%  SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12
%  (c) 1992-2001 Regents of the University of California, Santa Cruz
%
%          Sequence Alignment and Modeling Software System
%         http://www.cse.ucsc.edu/research/compbio/sam.html
%
% ----------------- Citations (SAM, SAM-T99, HMMs) --------------------
% R. Hughey, A. Krogh, Hidden Markov models for sequence analysis:
%  Extension and analysis of the basic method, CABIOS 12:95-107, 1996.
% K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting
%  remote protein homologies, Bioinformatics 14(10):846-856, 1998.
% A. Krogh et al., Hidden Markov models in computational biology:
%  Applications to protein modeling, JMB 235:1501-1531, Feb 1994.
% ---------------------------------------------------------------------
%  stridefoo.1.YGR016W.t2k-100-30-stride-ebghtl   Host: cc41    Fri Nov  8 17:06:21 2002
%  karplus                                        Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR016W
% ---------------------------------------------------------------------
% Inserted Files: 
% Database Files:  /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds
%
% Subsequence-submodel (local) (SW = 2)
% Simple scores adjusted by ln(seq len) (adjust_score = 2)
% Track 0 FIMs added (geometric mean of match probabilities (6))
% Track 0 Coeff 1.000 File YGR016W.t2k-w0.5.mod
% Track 1 FIMs added (the generic node (5))
% Track 1 Coeff 0.300 File YGR016W.t2k.stride-ebghtl.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 7310 sequences, 1706072 residues, 191 nodes, 128.72 seconds
%
% Sequence scores selected if better than:
%	 E-value (Emax 4.0e+01) (select_score=4)
%
% Simple: NLL-NULL using FIM probabilities
% Reverse: NLL-NULL for the reverse sequence NULL model
%    Calculated when Simple < simple_threshold (0.00)
% E-value on N (=7316) sequences:
%    N / (1 + exp(-(lambda(=1.6405) * Reverse)^tau(=0.7791)))
%    Calculated when Simple < simple_threshold (0.00)
%    Rescale E-values or use -dbsize for multiple scoring runs.
% Scores sorted by E-value, best first
%
% Sequence ID   Length      Simple     Reverse     E-value      X count
1g5hA             454       -36.06      -12.21     2.38e-01
1qj4A             257       -31.86      -10.93     5.58e-01
1yasA             257       -31.55      -10.65     6.76e-01
1go5A              69       -25.52       -8.12     3.97e+00
1g99A             408       -30.60       -7.74     5.24e+00
1b43A             340       -29.15       -7.16     7.98e+00
1howA             373       -29.78       -7.16     8.01e+00
1hnoA             280       -29.75       -7.08     8.48e+00
1hzpA             335       -28.35       -7.06     8.64e+00
1bmfA             510       -29.69       -6.99     9.05e+00
1yprA             125       -27.47       -6.79     1.06e+01
1ap6A             198       -27.63       -6.57     1.24e+01
1abmA             198       -27.63       -6.55     1.27e+01
1f00I             282       -26.68       -6.54     1.28e+01
1eyeA             280       -28.39       -6.46     1.36e+01
1e79A             510       -29.26       -6.34     1.49e+01
1h8eA             510       -29.20       -6.28     1.55e+01
1hnuA             280       -28.76       -6.22     1.63e+01
1fp1D             372       -29.50       -6.03     1.88e+01
1qklA             127       -25.48       -5.97     1.97e+01
1dofA             403       -29.32       -5.82     2.20e+01
1f44A             324       -27.45       -5.78     2.27e+01
1b24A             188       -29.66       -5.77     2.30e+01
1itxA             419       -27.68       -5.72     2.39e+01
1hv2A              99       -25.26       -5.55     2.72e+01
1gwcA             230       -29.31       -5.33     3.23e+01
1bk0              331       -27.05       -5.33     3.25e+01
1pyaB             228       -26.84       -5.28     3.36e+01
1ukz              203       -27.17       -5.24     3.49e+01
1fpqA             372       -28.82       -5.17     3.66e+01
1knqA             175       -28.00       -5.08     3.96e+01