I am using the freeware STRAP.bat for aligning proteins and I want to export the alignment to a PDF. I had problems getting the sequence to fit on the page correctly, so I updated the software. Now when I export the alignment, the proteins are aligned from the very beginning; all the proteins align at the first amino acid, which is not correct and is not seen in the alignment in the program before exporting. Does anyone have any tips on how to correct this?