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pBluescript II SK(+) digested with HphI
HphI recognises GGTGA and cuts circular pBluescript II SK(+) (GenBank X52328.1, 2,961 bp) at 6 sites, so a complete digest gives 6 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
1,661
229
1,889
2
227
1,890
2,116
3
416
2,117
2,532
4
206
2,533
2,738
5
35
2,739
2,773
6
416
2,774
228
The fragments add up to 2,961 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Site reads on
Cuts after base (top strand)
1
236
bottom strand
228
2
1,897
bottom strand
1,889
3
2,124
bottom strand
2,116
4
2,520
top strand
2,532
5
2,746
bottom strand
2,738
6
2,761
top strand
2,773
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 HphI
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
HphI: GGTGA, cut GGTGANNNNNNN_N^N, leaving a 1-base 3′ overhang whose bases are not fixed by the recognition site.
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.