-14 +15 winleft, winright: left and right ends of window
-10 10 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
1 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