hy Phuc Tran

Retrieve the sequence from the sequencing results and look for alignment to identify the starting point on the gene (flanks). You can then design the primers manually or you can use that sequence to look for auto primer pairs on primer blast, primer3, primer quest, mfe primers etc..

If they sequenced in both directions then you will see the reverse somplement of the forward primer at the end of the reverse sequence and vice versa, In sanger sequencing you do not see the f primer in the f sequence or the r primer in the r sequence because the measured sequence only starts about 30 bases in from the sequencing primer. Blasting you sequence will give you the amplimer sequence and you can add about 60 bases to that sequence and ise primer blast or primer 3 to design primers

You can contact them to ask. I assume your samples were PCR amplified before the Sanger sequencing. Typically, one of those primers will be used for the Sanger reaction.

Did you add on a common "universal" primer to your PCR primers? Some folks will add in M13 or T7 primer sequence so that all their reactions can be sequenced using those primers, regardless of the original template.

The company usually used a degenerate primer, it may be challenging to identify the specific primer they used. Extracting the start or stop region of the amplicons may only provide specific information, and not necessarily the full degenerate primer sequence. This can make it difficult to replicate the identification using the same primer, but it will work for your case.

For bacteria or fungi, the use of degenerate primers is common for amplification. Searching relevant research articles on PubMed may be a useful approach to identify appropriate degenerate primers for specific applications. This can provide information on previously published methods and primer sequences that have been successfully used in similar studies, allowing for greater reproducibility and comparability between experiments.

Thank you everyone