---
name: "last-pair-probs"
section: "1"
platform: "linux"
package: "last-align"
version: "1609-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/last-pair-probs"
---

# last-pair-probs(1)

Read alignments of paired DNA reads to a genome, and do estimations

## NAME

last-pair-probs - Read alignments of paired DNA reads to a genome, and do estimations

## SYNOPSIS

*last-pair-probs* \[options\] interleaved-alignments

*last-pair-probs* \[options\] alignments1 alignments2

## DESCRIPTION

Read alignments of paired DNA reads to a genome, and: (1) estimate the distribution of distances between paired reads, (2) estimate the probability that each alignment represents the genomic source of the read.

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **-r**, **--rna**

  assume the reads are from potentially-spliced RNA

- **-e**, **--estdist**

  just estimate the distribution of distances

- **-m** M, **--mismap**=*M*

  don't write alignments with mismap probability \> M (default: 0.01)

- **-f** BP, **--fraglen**=*BP*

  mean distance in bp

- **-s** BP, **--sdev**=*BP*

  standard deviation of distance

- **-d** PROB, **--disjoint**=*PROB*

  prior probability of disjoint mapping (default: 0.02 if **-r**, else 0.01)

- **-c** CHROM, **--circular**=*CHROM*

  specifies that chromosome CHROM is circular (default: chrM)

- **-V**, **--version**

  show program's version number and exit