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use strict;
use warnings;

...
        $line = $followingLine;
    }
}

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KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.1    2e-139     497
KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.1    4e-46     187
KN-1791-LAST_rep_c7834    IMGA|Medtr4g125100.2    4e-46     187