---
name: "tantan"
section: "1"
platform: "linux"
package: "tantan"
version: "51-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/tantan"
---

# tantan(1)

low complexity and tandem repeat masker for biosequences

## NAME

tantan - low complexity and tandem repeat masker for biosequences

## SYNOPSIS

**tantan** \[*options*\] *fasta-sequence-file(s)*

## DESCRIPTION

Find simple repeats in sequences

### Options (default settings):

- **-p**

  interpret the sequences as proteins

- **-x**

  letter to use for masking, instead of lowercase

- **-c**

  preserve uppercase/lowercase in non-masked regions

- **-m**

  file for letter pair scores (+1/-1, but **-p** selects BLOSUM62)

- **-r**

  probability of a repeat starting per position (0.005)

- **-e**

  probability of a repeat ending per position (0.05)

- **-w**

  maximum tandem repeat period to consider (100, but **-p** selects 50)

- **-d**

  probability decay per period (0.9)

- **-a**

  gap existence cost (0)

- **-b**

  gap extension cost (infinite: no gaps)

- **-s**

  minimum repeat probability for masking (0.5)

- **-f**

  output type: 0=masked sequence, 1=repeat probabilities,

-

  2=repeat counts, 3=BED (0)

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

  show help message, then exit

- **--version**

  show version information, then exit

## REPORTING BUGS

Report bugs to: tantan@cbrc.jp\
 Home page: http://www.cbrc.jp/tantan/