pairwiseLength = 0;
// string dummy;
-// while(dummy != "query:"){ cout << dummy << endl;blastFile >> dummy; }
+// while(dummy != "query:"){ mothurOut(dummy, ""); mothurOutEndLine(); blastFile >> dummy; }
// blastFile >> seqBend;
-// cout << seqBend << endl;
+// mothurOut(toString(seqBend), ""); mothurOutEndLine();
// for(int i=0;i<seqBend;i++){
// seqAaln += 'Z';
// seqBaln += 'X';