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$ perl -E '
$s1 = q{gctgc};
...
0x04
0x00
$

use strict;
use warnings;
...
    substr $baseStr, $_, 1, q{X} for @posns;
    return $baseStr;
}

at
gctgctaggctgtgctgccaactggatcctgcgcgggacgtcctttgtctacgtcccgtcggcgctgaat
+cctgcggacgacccctctcgtggtcg
ttggggctct
ccgccctcttctccgcctgccgttc
ggc

use strict;
use warnings;
...

    $diffPosns{ pos $diff } ++ while $diff =~ m{(?=[^\0])}g;
}