---
name: "exonpairs"
section: "1"
platform: "linux"
package: "snap"
version: "2013-11-29-11"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/exonpairs"
---

# exonpairs(1)

SNAP module exonpairs

## NAME

exonpairs - SNAP module exonpairs

## SYNOPSIS

**exonpairs** \[*options*\] \<**HMM file**\> \<**FASTA file**\> \[*options*\]

## OPTIONS

- **-min-intron** \<int\>

  minimum Intron length \[30\]

- **-max-intron** \<int\>

  maximum Intron length \[10000\]

- **-einit-length** \<int\>

  minimum Einit length in bp \[10\]

- **-eterm-length** \<int\>

  minimum Eterm length in bp \[10\]

- **-exon-length** \<int\>

  minimum Exon length in bp \[30\]

**-intron-score** \<float\> minimum Intron score in bits \[-5\]

- **-einit-score** \<float\>

  minimum Einit score in bits \[-5\]

- **-eterm-score** \<float\>

  minimum Eterm score in bits \[-5\]

- **-exon-score** \<float\>

  minimum Exon score in bits \[-5\]

- **-pair-score** \<float\>

  minimum pair score (exon-intron-exon) \[10\]

- **-flank-length** \<int\>

  length of flanking sequence per exon \[20\]

- **-lcmask**

  treat lowercase as N