And this is, we have four characters in our alphabet.
So, I'm going to make this a five by five array.
So we'll have the mismatch of each character to each other character.
As well as the skips, the pounding for skipping each character.
So, the top left.
Four by four of this array will have the mismatches in each character against
each other character.
So A against A is a match, so we're not going to penalize that at all.
A mismatch of A to C would be a penalty of four.
A mismatch of A to G would be a penalty of two.
And a mismatch of A to T will be a penalty of four.
So, since A and G are both purines right?
>> Mm-hm.
>> Since those are both purines, they're more likely to have a mismatch
there than A against C or T, which are a different permadines is
a different type of nucleotide, a different, slightly different structure.
So we're penalizing the C and T more than G, right?
And then the last character in this row will just be if there, if an A is skipped,
so we're going to gives a penalty of E.