We must search for the complement of 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 5' of the search string which means that the position reported will that of the first base in the reading. We search for the -20 forward primer in M13MP18, shown as forwardP 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=forward ? String(s)='actggcc ? Name= ? select names (y/n) (y) = n 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 forward 'actggcc 6290 7249 7249
A search for the -20 forward primer in M13MP18.
So the absolute position is 6290 and the relative position is 6290-6249 = 41