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#!/usr/bin/perl -w
use strict;
...
    }
    return @hyph_padded_seq;
}

Query: "A C D"     Query: "A B C"    Query: "A B"   Query: "C D"
Answers:           Answers:          Answers:       Answers:
...
  'ABICID',        ]                  'A--B'         'CAD',
]                                    ]               'CID'
                                                    ]

Take Query "A C D" as an example:

...
        S1-> AB-C-D
        S2-> A--C-D
        S4-> ABICID