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     gene            337..2799
                     /gene="thrA"
                     /locus_tag="t0002"
...
                     ISQQVPGFDEWLWVLAYPGIKVSTAEARAILPAQYRRQDCIAHGRHLAG
+FIHACYSRQ
                     PQLAAALMKDVIAEPYRARLLPGFSQARQAVSEIGALASGISGSGPTLF
+ALCDKPETA
                     QRVADWLSKHYLQNQEGFVHICRLDTAGARVVG"

ORIGIN      
        1 agagattacg tctggttgca agagatcata acaggggaaa ttgattgaaa ataaa
+tatat
...
  4791901 tttggtccat gatattgaaa aaaaactaac aaaataacgt gttgtaattt ttaaa
+ataat
  4791961 a
//

#!/usr/bin/perl

...
    print "</table>\n";
    print "</body>\n</html>";
}

#!/usr/bin/perl

...
    $mutations{total} = $mutations{tt} + $mutations{ct} + $mutations{c
+c};
    return %mutations;
}