%  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.YGR008C.t2k-100-30-stride-ebghtl   Host: cc67    Fri Nov  8 15:58:14 2002
%  karplus                                        Dir:  /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR008C
% ---------------------------------------------------------------------
% 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 YGR008C.t2k-w0.5.mod
% Track 1 FIMs added (the generic node (5))
% Track 1 Coeff 0.300 File YGR008C.t2k.stride-ebghtl.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 7310 sequences, 1706072 residues, 85 nodes, 57.04 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(=2.2833) * Reverse)^tau(=0.7543)))
%    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
1kkoA             413       -31.12       -8.31     7.33e-01
1jjfA             268       -27.02       -7.47     1.49e+00
1gkkA             297       -27.19       -6.94     2.37e+00
1gklA             297       -26.86       -6.56     3.30e+00
1efdN             266       -25.87       -5.77     6.70e+00
1poiA             317       -25.40       -5.64     7.59e+00
1g5gB             481       -26.45       -5.45     9.01e+00
1exeA              99       -22.43       -5.42     9.29e+00
1jcv              153       -24.06       -5.31     1.02e+01
1b06A             210       -23.99       -5.24     1.10e+01
1ah6              220       -23.96       -5.16     1.19e+01
1azwA             313       -25.16       -4.94     1.46e+01
1ghtA             105       -22.44       -4.93     1.46e+01
1iknD             236       -24.36       -4.86     1.57e+01
1ha9A              34       -20.33       -4.79     1.68e+01
1aun              208       -24.35       -4.59     2.04e+01
1poiB             260       -24.55       -4.58     2.04e+01
1jj2Z              56       -21.97       -4.50     2.21e+01
1dabA             539       -26.01       -4.36     2.55e+01
1k8cA             322       -25.28       -4.29     2.71e+01
1le6A             123       -22.36       -4.29     2.73e+01
1m1cA             680       -26.49       -4.27     2.77e+01
1ae7              119       -22.31       -4.25     2.82e+01
1a4iA             301       -23.96       -4.18     3.04e+01
3cms              323       -23.14       -4.16     3.10e+01
1a0hA             159       -24.37       -4.12     3.21e+01
1g8yA             279       -23.37       -4.06     3.40e+01
1ezvG              93       -22.98       -4.03     3.52e+01
1rpxA             230       -24.42       -4.03     3.52e+01
2rslA             140       -21.50       -4.02     3.54e+01
4cms              323       -23.21       -4.02     3.56e+01
1fcqA             350       -24.54       -3.96     3.77e+01