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#!/usr/bin/perl

...
  }

use Data::Dump 'dd'; dd sort values %unique;

(
  ">4kt0_M|P72986\nMALSDTQILAALVVALLPAFLAFRLSTELYK\niiiiiiiiiMMMMMMMMM
+MMMMMMMMIIIII\n",
  ">5oy0_m|P72986\nMALSDTQILDIFFERENTAFLAFRLSTELYK\niiiiiiiiiMMMMMMMMM
+MMMMMMMMIIIII\n",
  ">7oy0_m|P72996\nMALSDTQILAALVVALLPAFLAFRLSTELYK\niiiiiiiiiMMMMMMMMM
+MMMMMMMMIIIII\n",
)