# Sequence search **TL;DR:** The linear genome view's **Sequence search** menu item searches the reference sequence itself and adds the hits as a new track, whether or not a sequence track is displayed. Three modes: - Sequence pattern - find every occurrence of a single DNA motif or regex across the reference. - CRISPR guide RNAs - discover candidate guides and their PAM sites directly against the reference. - Motif list - search many named motifs at once, pasted as one per line. This is the mode for restriction enzymes; see below. ## Sequence pattern Enter a sequence to find every occurrence in the reference. The field is a regex, so `GAATTC` matches exactly and `TATA[AT]A[AT]` matches either variant. Both strands are searched, case-insensitively; either can be turned off. Most restriction sites are palindromic — the site reads the same on both strands, which is how one enzyme cuts both — so such a hit is reported once, unstranded, rather than twice at one position. This needs bare `ACGT`: regex syntax has no reverse complement, and IUPAC codes are not regex (`N` matches a literal N). Use [Motif list](#restriction-enzymes-and-other-named-motifs) for IUPAC sites. ## CRISPR guide RNAs Choose an enzyme preset (SpCas9 `NGG`, SaCas9 `NNGRRT`, Cas12a `TTTV`, ...) or set the PAM, guide length, and PAM location by hand, and search either or both strands. Each guide is drawn with a dedicated guide-RNA glyph: the protospacer box, the PAM overpainted, and the predicted cut — one tick for a blunt cutter like SpCas9, a staggered pair for Cas12a. Clicking a guide reports its sequence, PAM, cut position, GC%, and two flags. `hasPolyT` marks the `TTTT` run that terminates transcription from the pol III promoters guides are usually expressed from. `softMasked` means the reference lower-cased this protospacer, which marks it as repetitive. Both describe the protospacer's own sequence; scoring a guide's specificity takes a genome-wide search, and this mode runs a scan of the region in view. A protospacer that reaches into an assembly gap is skipped. To order oligos from a search, use **Save track data** on the track's menu. The GFF3 export carries the guide sequence, PAM, cut positions, and flags as attributes. ## Restriction enzymes and other named motifs The **Motif list** mode takes a pasted list in the notation REBASE already uses, one motif per line, with an optional name and an optional cut marker: ``` # name site EcoRI G^AATTC BamHI G^GATCC PstI CTGCA^G BsaI GGTCTC(1/5) ``` There are two cut notations because there are two kinds of enzyme. A `^` marks a cut inside the recognition site. The `(n/m)` form is for the type IIS enzymes that cut _downstream_ of their site — BsaI, BsmBI, BbsI, SapI, AarI, the Golden Gate workhorses — where `n` and `m` count from the site's 3' end to the top- and bottom-strand cuts (negative numbers count back into the site). The panel is prefilled with common cloning enzymes; wipe it and paste your own set from REBASE or anywhere else. Sites may use [IUPAC ambiguity codes](https://www.bioinformatics.org/sms/iupac.html) (e.g. `GGTNACC`), blank lines and `#` comments are ignored, and a bare site with no name names itself. The cut notation carries the cuts themselves. `(n/m)` pins both strands' cuts outright; a `^` pins the top-strand cut, and for a palindromic site the bottom-strand cut mirrors it. So each hit reports both cut positions and whether the enzyme leaves a 5' overhang, a 3' overhang, or a blunt end. The strand checkboxes only appear when the list contains a motif that is actually stranded. Because the list is just text, the same mode works for primers, adapters, polylinker sites, or any other named motif set. With more than one motif in the list, **Launch as one track** puts every motif's matches in one track, distinguishable only by name, and **Launch one track per motif** gives each its own lane.