Another problematic case is searching for sequences in repeats or transposons. BLAT skips the most repetitive parts of the query and limits the number of matches it finds, leading to missing matches for these repeat sequences. The online version of BLAT masks 11mers from the query that occur more than 1024 times in the genome and limits results to 16 matches per chromosome strand. This means that at most 32 locations per chromosome are returned. This is done to improve speed, but can result in missed hits when you are searching for sequences in repeats.
Often for repeat sequences, you can use the self-chain track to find the other matches, but only if the other matches are long and specific enough. You can check whether any sequence is present at a particular location by using the "Short match" track if your sequence is less than 30 bp. -You can work around this minimum length limitation but adding more flanking sequence to your query +You can work around this minimum length limitation by adding more flanking sequence to your query to make the query unique enough. 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. When using the command line version of BLAT, you can set the repMatch option to a large value to try to improve finding matches in repetitive regions and do not use one of the default 11.ooc repeat masking files.
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.