multiple alligments using accession numbers

[lvcl]

Hello,

I am new to the field of bioinformatics so please excuse my stupid question

I need to design primers to identify strains within a species of bacteria. This bacteria is closely related to a group of other bacteria too. so in theory, I need to find seuqnces of a particular gene which is used to strain type the given bacteria, that are unique by comparing it with the seuqnces of the given gene in other strains of the same bacteria and also the closely related other species. Full sequences of the gene in the different strains (about 100 strains) are available. However, when it comes to the other related bacteria which are about 20 in number, complete genome is available for some and un annotated shot gun sequences of the whole genome is available for most (up to about 1000 varieties for some specicies). Theoretically I need to allign all of them. As donwloading the fasta files of nearly 2000 sequences is time consuming, I would like to know if there are any free software that would work with the accession numbers only. So that I can do a gene bank search for the given bacteria, select accession number as the display option, copy and pase to allign. Thanks in advance