Homology Based Cloning can create the following outputs:
- Report A report containing the following sections:
- Summary Contains the number of fragments and primers used in the cloning reaction as well as their lengths and any warnings.
- Fragments Lists the vector and fragments used in the cloning reaction.
- Warnings Lists the warnings given for primer pairs.
- Primer pairs Lists fragments for which primers were designed together with pair annealing and pair end annealign values for the primer pairs. See Standard PCR output table for information about annealing values.
- Primers Lists individual primers and their sequence. Primer sequence is written with capital letters, whereas added bases and overhangs are in lowercase.
- Primer parts Lists full and subparts of designed primers with characteristics such as length and G/C content. The following terms are used:
- Full The full primer including overhang and added bases.
- Anneal The part of the primer annealing to the original fragment (primer without overhang or any added bases).
- Overhang The overhang added to primers to generate homologous sequence between fragments.
- Added The bases inserted between primer and overhang.
- Assembled vector The vector as it will appear after all fragments have been assembled. The assembled vector will be annotated with the positions of primers, added bases and overhangs as well as with inserts and vector sequence. When the vector is opened, you can select which annotations should be shown on the sequence in the side panel under Annotation types.
Note: the assembled vector can be used as input to Homology Based Cloning if you wish to adjust a previous design.
- Primers sequence list A sequence list containing the designed primers. The primers are annotated with primer, added bases and overhang, where primer is the part of the sequence that originally aligned to the insert or vector that was amplified.
- PCR fragments sequence list The PCR fragments generated from input sequences and designed primers including additional bases and overhangs.
- Primer pairs table A table providing information about melting temperatures, secondary structure, etc., for primer pairs with and without overhangs. For a description of each of the columns in the Primer Pairs table, see Standard PCR output table.