<p>I have a 20 nucleotide pattern. Now I want to find ALL of its occurences in a fasta file with about 200 sequences.</p>

<p>Then I want to ouput the positions either to a gff or into a sam file to be able to load into IGV. What is the most efficient way to do that?</p>

<p>It can have about 1-2 indels and about 2-4 SNPs. It is just important to find where the approximate pattern occurs often...</p>

<p>How about good old blat or gmap?</p>
