-10 +10 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 500 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