We must search for the primer sequence in the vector and find where its last base lies relative to the cloning site. Note that we define the cut site to be 3' of the search string which means that the position reported will that of the first base in the reading. We search for a reverse primer in M13MP18, shown as reverseP in the figure above. See section The positions of SmaI site and a forward and reverse primer for M13MP18.
Select operation X 1 Search 2 List enzyme file 3 Clear text 4 Clear graphics ? Selection (1-4) (1) = Select input source 1 All enzymes file X 2 Six cutter file 3 Four cutter file 4 Personal file 5 Keyboard ? Selection (1-5) (2) =5 Define search strings by typing a string name followed by the string(s) ? Name=reverse ? String(s)=gaccatg' ? Name= ? Search for all names (y/n) (y) = Select results display mode X 1 Order results enzyme by enzyme 2 Order results by position 3 Show only infrequent cutters 4 Show names above the sequence ? Selection (1-4) (1) = ? List matches (y/n) (y) = ? The sequence is circular (y/n) (y) = ? Search for definite matches (y/n) (y) = Working Matches found= 1 Name Sequence Position Fragment lengths 1 reverse gaccatg' 6225 7249 7249
A search for a reverse primer in M13MP18.
So the absolute position is 6225 and the relative position is 6225-6249 = -24.