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