Strategies to include:
1. Strategy with the longest upstream piece.
2. Strategy including as much coding sequence as possible (plus large upstream)
[Note that in all cases, the total size of upstream + coding should be no more than approx. 10 kb]
After those, try to create a set of strategies deleting progessively more upstream and/or coding sequence, in about 500 - 2000 bp increments, and with a minimum of about 500 - 1000 bp of upstream sequence.
| Strategy | 5' Site | Location | 3' Site | Location | Fragment size (bp) | Upstream (bp) | Comments |
| 1 | NsiI | 17637 | XhoI | 26402 | 8765 | 6412 | directional; cut vector with PstI, SalI |
| 2 | SalI | 17666 | XhoI | 26402 | 8736 | 6383 | non-directional; cut vector with SalI |
| 3 | HindIII | 19329 | XhoI | 26402 | 7073 | 4720 | directional; cut vector with HindIII, SalI |
| 4 | XbaI | 20470 | XbaI | 26820 | 6350 | 3579 | non-directional; cut vector with XbaI |
| 5 | PstI | 20789 | XbaI | 26820 | 6031 | 3260 | directional; cut vector with PstI, XbaI |
| 6 | PstI | 20789 | XhoI | 26402 | 5613 | 3260 | directional; cut vector with PstI, SalI |
| 7 | NgoMI | 21811 | NgoMI | 24113 | 2302 | 2238 | non-directional; cut vector with XmaI |
| 8 | BspEI | 21912 | BspEI | 24753 | 2841 | 2137 | non-directional; cut vector with XmaI |
| 9 | BspEI | 21912 | NgoMI | 24113 | 2201 | 2137 | non-directional; cut vector with XmaI |
| 10 | NheI | 22037 | XbaI | 26820 | 4783 | 2012 | non-directional; cut vector with XbaI |
| 10 | NheI | 22037 | BspEI | 24753 | 2716 | 2012 | directional; cut vector with XbaI, XmaI |
| 11 | NheI | 22037 | NgoMI | 24113 | 2076 | 2012 | directional; cut vector with XbaI, XmaI |
| 12 | SphI | 22902 | XbaI | 26820 | 3918 | 1147 | directional; cut vector with SphI, XbaI |
| 13 | SphI | 22902 | XhoI | 26402 | 3500 | 1147 | directional; cut vector with SphI, SalI |
| 14 | SphI | 22902 | BspEI | 24753 | 1851 | 1147 | directional; cut vector with SphI, XmaI |
| 15 | SphI | 22902 | NgoMI | 24113 | 1211 | 1147 | directional; cut vector with SphI, XmaI |
Correct Vector for preserving reading frame for 3' (in exon) sites:
| 3' Site | Vector |
| NgoMI | "Frame 1" |
| BspEI | "Frame 1" |
| XhoI | "Frame 2" |
| XbaI | "Frame 2" |