remove the cpDNA-containing scaffolds

Question

[AHP]

My reference contains 4000+ scaffolds of which several are cpDNA. Separately we obtained the cpDNA from Dr. Jarvis. Before I can add the cpDNA to the reference, I needed to remove the cpDNA-containing scaffolds. This was done by first blasting the reference with the scaffolds to the cpDNA sequence with ncbi's blast locally. I know that the E. value is the number of Blast hist so E-value for example 5.33e-105 or 0 (E.value< 1 e-179) indicates that two identical sequences and the query has found strong matches in the database probably not by chance. As I new to this topic can anyone help me what can be a good cut-off base on this results?

Thank you in advance and This is part of my results

pident    98.165
slen          151799
qlen        249999
length     218
mismatch     4
evalue    5.33E-105