Hello,

I want to set parameters for Blastn (reward / penalty- gap / gapextend). I read on the blast site:

It is important to choose reward/penalty values appropriate to the sequences being aligned with the (absolute) reward/penalty ratio increasing for more divergent sequences. A ratio of 0.33 (1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5 (1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1) is best for sequences that are 75% conserved

I want to know what that means "99% conserved" and "95% conserved" and "75% conserved"? And if reward>penalty, how can one say of these sequences?

Because in the table there are:

r/p     gap/gapext
3/-2    5/5
5/-4    10/6, 8/6

Thank you for your help.