Using PrimerPro, you should get an output file called "[name] .fasta.results.csv".  This result file contains the orignal misa output as up to 3 of the best primer pairs found by Primer3 along with their properties.

So this file should contain the 3 best primer pairs found. The first pair should also be the best pair. Which file are you looking at and how many primers are there?

Nicholas Wagner,

thanks for the answer but i have more then 5000 primers i reduced on the basis of GC and tep but i want to reduce them up to 100.