Seems command line BLASTn is segmenting some of my hits in two HSPs due to this filter, but homology is 100% for both HSPs and they overlap. Have a look at this one:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovs qcovhsp
gi|1006752541|gb|LKUW01000052.1|:59772-65114 Scaffold_1 100.00 3428 0 0 1 3428 1245417 1241990 0.0 6331 100 64
gi|1006752541|gb|LKUW01000052.1|:59772-65114 Scaffold_1 100.00 1992 0 0 3352 5343 1241789 1239798 0.0 3679 100 37
Thanks
Thanks for the command @a.zielezinski. Unfortunately still giving me some segmented hits, as well as some unspecific hits. Anyway, I will have to look manually at this ones.