SSR Motif Class

Reduce an SSR motif to its primitive repeat unit and classify its base length.

Description

A simple sequence repeat motif can itself contain repeated smaller units.

A simple sequence repeat motif can itself contain repeated smaller units. Its primitive unit determines the motif-length class.

Reduce an SSR motif to its primitive repeat unit and classify its base length.

When to use SSR Motif Class

Use this for the following task: Reduce an SSR motif to its primitive repeat unit and classify its base length.

Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.

How to use SSR Motif Class 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 motif using the field table, then run the tool.
Read primitiveMotif, primitiveLength, motifClass. 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
motif	Motif	string; minimum text length 1; maximum text length 1000000; pattern ^\s[ACGTacgt]+\s$	Required

Normalize canonical DNA, use prefix-period information to reduce complete repetitions, and label lengths 1–6 as mono through hexa; larger units are longer.^[1]

primitive period = shortest length that exactly tiles the supplied motif

This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.

Output field	Meaning	Value type
primitiveMotif	Primitive motif	string
primitiveLength	Primitive length	integer
motifClass	Motif class	string

json

{
  "input": {
    "motif": "ATAT"
  },
  "output": {
    "primitiveMotif": "AT",
    "primitiveLength": 2,
    "motifClass": "di"
  }
}

Limitations and assumptions

Rotated or reverse-complement motif equivalence is not canonicalized. This classifies a motif, not a repeat interval.

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 Tandem Repeat Copy Number for this operation: Find the longest exact DNA motif run at zero-based half-open positions, choosing the earliest tie. For a complementary task, use STR Microvariant Formatter for this operation: Format an STR microvariant allele from complete repeats and residual bases; decimal suffix is not a fraction.

The implementation reference documents the exact calculation, supported input shapes and returned fields.

References

SSR Motif Class — tool.io

Similar or alternative tools

Tandem Repeat Copy Number
Find the longest exact DNA motif run at zero-based half-open positions, choosing the earliest tie.
STR Microvariant Formatter
Format an STR microvariant allele from complete repeats and residual bases; decimal suffix is not a fraction.