. For

I = TTGGAATACCATC and J = GGCATAATGCACCCC, make dot

matrices for the k-tuple hits for k = 1, 2, and 3.

. The

E. coli F plasmid transfer

origin region contains the sequence

I:

5_-ATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTT

AAAAAAGCG-3_

The TraY protein has been shown to

bind to a region some 1600 bp away at

a site that contains the sequence

J:

5_-TAACACCTCCCGCTGTTTAT-3_

Perform dot-matrix analyses for k

= 1 and k = 2 to locate in I a subsequence

that is similar to J. This

identifies a potential binding site for TraY in sequence

I. [Hint: Use R to construct a

matrix having dimensions determined

by the lengths of J and I,

initialize elements to zero, and then substitute the

appropriate elements with the

number 1 to indicate matches. Produce two

matrices: one for k = 1 and

another for k = 2.]