<div dir="ltr">Dear developers<div><br></div><div>Please consider this genomic sequence:</div><div><br></div><div><p class="MsoNormal">CTTTCTCTTTCTTTCTTTCTTTCTTTTTTCTTTCTTTTCTTTCTCCCTCTCTCTCTCCCT</p><p class="MsoNormal"><br></p><p class="MsoNormal">I got it from ensembl directly on GRCh37 on coordinates (X:153,795,306-153,795,365)</p><p class="MsoNormal"><br></p><p class="MsoNormal"><span style="color:rgb(31,73,125)">Sequence export:</span></p><p class="MsoNormal"><span style="color:rgb(31,73,125)"> </span></p><p class="MsoNormal">



</p><p class="MsoNormal"><span style="color:rgb(31,73,125)"><a href="http://grch37.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=X:153795306-153795365;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text">http://grch37.ensembl.org/Homo_sapiens/Export/Output/Location?db=core;flank3_display=0;flank5_display=0;output=fasta;r=X:153795306-153795365;strand=feature;coding=yes;cdna=yes;peptide=yes;utr3=yes;exon=yes;intron=yes;genomic=unmasked;utr5=yes;_format=Text</a></span></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal">However, if I blat this very same sequence on your own blat servers I get no perfect hit (please see attached text file).<br></p><p class="MsoNormal"></p></div><div><br></div><div>If, however, I blat it on UCSC blat servers I get 1 perfect matched hit at the expected coordinates:</div><div><br></div><div><pre style="color:rgb(0,0,0);font-size:medium;background-color:rgb(255,254,232)"><h2 style="font-family:Arial,Helvetica,sans-serif;white-space:normal">BLAT Search Results</h2><tt style="white-space:normal"><pre>   ACTIONS      QUERY           SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
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<a href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chrX:153795306-153795365&db=hg19&ss=../trash/hgSs/hgSs_genome_2fc2_484490.pslx+../trash/hgSs/hgSs_genome_2fc2_484490.fa&hgsid=414875813_bYZ83pe63bElHH1MYpoaOoXfSIuQ" style="color:rgb(18,30,154)">browser</a> <a href="http://genome.ucsc.edu/cgi-bin/hgc?o=153795305&g=htcUserAli&i=../trash/hgSs/hgSs_genome_2fc2_484490.pslx+..%2Ftrash%2FhgSs%2FhgSs_genome_2fc2_484490.fa+YourSeq&c=chrX&l=153795305&r=153795365&db=hg19&hgsid=414875813_bYZ83pe63bElHH1MYpoaOoXfSIuQ" style="color:rgb(18,30,154)">details</a> YourSeq           60     1    60    60 100.0%     X   +  153795306 153795365     60</pre></tt></pre></div><div><br></div><div>Can you explain the discrepancy?</div><div><br></div><div>Best regards</div><div><br></div><div>Duarte</div><div><br></div><div><div>
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