I would further recommend a general adjustment of how you approach it. You are doing black list filtering, i.e., I don't want "\s." White listing is safer and makes it harder to violate expectations. The following is a stab at it from your sample data.

$temp =~ /\b(mmu-miR-\d\d[ab\d])\b/;
print "$1 is all I want\n";
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Like ikegami said, encoding issues might need to be handled first.