-20 -4  winleft, winright: left and right ends of window
-8 6   shiftmin, shiftmax: minimum and maximum shift of aligned base
54321    iseed: integer random seed
0        nranseq: number of random sequences, or 0 to use sequences in book
1000        nshuffle: number of times to redo alignment after random shuffle
0        ifpaired: 1 for pairs of complementary sequences for symmetric site
1        standout: -1 no, 0 limited, 1 full standard output
1        npassout: output H and alignment every npassout passes
1        nshiftout: output H(L) every nshiftout shifts, every pass if 0, -1 no
0.0001   tolerance: tolerance in change of H
50       ntolpass: maximum number of passes with change less than tolerance