Task Name: find-repeats
Searches for repeats in sequences and saves the regions found as annotations.
Parameters:
in — semicolon-separated list of input files. [String, Required]
out — output file with the annotations. [String, Required]
name — name of the annotated regions. [String, Optional, Default: “repeat_unit”]
min-length — minimum length of the repeats. [Number, Optional, Default: 5]
identity — percent identity between repeats. [Number, Optional, Default: 100]
min-distance — minimum distance between the repeats. [Number, Optional, Default: 0]
max-distance — maximum distance between the repeats. [Number, Optional, Default: 5000]
inverted — if true, searches for the inverted repeats. [Boolean, Optional, Default: false]
Example:
| Code Block |
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ugene find-repeats --in=murine.gb --out=murine_repeats.gb --identity=99 |