Format: [motif>r]n.p
| Element | Meaning |
|---|
| [AAG] | Canonical motif, no rotation |
| [AAG>1] | Canonical rotated 1 position left: AAG → AGA |
| [~AAG] | Reverse complement of canonical: AAG → CTT |
| [~AAG>2] | RC of canonical rotated 2 left: AAG → GAA → TTC |
| ]3 | 3 complete repeats |
| ]3.1 | 3 complete repeats + 1 partial base |
| [N]5 | 5-base gap between stretches |
| [N]-2 | 2-base overlap between stretches |
| (ACGT) | Literal gap sequence — shown when Full sequence in gaps is on |
Options
| Option | Effect |
|---|
| Hide N gaps | Suppress all [N] gap/overlap markers |
| Full sequence in gaps | Show actual bases in (parentheses) instead of [N]n |
| Strip prefix/suffix N | Suppress only the leading and trailing [N] markers; keep internal ones |
| Trim front / end | Remove a fixed number of bases from the start/end of each sequence before analysis (under Advanced options) |
Examples
| Input | Output | Notes |
|---|
| AAGAAGAAG | [AAG]3 | canonical, no rotation |
| AGAAGAAGAA | [AAG>1]3.1 | AGA×3 + partial A |
| TTCTTCTTCTTCTT | [~AAG>2]4.2 | TTC×4 + partial TT |
| TGCAAGAAGAAG | (TGC)[AAG]3 | with Full sequence in gaps on |
| TGCAAGAAGAAG | [AAG]3 | with Strip prefix/suffix N on |
Paste a nomenclature (with plain digits) to convert it back to a sequence. Literal gap sequences in (parentheses) are also expanded.