Hello Jinyan, A correction to my email - it should read:
"In your query 21 of the 25 bases align to danRer5 at chr4:39,278,984-39,279,004." Apologies for any confusion. Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Pauline Fujita wrote: > 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 > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
