Hello Jinyan, This sequence is actually long enough to blat. Blat will find perfect sequence matches of 25 bases, and sometimes find them down to 20 bases. In your query 21 of the 25 bases align to dm5 at chr4:39,278,984-39,279,004.
For sequences that are 20bp or shorter you can search in the "Short Match" track. We also have tracks that detail different types of repeats (Interrupted Rpts, Simple Repeats) in the Zebrafish browser if you are interested in repeats. Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Jinyan Huang wrote: > Dear Prof. > > I want to know how many repeats of this sequence in Zebrafish: 5' > acacccttgtgcctttatctcccat 3'. This sequence is beta-arrestin 1 > morpholino. But it is too short to blat it. > How can I do this? > Thank you very much in advance. > > > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
