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pBluescript II SK(+) digested with Sau96I
Sau96I recognises GGNCC and cuts circular pBluescript II SK(+) (GenBank X52328.1, 2,961 bp) at 8 sites, so a complete digest gives 8 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
289
219
507
2
152
508
659
3
1
660
660
4
1,428
661
2,088
5
79
2,089
2,167
6
17
2,168
2,184
7
222
2,185
2,406
8
773
2,407
218
The fragments add up to 2,961 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Cuts after base (top strand)
1
218
218
2
507
507
3
659
659
4
660
660
5
2,088
2,088
6
2,167
2,167
7
2,184
2,184
8
2,406
2,406
Positions are in the numbering of GenBank X52328.1. A cut after base n leaves base n at the end of one fragment and the next base at the start of the next. A fragment that runs past the record's last base continues from its first. A vendor's map, or your own stock, may differ from this record.
The same question is open below in Drybench Plasmid. Change the enzymes, the host's methylation or the vector there; nothing you do here is saved unless you save it.
Reference dataset active
pBluescript II SK(+) (X52328.1) digested with Sau96I
Opening what was sent…
Not medical advice. For research and education only, and not medical advice: this app designs restriction, Golden Gate and Gibson products from the sequences you supply; a designed product is not evidence that the reaction occurred, and nothing here predicts whether a reaction works, how well, or whether the product is expressed.
Ends
Sau96I: GGNCC, cut G^GNC_C, leaving a 3-base 5′ overhang (GNC).
Methylation
Every one of these sites is cut in unmethylated DNA and in DNA from a dam and dcm methylating host, by the recorded dam and dcm sensitivities. Only dam and dcm are considered; CpG, EcoKI and other modifications are not modelled.
Source: McClelland M, Nelson M, Raschke E. Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res 1994;22:3640-3659 (doi 10.1093/nar/22.17.3640), Table I, read 6 October 2026.
The workspace draws a schematic gel of these fragments, not a prediction of where bands will run. Fragments under 100 bp are listed here but not drawn there, and fragments within 5 percent of each other are drawn as one band.
How this page was made
Computed when the site was built by the Drybench Plasmid engine, version 1.0.0, from /data/plasmid-map/examples/pbluescript-sk.1.json (GenBank X52328.1, SHA-256 b332229320366853c638f602edbd368bdc515b1846fc1ab95600813c1e0a2514) and enzyme table version 1, /data/plasmid-map/enzymes.8829d35c83.json (2026-10-06). Every cut position and fragment length on this page was compared with Biopython 1.88 (REBASE release 404, recorded 2026-11-07); a disagreement stops the build.