How's this:

use List::Util 'sum';

my %collect;
for my $i ( 0 .. $#@sequences ) {
  push @{ $collect{ $sequences[ $i ] } }, $numbers[ $i ]; 
}

for my $sequence ( keys %collect ) {
  my $avg = ( sum @{$collect{$sequence}} )/@{$collect{$sequence}};
  printf "sequence: $sequence = %.1f\n", $avg;
}
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