Enter a comma separated list of nucleotide sequences that should be excluded from the final output (e.g. Restriction Sites). Each exclusion sequence within the list should contain at least 4 unambiguous bases (ACGTU). Exclusion sequences may also contain ambiguous bases Y,R,W,S,K,M,D,V,H,B,N.
Note that sequences entered here will only be excluded on the forward strand and not the complementary strand, unless the sequence is palindromic (forward and complement are the same). E.g. if you enter ATGATG, the algorithm will not automatically exclude the complementary sequence CATCAT. In order to exclude both ATGATG and CATCAT, enter each one seperately. You can select common Restriction Enzyme Sites and Translation Initiation sites (e.g. Kozak), from the menu below. Clicking on a site name, will add its sequence to the textbox.
Note: You may choose to remove sequence as either a constraint or a parameter. When selected as a constraint, the algorithm will prioritize satisfying the selected option over any other non-constraint design criteria.
Warning: a sequence with too few unambiguous bases (ACGTU) will result in too many matches and thus will reduce the codon optimization algorithm's effectiveness.
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