[BiO BB] Inconsistent Blast Results

[Rebekah Rogers]

Hi:

I'm currently running blast 2.2.14 locally on my mac.  I've noticed
that the printout from a blastn run at an E cutoff of 10^-10 reads
differently than a blast run at an E cutoff of 10^-7 when hits worse
than 10^-10 are ignored.   Suddenly at 10^-7 new hits with evals of
10^-11 appear that weren't there before and even the relative strength
of different hits can change.

I'm not certain I understand why this is true and it has a huge impact
on my results.  I know that the Eval is dependent on certain constants
taken from the compared sequences, but I don't understand how this
could possibly change when I'm using the exact same input file and
database.

Does anyone have an explanation?

-Rebekah