Please debug this code for me

I'm trying to make a program based on this tutorial:

http://www.mathworks.com/help/bioinfo/examples/using-scoring-matrices-to-measure-evolutionary-distance.html

plz use AAA69808, NP_989750 as input, as it's shown in the example, plz fix the code to achieve same results in the example

plz feel free to adjust and tweak as u wish, the output needs to be posted to new lines instead of being next to each other, the dots need to appear slowly corresponding to the time it takes, i want the program to continue running for more input after the first run...etc

[Geoff Hayes]

Ahmad - what is preventing you from debugging the code? If you are observing a particular error, then copy and paste the full error message to your question and hopefully someone will be able to offer guidance and help you resolve the issue.