Shell Programming and Scripting

gawk '
{
   key[NR]=$1;
   for(i=1;i<length($2);i+=2) {
       site[i,NR]=substr($2,i,2)
       if(i>maxi)maxi=i
   }
}
END {
    c=0
    for(i=1;i<=maxi;i+=2) {
           v=""
           mismatch=0
           for(r=1;r<=NR;r++) {
              if(v=="" && !(site[i,r]~"-"))v=site[i,r];
              else if(length(v)&&site[i,r]!=v) {
                 if(++mismatch>1) {
                     keep[++c]=i;
                     r=NR
                 }
              }
           }
        }
        for(r=1;r<=NR;r++) {
           printf "%s ", key[r]
           for(i=1;i<=c;i++) printf "%s", site[keep[i],r]
           printf "\n"
        }
}' infile