%  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.YDR525W.t2k-100-30-stride-ebghtl   Host: cc34    Sat Dec  7 04:38:24 2002
%  karplus                                        Dir:  /projects/compbio/experiments/protein-predict/yeast/YDR5/YDR525W
% ---------------------------------------------------------------------
% 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 YDR525W.t2k-w0.5.mod
% Track 1 FIMs added (the generic node (5))
% Track 1 Coeff 0.300 File YDR525W.t2k.stride-ebghtl.mod
% Score DP Method: forward all-paths (dpstyle = 0)
% Align DP Method: viterbi (adpstyle = 1)
% 7458 sequences, 1753770 residues, 110 nodes, 75.79 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(=2.1190) * Reverse)^tau(=0.7432)))
%    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
1ocrC             261       -29.91       -9.77     5.43e-01
2occC             261       -29.91       -9.76     5.48e-01
1bsmA             201       -25.91       -6.66     5.73e+00
1avmA             201       -25.77       -6.52     6.41e+00
2pna              104       -23.31       -5.81     1.14e+01
1fzaB             328       -27.61       -5.71     1.24e+01
1fj7A             101       -24.40       -5.64     1.31e+01
1b8xA             280       -26.96       -5.61     1.35e+01
1fjeB             175       -25.14       -5.61     1.35e+01
1eb7A             323       -26.94       -5.28     1.78e+01
1ev7B             317       -25.17       -5.00     2.25e+01
1cto              109       -23.29       -4.97     2.32e+01
1rtu              114       -23.13       -4.95     2.35e+01
1idsA             207       -24.71       -4.93     2.40e+01
5csmA             256       -24.53       -4.92     2.42e+01
1csmA             256       -24.56       -4.88     2.50e+01
1mgsA              73       -22.06       -4.85     2.56e+01
1a88A             275       -25.12       -4.80     2.67e+01
1iu4A             331       -26.90       -4.80     2.69e+01
1b9oA             123       -22.63       -4.74     2.82e+01
1i0vA             104       -23.50       -4.72     2.86e+01
9rnt              104       -23.47       -4.67     2.99e+01
3rnt              104       -23.48       -4.64     3.09e+01
1kp0A             402       -26.06       -4.58     3.26e+01
1axh               37       -20.11       -4.54     3.37e+01
1fgyA             127       -23.62       -4.50     3.46e+01
1bkb              136       -22.52       -4.42     3.72e+01
1qtfA             246       -24.14       -4.39     3.84e+01
1lnzA             342       -27.99       -4.35     3.95e+01