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use strict;
use warnings;
...
       map { $common_letters[ $_ ] || '-' }
       0 .. length( $reference ) - 1;
}

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pat_mc : -oo----
almut  : -oo----
Can't use an undefined value as an ARRAY reference at ./spw731537C lin
+e 48.

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...
sub pat_mc {
...
       map { $common_letters[ $_ ] || '-' }
       0 .. length( $reference ) - 1;
}

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pat_mc : -oo----
almut  : -oo----
pat_mc : -oo----
almut  : -oo----

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almut  : -oo----
johngg : -oo----
...
johngg  256/s    15%     --   -89%   -97%
pat_mc 2416/s   984%   843%     --   -75%
almut  9772/s  4284%  3714%   304%     --

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...
sub pat_mc {
...
       map { $common_letters[ $_ ] || '-' }
       0 .. length( $reference ) - 1;
}

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pat_mc : -oo----
almut  : -oo----
pat_mc : -oo----
almut  : -oo----