Inverted Repeat Scan
Find reverse-complement DNA arms separated by a caller-selected spacer length.
Description
An inverted repeat contains DNA arms that are reverse complements separated by a spacer.
An inverted repeat contains DNA arms that are reverse complements separated by a spacer. Exact scanning identifies locations matching a supplied arm/spacer geometry.
Find reverse-complement DNA arms separated by a caller-selected spacer length.
When to use Inverted Repeat Scan
Use this for the following task: Find reverse-complement DNA arms separated by a caller-selected spacer 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 Inverted Repeat Scan 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, armLength, spacerLength using the field table, then run the tool.
- Read leftArmStarts, rightArmStarts, repeatCount. 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 |
| armLength | Arm length | integer; minimum 1 | Required |
| spacerLength | Spacer length | integer; minimum 0 | Required |
Normalize canonical DNA and test all windows that fit the fixed geometry. Return zero-based arm starts for exact reverse-complement matches; an oversized geometry returns empty lists.1
rightStart = leftStart + armLength + spacerLength This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| leftArmStarts | Left arm starts | list of integer |
| rightArmStarts | Right arm starts | list of integer |
| repeatCount | Repeat count | integer |
{
"input": {
"sequence": "ATGCAT",
"armLength": 3,
"spacerLength": 0
},
"output": {
"leftArmStarts": [
0
],
"rightArmStarts": [
3
],
"repeatCount": 1
}
}Limitations and assumptions
Mismatches and variable spacers are not allowed. Operation and output 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 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 K-mer Frequency Table for this operation: Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.
The implementation reference documents the exact calculation, supported input shapes and returned fields.
References
-
Inverted Repeat Scan — 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.
- K-mer Frequency Table
Tabulate overlapping k-mer frequencies with optional reverse-complement canonicalization.