Template - the template sequence is the nucleotide sequence you want to view. Four formats are accepted:

• GenBank - the format used in the NIH (National Institutes of Health) sequence database. View sample.
• EMBL - the format used in the EMBL (European Molecular Biology Laboratory) sequence database. View sample.
• FASTA - consists of a single line description followed by sequence data. The description line is marked by the > symbol, and the description is followed by a carriage return. View sample.
• Raw - consists only of sequence information. Non-IUPAC codes are automatically removed. View sample.

Primers - the primer sequences are compared to the template sequence and potential annealing sites are marked. Primer sequences are entered as follows: the sequence of the primer is entered first, followed by a blank space, and then the name of the primer. Primer entries are separated by a comma. Degenerate IUPAC codes can be included in the primer sequence. "I" for inosine is treated the same as "N".

Genetic code - the genetic code used when translations are calculated for FASTA or raw entries.

Restriction set - the set of restriction patterns searched for in the template sequence.

Translate reading frame - the reading frames to be translated for FASTA or raw entries.

• one - show the translation for reading frame one.
• two -show the translation for reading frame two.
• three - show the translation for reading frame three.
• one to three - show the translation for reading frames one, two, and three.
• all six - show the translations for all six reading frames.
• uppercase one - treat uppercase text as a continuous reading frame, and start the translation in reading frame one.
• uppercase two - treat uppercase text as a continuous reading frame, and start the translation in reading frame two.
• uppercase three - treat uppercase text as a continuous reading frame, and start the translation in reading frame three.

Topology - the topology of the sequence (linear or circular). The distinction alters how restriction patterns and primer sites are found. With linear sequences, the search is performed using the sequence as entered. For circular sequences, the end and beginning of the sequence are joined so that patterns spanning the ends of the entered sequence can be detected.

Allow primers to have mismatched:

• 5' tails - detect primer sites in which the 5' tail of the primer contains bases that do not perfectly anneal with the template.
• 3' tails - detect primer sites in which the 3' tail of the primer contains bases that do not perfectly anneal with the template.

Matching bases required when mismatching bases allowed - when mismatching 5' tails or 3' tails are allowed, this option sets the minimum number of annealing bases required for a primer site to be detected.

Bases per line - the number of bases of template sequence shown per line in the returned figure.

Show - use these options to adjust the appearence of the sequence portion of the figure:

• Reverse strand - display the reverse strand of the template sequence.
• Number line - display a line indicating base number below the template sequence.
• Spacer line - display a line of dashes between each line of template sequence.

Return - use these options to adjust what extra information is returned with the sequence figure.

• Restriction summary - display a summary of restriction patterns searched for, and the positions of restriction sites when found.
• Primer summary - display a summary of primer patterns searched for, and the positions of primer sites when found.
• Help information - display a brief description of how to interpret and use the returned figure.
• Coding sequence links - display a group of links for viewing the coding sequences of the template in a separate window.
• Translation links - display a group of links for viewing the protein translations of the template sequence in a separate window.
• Options selected - display a summary of the options selected.