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@@ -91,30 +93,49 @@ The online version of Blat masks 11mers from the query that occur more than 1024 times in the genome. This is done to improve speed, but may result in missed hits when you are searching for sequences in repeats.If your input sequence is not one of the very repetitive sequences, but still present a few dozen times on a chromosome, note that Blat results are limited to 16 results per chromosome strand. This means that at most 32 locations per chromosome are returned.
To find all matches for repetitive sequences with the online version of Blat, you can add more flanking sequence to your query. If this is not possible, the only alternative is to download the executables of Blat and the .2bit file of a genome to your own machine and use BLAT on the command line. See Downloading BLAT source and documentation for more information.
+ ++This usually occurs on the newer genome assmeblies, such as hg38, when you search a sequence that +has an "alternate" or "fix" sequence. To improve the quality of the these +assemblies, curators have added multiple versions of some important loci, e.g. the MHC regions. +They also add fix sequences to resolve errors without changing the reference. See our patches blog post for more +information.
++When you BLAT or isPCR a sequence which matches a chromosome location that also has a fix or alt +sequence, you will see a match on the reference chromosome (e.g. "chr1") and another +match on the patch sequence (e.g. chr1_KN196472v1_fix). In most cases it is safe to ignore the +patch hit, as a human genome will not contain both the reference and alternate sequence at the +same time. For more information on the specific kinds of patch sequences see our FAQ entry on the topic.
+Due to the high demand on our Blat servers, we restrict service for users who programmatically query the BLAT tool or do large batch queries. Program-driven use of BLAT is limited to a maximum of one hit every 15 seconds and no more than 5,000 hits per day. Please limit batch queries to 25 sequences or less.
For users with high-volume Blat demands, we recommend downloading the BLAT tool for local use. For more information, see Downloading BLAT source and documentation.