I'm running BLAT with this command:

    blat genome.fasta query.fasta blat_90.csv -minIdentity=90 -noHead

And I'm surprised that I've counted the results and order by count. 


    import pandas as pd
    import sys
    df_blat = pd.read_csv('blat_90.csv', index_col=False, sep='\t')
    s = df_blat.qName.value_counts()
    count = 1
    for k in s.head(100).index.tolist():
        count += 1
        print(s[k],k)
    

The interesting thing is that the max results per query is 672 and this number is repeated about 30 times. Then I have queries that were repeated 671 times again many times. 


    672 MITE_T_71978|chr3D|340455280|340455443|AT|175|F2975
    672 MITE_T_97305|chr7B|194283260|194283371|AT|29|F4298
    672 MITE_T_110543|chr5D|34445518|34445608|TA|94|F5023
    672 MITE_T_72475|chr3D|503092467|503092630|AT|174|F2988
    ...


So this makes me wonder if there's a limit in the number of times a query is search. I've repeated this script with no different results. 


UPDATE:
I've notice that running only one query with each wheat chromosome in a separate thread, the max results per search is 32.

This is how the results look like when I search only one sequence agains each chromosome at the time:
   

     wc -l b*
               32 b1A.csv
               32 b1B.csv
               32 b1D.csv
               32 b2A.csv
               32 b2B.csv
    ...

Max 32 hits per search (accordingly 32 x 21 chromosomes is 672)


There must be a limit in the code but I'm still not able to find it


As responded by UCSC itself:


> The 32 results are indeed a consistent limitation where BLAT only
> allows 16 results per chromosome and per strand. BLAT is unable to
> exhaustively return results for queries with repetitive sequences that
> map to many places in the genome. There may be many other sequence
> aligning programs available that do not have such limits, but we do
> not have any specific recommendations about which to use.
> 