Documentation

Pairing

Pairing[seqA, seqB]⟹pairs

returns all possible pairings of seqA and seqB.

Pairing[{seqA,intervalA, seqB]⟹pairs

returns only pairs touching some part of intervalA on seqA.

Pairing[seqA, {seqB,intervalB}]⟹pairs

returns only pairs touching some part of intervalB on seqB.

Pairing[{seqA,intervalA, {seqB,intervalB}]⟹pairs

returns only pairs touching some both part of intervalA on seqA and part of intervalB on seqB.

Details

Note that interval specification is different for sequences, strands, and structures

Input

Output

General Options

Examples

Basic Examples (2)

Pair two sequences:

Specify interval for first Strand:

Additional Examples (9)

Specify interval for both structures:

Pair two strands:

Pair two structures:

Specify interval for second sequences:

Specify interval for both sequences:

Specify interval for second Strand:

Specify interval for both strands:

Specify interval for first Structure:

Specify interval for second Structure:

Options (7)

Consolidate (1)

Do not consolidate subpairings:

Depth (2)

Return things with up to 1 Pairing:

Return things with exactly 1 Pairing:

MaxMismatch (1)

Maximum number of mismatches allowed in a pair:

MinLevel (1)

Specify minimum number of consecutve bases in each Pairing:

MinPieceSize (1)

Maximum number of mismatches allowed in a pair:

Polymer (1)

Specify polymer type: