Since I do not have a reference genome, I run the blast between the treated and control of the single species. As a result of the blast, I was able to find the three transcripts that are the top hits for the single transcript in the query. As an example, transcript/1 in query matches transcript/2, transcript/3, and transcript/4 - For each of these transcripts, the identity percentage (%) is identical, the evalue is identical, and the score is identical as well. Can you please let me know which transcript is the best fit for transcript/1 in the query? Also, under what conditions this transcript is best suitable? The objective of this experiment is to run the differential expression.

In-advance Thank you fro your response.