Finding Repeats

Task Name: find-repeats

This task searches for repeats in sequences and saves the regions found as annotations.

Parameters:

• in — a semicolon-separated list of input files. [String, Required]
• out — the output file with the annotations. [String, Required]
• name — the name of the annotated regions. [String, Optional, Default: “repeat_unit”]
• min-length — the minimum length of the repeats. [Number, Optional, Default: 5]
• identity — the percent identity between repeats. [Number, Optional, Default: 100]
• min-distance — the minimum distance between the repeats. [Number, Optional, Default: 0]
• max-distance — the maximum distance between the repeats. [Number, Optional, Default: 5000]
• inverted — if true, searches for the inverted repeats. [Boolean, Optional, Default: false]

Example:

ugene find-repeats --in=murine.gb --out=murine_repeats.gb --identity=99