does, you're on safe ground.

Thanks, I did that and the data are confirmed. Later, I noticed that when I submitted the query I had left the low complexity filter on. I then resubmitted the query with the filter off and got updated results. In general the sequence is the same with the corresponding change in the e-value(the sequences become more "significant"). I have also looked at fumarase and 40S ribosomal protein S4. These do not change much. The ribosomal protein shows that the chicken is closer to human than mammals outside of primates.(in terms of that protein)

Query = gi|16307477|gb|AAH10286.1|AAH10286 ribosomal protein S4, Y-linked [Homo sapiens] (263 letters)

I also ran the X-linked ribosomal protein. In that analysis the chicken is closer to human than the primates. Go figure.

Query = gi|12653405|gb|AAH00472.1|AAH00472 ribosomal protein S4, X-linked [Homo sapiens] (263 letters)

I have also looked at fumarase and 40S ribosomal protein S4. These do not change much. The ribosomal protein shows that the chicken is closer to human than mammals outside of primates.(in terms of that protein)

Well, I warned you about canned programs. The human protein has an extra N-terminal and C-terminal that most mammals lack (you can count each deletion as a single mutation, if you like), but if you focus on the common sequence, I get 4 differences between Sus scrofa (pig; go figure) and H. sapiens; and 12 between Gallus gallus and H. sapiens. Bos taurus is almost identical to S. scrofa (1 change)

My chicken is the chicken rps4 (P47836); human is the Y-linked rps4 (AAH10286) and the pig is BAA21081; pigs only have one sex-chromosome linked rps4. Cow is BAA21078.

I can post the aligned sequences on a web page., if anyone wants to see for himself.