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#!/usr/bin/perl

...
AUUGGUACUAUCUUNAUUGUUAUCAUAAUUGACGUGUGUUUAAGUUCNNNNNNNNNNNNN
NNNNN

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Contig1
AAAAU*CCAAUAUUUCCAU*AUUUU => 1
...
UCGUC*GGUACUC*GACGA => 1
UCGUCG*GUACU*CGACGA => 1