Pairwise - Two Sequence Alignment Tool

Instructions: Paste two sequences into each of the sequence editors at the top of this applet. Use the pulldown to switch editors. Each sequence can be reverse-complemented with the R/C button, limits of alignment can be set using the from/to fields.

Please note that there is no feedback during the alignment process, long sequences may take quite a bit of time.

HINT: Use the "Linear" instead of "Square" memory model to get an idea of the region of best fit, then use the limit box to start the alignment prior the reported end. Put another way, the linear memory model gives you the end of best alignment. Keep adjusting the "from" setting toward the beginning of your sequences until the alignment drops off.