for(int i=0;i<alignLength;i++){
if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
for(int i=0;i<alignLength;i++){
if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
start = i;
break;
}
}
for(int i=alignLength-1;i>=0;i--){
if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;
break;
}
}
for(int i=alignLength-1;i>=0;i--){
if(seqA[i] != '.' && seqB[i] != '.' && seqA[i] != '-' && seqB[i] != '-' ){
end = i;