I'm having some problems with running TBLASTN locally that I was hoping someone here might have some ideas on what to do with.
I have a smallish fungal genome, and in that genome I have an open reading frame in a single exon forming a contigous 405 bp nucleotide sequence from start codon to stop codon. If I take this 405 bp nucleotide sequence and use blastn on the genome, I find the complete sequence. But if I convert the nucleotide sequence into an 134 amino acids long protein sequence (excluding the stop codon) and use tblastn on the same genome, the hit I get is only 113 amino acids long. I've tried several versions of BLAST from 2.2.31 to 2.7.1, and I've tweaked a number of parameters, for instance window_size, threshold and word_size, but nothing helps and I always get the same 113aa sequence.
Does anyone have any idea on what could cause this, and if is there anything I could try to improve the tblastn results? Alternatively, is there some other piece of software that I can try instead?