find_repeats

find_repeats
 -io            io_handle:integer
 -contigs       identifiers:strings
?-direction     direction:integer(3)?
?-min_match     length:integer(25)?
?-outfile       filename:string()?
?-tag_types     types:string()?

The command searches for perfect matches between two or more fragments in the consensus sequences. This information is plotted on the Contig Selector. The command will not work if the Contig Selector is not displayed. The function returns no value but will generate a Tcl error if an error occurs.

-io io_handle

The database IO handle returned from a previous open_db call.

-contigs identifiers

This specifies the list of contigs to search. The {contig start end} syntax may be used for an identifier to search only a region of the contig, otherwise all of it is searched.

-direction direction

This specifies whether forward repeats (1), reverse repeats (2), or both (3) are to be found. The default is 3 (both).

-min_match length

This specifies the minimum length of a repeat to be searched for. The default is 25. The minimum allowed is 8.

-outfile filename

This specifies a file in which to save the tag hits. The results are written in the form of REPT annotations which are suitable for passing onto the enter_tags command. The default is a blank string, which implies no file should be created.

-tag_types types

If types is a non blank list of tag types then masking will be applied to remove sequence covered by tags of these types from the repeat searching. The default is a blank list, which means no masking will be performed.