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#!/usr/bin/perl

...
print "$key => $value\n";
   }
exit;

Contig1
NAAAAGUAUAGGCUCGAGAGAGAAGUCCUGGCCUAUCGGAUUACACCACGNGUCAGAUCU
...
GUUACUUUAGAUCAGAUCUGUANUUCCCUUUGUAUUGUUCAGGNUUUCCAACCAUAAAUU
AUUGGUACUAUCUUNAUUGUUAUCAUAAUUGACGUGUGUUUAAGUUCNNNNNNNNNNNNN
NNNNN

Contig1
GACGG*UUG*CCGUC => 1
...
GAUAU*GU*AUAUC => 1
AAAAU*CCAAUAUUUCCAU*AUUUU => 1