HhaI Recognition Site
HhaI at a glance
5' GCG|C 3' 3' C|GCG 5'
| Recognition site | 5'-GCGC-3' |
| Cut | GCG^C |
| Ends | a 2-base 3' overhang (CG) |
| Expected frequency | about once every 256 bp in random DNA |
How to find HhaI sites in a sequence
- Paste a DNA sequence or FASTA record into the box above. HhaI is already entered under Only these enzymes.
- Tick Circular DNA for a plasmid, so a site that spans the end and the start is found.
- The map marks each HhaI cut with its position. Copy or download the output below it.
Frequently asked questions
What sequence does HhaI cut?
HhaI recognizes GCGC (written 5' to 3') and cuts the top strand at GCG^C.
Does HhaI leave sticky or blunt ends?
Sticky ends: a 2-base 3' overhang (CG).
How often does HhaI cut?
A site like GCGC turns up about once every 256 bp in random DNA. Real sequences vary, so check yours above.
Restriction enzymes
Restriction MapAatII Recognition SiteAccI Recognition SiteAflII Recognition SiteAgeI Recognition SiteAluI Recognition SiteApaI Recognition SiteApaLI Recognition SiteAscI Recognition SiteAvaI Recognition SiteAvrII Recognition SiteBamHI Recognition SiteBclI Recognition SiteBglII Recognition SiteBsiWI Recognition SiteBspHI Recognition SiteBsrGI Recognition SiteBssHII Recognition SiteBstBI Recognition SiteClaI Recognition SiteDraI Recognition SiteEagI Recognition SiteEcoRI Recognition SiteEcoRV Recognition SiteFseI Recognition SiteHaeIII Recognition SiteHincII Recognition SiteHindIII Recognition SiteHinfI Recognition SiteHpaI Recognition SiteKpnI Recognition SiteMfeI Recognition SiteMluI Recognition SiteMseI Recognition SiteMspI Recognition SiteNaeI Recognition SiteNcoI Recognition SiteNdeI Recognition SiteNheI Recognition SiteNotI Recognition SiteNruI Recognition SiteNsiI Recognition SitePacI Recognition SitePmeI Recognition SitePstI Recognition SitePvuI Recognition SitePvuII Recognition SiteRsaI Recognition SiteSacI Recognition SiteSacII Recognition SiteSalI Recognition SiteSau3AI Recognition SiteScaI Recognition SiteSfiI Recognition SiteSmaI Recognition SiteSnaBI Recognition SiteSpeI Recognition SiteSphI Recognition SiteSspI Recognition SiteStuI Recognition SiteSwaI Recognition SiteTaqI Recognition SiteXbaI Recognition SiteXhoI Recognition SiteXmaI Recognition Site
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