if( p1[ i ] != p2[ i ] && p1[ i ] != 'N' && p2[ i ] != 'N' ) {

##</code><code>##

        if (c_map[ str1[i] ^ str2[i] ]) {

##</code><code>##

int seqDiff ( SV *s1, SV *s2 ) {
    STRLEN bytes1, bytes2;
    char *p1, *p2;
    int i;

    p1 = SvPV( s1, bytes1 );
    p2 = SvPV( s2, bytes2 );
    if( bytes1 != bytes2 ) return 0;

    for( i = 0; i < bytes1; ++i ) {
        if( p1[ i ] != p2[ i ] && p1[ i ] != 'N' && p2[ i ] != 'N' ) {
            return 0;
        }
    }
    return 1;
}

##</code><code>##

C:\test>SeqDiffDC_mark_1
comparing strings of length 240003
          Rate bitmask  inline     buk   
bitmask 50.8/s      --    -92%    -95%   
inline   634/s   1146%      --    -34%   
buk      967/s   1802%     53%      --   
benchmark results expected

C:\test>SeqDiffDC_mark_1 -LEN=10
comparing strings of length 243
            Rate bitmask  inline     buk
bitmask  25730/s      --    -65%    -93%
inline   72894/s    183%      --    -81%
buk     393465/s   1429%    440%      --
benchmark results expected

##</code><code>##

int seqDiff32 ( SV *s1, SV *s2 ) {
    STRLEN bytes1, bytes2;
    char *p1, *p2;
    STRLEN dwords;
    STRLEN lastBytes;
    U32 *up1, *up2;
    int i;

    p1 = SvPV( s1, bytes1 );
    p2 = SvPV( s2, bytes2 );
    if( bytes1 != bytes2 ) return 0;

    up1 = (U32*)p1;
    up2 = (U32*)p2;
    dwords = bytes1 >> 2;
    lastBytes = bytes1 % 4;
    p1 += dwords << 2;
    p2 += dwords << 2;

    while( dwords-- ) {
        if( *up1 != *up2 ) {
            for( i = 0; i < 4; ++i ) {
                char c1 = ( (char*)up1 )[ i ];
                char c2 = ( (char*)up2 )[ i ];
                if( c1 != c2 && c1 != 'N' && c2 != 'N' ) {
                    return 0;
                }
            }
        }
        up1++; up2++;
    }

    for( i = 0; i < lastBytes; ++i ) {
        char c1 = ( (char*)p1 )[ i ];
        char c2 = ( (char*)p2 )[ i ];
        if( c1 != c2 && c1 != 'N' && c2 != 'N' ) {
            return 0;
        }
    }
    return 1;
}

##</code><code>##

C:\test>SeqDiffDC_mark_1 -LEN=1
comparing strings of length 27
            Rate bitmask  inline   buk64     buk   buk32
bitmask  43724/s      --    -42%    -93%    -93%    -93%
inline   75272/s     72%      --    -88%    -88%    -88%
buk64   613799/s   1304%    715%      --     -1%     -6%
buk     620545/s   1319%    724%      1%      --     -5%
buk32   651674/s   1390%    766%      6%      5%      --

C:\test>SeqDiffDC_mark_1 -LEN=10
comparing strings of length 243
            Rate bitmask  inline     buk   buk64   buk32
bitmask  25730/s      --    -65%    -93%    -94%    -95%
inline   72894/s    183%      --    -81%    -84%    -86%
buk     393465/s   1429%    440%      --    -12%    -22%
buk64   447289/s   1638%    514%     14%      --    -11%
buk32   504399/s   1860%    592%     28%     13%      --
benchmark results expected

comparing strings of length 240003
          Rate bitmask  inline     buk   buk64   buk32
bitmask 50.9/s      --    -92%    -95%    -97%    -98%
inline   629/s   1136%      --    -35%    -59%    -75%
buk      962/s   1790%     53%      --    -38%    -62%
buk64   1545/s   2935%    146%     61%      --    -39%
buk32   2539/s   4889%    304%    164%     64%      --
benchmark results expected

##</code><code>##

my $seq1 = 'ATGCATCGATGN' x $LEN;
my $seq2 = 'ATGCATCGATGN' x $LEN;

##</code><code>##

C:\test>SeqDiffDC_mark_1 -LEN=1
comparing strings of length 27
            Rate bitmask  inline     buk   buk32   buk64
bitmask  43145/s      --    -43%    -93%    -94%    -94%
inline   76220/s     77%      --    -88%    -89%    -89%
buk     651920/s   1411%    755%      --     -2%     -2%
buk32   664615/s   1440%    772%      2%      --     -1%
buk64   668000/s   1448%    776%      2%      1%      --
benchmark results expected

C:\test>SeqDiffDC_mark_1 -LEN=10
comparing strings of length 243
            Rate bitmask  inline     buk   buk32   buk64
bitmask  25665/s      --    -65%    -94%    -96%    -96%
inline   73346/s    186%      --    -84%    -88%    -88%
buk     450664/s   1656%    514%      --    -23%    -29%
buk32   587556/s   2189%    701%     30%      --     -7%
buk64   632327/s   2364%    762%     40%      8%      --
benchmark results expected

C:\test>SeqDiffDC_mark_1 -LEN=100
comparing strings of length 2403
            Rate bitmask  inline     buk   buk32   buk64
bitmask   4723/s      --    -87%    -96%    -99%    -99%
inline   37224/s    688%      --    -66%    -88%    -91%
buk     108924/s   2206%    193%      --    -66%    -75%
buk32   321561/s   6709%    764%    195%      --    -26%
buk64   432770/s   9063%   1063%    297%     35%      --
benchmark results expected

C:\test>SeqDiffDC_mark_1 -LEN=1000
comparing strings of length 24003
           Rate bitmask  inline     buk   buk32   buk64
bitmask   506/s      --    -91%    -96%    -99%    -99%
inline   5834/s   1054%      --    -54%    -90%    -94%
buk     12793/s   2431%    119%      --    -77%    -86%
buk32   55949/s  10966%    859%    337%      --    -41%
buk64   94726/s  18637%   1524%    640%     69%      --
benchmark results expected

C:\test>SeqDiffDC_mark_1 -LEN=10000
comparing strings of length 240003
           Rate bitmask  inline     buk   buk32   buk64
bitmask  51.3/s      --    -92%    -96%    -99%   -100%
inline    635/s   1139%      --    -51%    -90%    -94%
buk      1294/s   2425%    104%      --    -79%    -88%
buk32    6087/s  11774%    858%    370%      --    -45%
buk64   11162/s  21673%   1657%    762%     83%      --
benchmark results expected