Digest gel

The restriction digest's own plate as a canvas: every lane you set up, cut on the molecule you have open, migrated against a real ladder at the % agarose you would cast.

What it doesCopy Anchor Link

A restriction digest produces a list of fragment lengths, and a list of fragment lengths is not the result anyone acts on. The result is the gel — because what you will do next is run one, photograph it, and decide from the pattern whether the construct is what you think it is. Those are different questions: 4,361 bp cut by an enzyme into 2,100 / 1,400 / 861 is a fact; whether those three bands are separable on the gel you are about to cast is the one that decides the experiment.

This is that plate for the molecule you have open. Each lane you built in the digest panel — its enzymes, its name — is cut against the real sequence and drawn on one shared migration scale alongside the reference ladder, so a band is sized the way a band is really sized: against the marks beside it.

Picking a band selects its fragment, here and in the fragment table, so the band you are looking at and the row telling you its ends and its overhangs are the same object rather than two lists you match up by eye.

When you'd use thisCopy Anchor Link

• To check a diagnostic digest before you run it. An enzyme set that gives distinct-sounding numbers can still give co-migrating bands; the plate is where that shows up.
• Starting from a site you can see on the map. Right-click any cut site and open the restriction digest from it: the lane opens already loaded with that enzyme, cut against the molecule you have open, so the question "what would this site give me" takes one gesture rather than finding the enzyme again in a list of hundreds. It never disturbs lanes you have already set up: the enzyme takes an empty lane or a new one, and asking twice does not load it twice.
• To choose between two enzymes. Same molecule, a lane each, one scale — which is the comparison the numbers alone do not make.
• To read a gel you already ran. Set up the lanes you loaded and compare band positions against the same ladder your photograph used.
• When a fragment is missing from the photograph. A fragment can be too small to retain, too close to a neighbour to resolve, or absent because the enzyme did not cut; those look identical on a photograph and different here.

What this computesCopy Anchor Link

• The fragments of each lane, from cutting the open molecule with that lane's enzymes — circularity included, so a circular molecule cut once gives one linear fragment rather than none, and a site spanning the origin is a site.
• A migration distance per band, from an electrophoretic mobility model at the % agarose and the DNA form you set, so band positions move when the gel you described moves.
• Ladder-calibrated positioning — every band sits where the reference ladder's marks put it, not at a length printed beside it.
• The ends of every fragment — which enzyme cut each side and what overhang it left, which is what decides whether two fragments can be ligated.
• Co-migration, implicitly and then explicitly: bands that fall within the resolving window of the gel you described are flagged rather than drawn as two clean lines a real gel would not give you.
• Unresolved pairs on a real gel, on the status line: adjacent fragments in one lane closer than the smallest size difference QIAGEN's agarose guide states your percentage separates (more than 200 bp at 1.3% up to 2 kb, down to about 20 bp at 2.5–4.0% below 500 bp). At a percentage the guide does not name, above the fragment size its row is stated for, or on a ladder-calibrated gel, QIAGEN's general figure for standard agarose (about 20 bp, with no size dependence) is used, and the tooltip says which figure judged each pair. Field strength does not enter: neither the guide nor this simulation takes it.

What it does not doCopy Anchor Link

It is a prediction of migration, not of a photograph. It does not model loading amount, band intensity as a function of mass, smiling, overloading, partial digestion by default, or star activity. A lane whose enzyme does not cut is drawn uncut, which is a result — the absence of bands there is information, not an error.