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Identify conserved regions in SARS-COV2 virus based on Multiple sequence alignment for primer design

As a part of my project, i am supposed to download sequences from (GISAID) that are representative of the 3 waves inside Africa and perform multiple sequence alignment, based on which i should find the conserved region to use as a target for primer design. I am wondering if there is a certain tool or script that would do so? and what parameters can i set for choosing the most accurate conserved region in terms of length and position, gaps etc

alignment msa conserved primer design sequence multiple region
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written by Mohamed Elsherbieny • Mohamed Elsherbieny

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I gave them a quick read, couldn't find any mention of tools or scripts used to identify and extract conserved region from multiple sequence alignment file

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written by Mohamed Elsherbieny • Mohamed Elsherbieny

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