{
int length = sq.getLength();
boolean ssFound = false;
- Annotation asecstr[] = new Annotation[length + firstResNum - 1];
+ Annotation asecstr[] = new Annotation[length + (firstResNum-sq.getStart())];
for (int p = 0; p < length; p++)
{
if (secstr[p] >= 'A' && secstr[p] <= 'z')