Q1: You have the following alignment:
S1 ttgatatcataacgttcagc-ct
S2 ttcatatcat-accttcagcact
The alignment parameters were: Match = 5 pts, Mismatch = -4 points, Gap Penalty is -16 to open and -4 to extend by 1 residue. What is the raw alignment score based on these values?
Q2: Repeat the calculations for these two alignments:
S1 ttgatatcataacgttcagc-ct
S3 ttgata-cataacgt-cagcact
S2 ttcatatcat-accttcagcact
S3 ttgata-cataacgt-cagcact
Q3: What is the sum of the three alignment scores? NOTE: this is actually the Sum of Pairs score for the alignment containing S1, S2, and S3!
Q4: What is the probability of rolling a 19 on a 20-sided die? What is the probability of rolling a second 19 using the same 20-sided die? Compare that to the probability of simultaneously rolling two 20-sided dice and rolling 19 on both of them.
Q5: What is the probability of finding the sequence “AAAAAAAAAA” by random in a stretch of DNA?
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