buildTemplateProfile(parents);
createAlignMatrix(queryUnalignedLength, alignmentLength);
buildTemplateProfile(parents);
createAlignMatrix(queryUnalignedLength, alignmentLength);
else if(seq[j] == 'C') { profile[j].C++; }
else if(seq[j] == '-') { profile[j].Gap++; }
else if(seq[j] == '.') { profile[j].Gap++; }
else if(seq[j] == 'C') { profile[j].C++; }
else if(seq[j] == '-') { profile[j].Gap++; }
else if(seq[j] == '.') { profile[j].Gap++; }