Tandem Repeat Copy Number
Find the longest exact DNA motif run at zero-based half-open positions, choosing the earliest tie.
Description
A tandem repeat consists of adjacent exact motif copies.
A tandem repeat consists of adjacent exact motif copies. Reporting its interval requires a clear coordinate convention and a deterministic tie rule.
Find the longest exact DNA motif run at zero-based half-open positions, choosing the earliest tie.
When to use Tandem Repeat Copy Number
Use this for the following task: Find the longest exact DNA motif run at zero-based half-open positions, choosing the earliest tie.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use Tandem Repeat Copy Number and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter sequence, motif using the field table, then run the tool.
- Read longestCopyNumber, repeatStart, repeatEnd. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| sequence | Sequence | string; minimum text length 1; maximum text length 1000000; pattern ^\s*[ACGTacgt]+\s*$ | Required |
| motif | Motif | string; minimum text length 1; maximum text length 1000000; pattern ^\s*[ACGTacgt]+\s*$ | Required |
Normalize canonical DNA and scan possible starts for contiguous motif runs. Return the longest run, selecting the earliest tied start; use zero-based half-open positions and −1 when absent.1
end = start + longestCopies × motifLength This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| longestCopyNumber | Longest copy number | integer |
| repeatStart | Zero-based inclusive start; -1 if no full motif occurs. Ties choose the earliest start. | integer |
| repeatEnd | Zero-based exclusive end; -1 if no full motif occurs. | integer |
{
"input": {
"sequence": "ATATATGCATAT",
"motif": "AT"
},
"output": {
"longestCopyNumber": 3,
"repeatStart": 0,
"repeatEnd": 6
}
}Limitations and assumptions
Only exact supplied motif orientation is searched. No imperfect repeats or allele interpretation is performed; operation limits apply.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose SSR Motif Class for this operation: Reduce an SSR motif to its primitive repeat unit and classify its base length. For a complementary task, use Terminal Telomere Repeats for this operation: Count exact copies of the supplied motif at both sequence ends and report their combined span without counting overlaps twice.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Tandem Repeat Copy Number — tool.io
Similar or alternative tools
- SSR Motif Class
Reduce an SSR motif to its primitive repeat unit and classify its base length.
- Terminal Telomere Repeats
Count exact copies of the supplied motif at both sequence ends and report their combined span without counting overlaps twice.