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pACYC184 digested with AclI
AclI recognises AACGTT and cuts circular pACYC184 (GenBank X06403.1, 4,245 bp) at 2 sites, so a complete digest gives 2 fragments.
Fragments
Fragment
Length (bp)
From base
To base
1
1,765
2,397
4,161
2
2,480
4,162
2,396
The fragments add up to 4,245 bp, the length of the record.
Cut sites
Site
Recognition site: first base on the top strand
Cuts after base (top strand)
1
2,395
2,396
2
4,160
4,161
Positions are in the numbering of GenBank X06403.1. 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
pACYC184 (X06403.1) digested with AclI
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
AclI: AACGTT, cut AA^CG_TT, leaving a 2-base 5′ overhang (CG).
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/pacyc184.1.json (GenBank X06403.1, SHA-256 f9484eb2ae4c5d157b08c3c19af0933984ed1605753d8d73897728d914eee021) 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.