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pBluescript II SK(+) digested with SmlI
SmlI recognises CTYRAG and cuts circular pBluescript II SK(+) (GenBank X52328.1, 2,961 bp) at 5 sites, so a complete digest gives 5 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
591
669
1,259
2
262
1,260
1,521
3
277
1,522
1,798
4
868
1,799
2,666
5
963
2,667
668
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
668
668
2
1,259
1,259
3
1,521
1,521
4
1,798
1,798
5
2,666
2,666
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 SmlI
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
SmlI: CTYRAG, cut C^TYRA_G, leaving a 4-base 5′ overhang (TYRA).
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.