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UCSC BLAT miss some matches from hg38

Interesting result.

If you BLAT this sequence in hg38: TTTCTTTTGGATCTCCTGGTTAATTAGA

You will only receive 1 result, however, it do occur twice on human genome. How to understand it?

TTTCTTTTGGATCTCCTGGTTAATTAGAAACCTTTCCAATGTTTAAATTGTTAAATTAAGGACTTTTTCCCCAAATAACTTATCATACCACTCAGATATTTACATGCATTTGATACAAATAAATGGGATTAAAGCTGACATAGACTATTTCAGAATCAGTCCTGAAAAAATCAATATTGGGTATGATTTGACTTCTGCTCTTCAGTGACATGCTTCTTGAACTGCTTTCTTTTGGATCTCCTGGTTAATTAGA

hg38 ucsc blat
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updated by GenoMax GenoMax • written by Friyunnwoo • Friyunnwoo

1 answer

If you check the All results (no minimum matches) box before submitting the search you get three.

   ACTIONS      QUERY   SCORE START   END QSIZE IDENTITY  CHROM  STRAND  START       END   SPAN
-----------------------------------------------------------------------------------------------
browser details YourSeq    28     1    28    28   100.0%  chr7   -   140800064 140800091     28
browser details YourSeq    16     2    17    28   100.0%  chr9   -    17443841  17443856     16
browser details YourSeq    16    11    26    28   100.0%  chr10  +    24796926  24796941     16

But without that box checked you get one (as you note)

   ACTIONS      QUERY   SCORE START   END QSIZE IDENTITY  CHROM  STRAND  START       END   SPAN
-----------------------------------------------------------------------------------------------
browser details YourSeq    28     1    28    28   100.0%  chr7   -   140800064 140800091     28
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written by GenoMax GenoMax

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