Found it. in ajgraph.c starting at line 2760:
xa[0] = x;
ya[0] = y + incr;
xa[1] = x + incr;
ya[1] = y + size;
xa[2] = x + size;
ya[2] = y + incr;
xa[3] = x + incr;
ya[3] = y;
xa[4] = x;
ya[4] = y;
the last line should be
ya[4] = y + incr;
Regards,
David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech