RepeatsPlus is a set of programs that provides statistical filtering according to input sequence length and number of repeat occurrences, motif mask filtering and filtering related to ambiguous letters in input sequence and a large number of other options. RepeatsPlus package contains two batch-processing console programs StatRepeats and Repeats written in C++ and a graphical user interface RepeatPlus written in Python that simplifies execution one of the two console programs based on its options. The RepeatPlus package also contains two standalone batch-processing console programs MotifSearch (writen in C++) and DrawRepeats (written in C).