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Query  10550  CTTGGTTAGTACTGAATCCCATATATACTATGTTTTTCCTATACATATGTACTTAT
+GATA  10609
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+||||
Sbjct  74391  CTTGGATAGTACTGAATCCCATATATACTATGTTTTTCCTATACATATGTACTTAT
+GATA  74332

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Query  16319   CCCACTCGGGCCCGGCTCCAGCTCCTGCACCGCCTGGGCCAGCCTCCGCATGTTA
+AGGGC  16378
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+|||||
Sbjct  140831  CCCACTCGGGCCCCGCTCCAGCTCCTGCACCGCCTGGGCCAGCCACCGCATGTTA
+AGGGC  14077

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my $registry = 'Bio::EnsEMBL::Registry';
...
  }
  
 #}

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BLASTN 2.2.24+
Reference: Zheng Zhang, Scott Schwartz, Lukas Wagner, and
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Query  36924   CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTT
+TTATA  36983
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Sbjct  100370  CTGGTCTCCTTACACATTCGAAATTGGACATTTCCGACTATTTCCTTGGTATGTT
+TTATA  100311