I have a set of sequence files, where individual sequences look like this:
There is a primer sequence that has a few variable positions: TCCTSCGCTTATTGATATGC
However, this particular sequence has 26bp before the primer starts, that includes both an adaptor sequence and a barcode. In this case that sequence is: GACTACACGTAGTATATCTAGCGACT
So, the primer is always 20bp, but the leading adaptor and barcode can vary by 2bp in length, hence I can't just trim 46bp off the front. Is there a good way to handle this? Unforunately I dont have a file of adaptor and barcode sequences, just this information. It may be relevant that this is old 454 data.