I liked this algorithm. My problem now is sorting the fragments based on the start position because that info is stored somewhat deep in a hash;

 %details_of_match = (
                 $gene_model =>( ($position1, $orig_pos1, $sequence1)
                               , ($position2, $orig_pos2, $sequence2)
                               , ($position3, $orig_pos3, $sequence3)
                                 );
                   )
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