Many thanks to Michael Mitchell and Fred
The program REPRO (Heringa and Argos, 1993) is able to
recognize distant repeats in a single query sequence.
There is also some commercially available software with a capability of
repeats search in a SINGLE sequence. For example GeneQuest from DNA
Star package. But I have a lot of sequences. And I have to find
repeats, not to mask them
To find a repeats (like SINE, LINE)I have to compare all my sequences
to each other. Old famous PC-Gene is able of database creation and a
homology search. That could be done also in FASTA. Then it is going to
be N-1 runs. I.e. 499 runs of homology search for my 500 sequences. And
what shell I do than? How can I handle this data? It is also just a
little hard to perform 499 runs of homology search manually.