# The MEME Suite of motif-based sequence analysis tools.
# 
# version 4.7.0 (Release date: 4 PDT 20)
# 
# Program: mhmmscan
# File contents: Database search results
# Motif file: common/crp0.meme.html
# HMM file: mhmm/crp0.linear.mhmm
# Sequence file: common/crp0.fasta
# Create date: Tue Nov  1 11:41:26 2011
# 
# For further information on how to interpret these results or to get a copy
# of the MEME Suite software, please access http://meme.sdsc.edu.
# 
# If you use MCAST in your research, please cite
# 
#  Timothy Bailey and William Stafford Noble,
#  "Searching for statistically significant regulatory modules",
#  Bioinformatics (Proceedings of the European Conference on Computational Biology),
#  19(Suppl. 2):ii16-ii25, 2003.
# 
# *****************************************************************************
ID         E-value   Score      Start        End Description
 -----------------------------------------------------------------------------------------------------------------------------------
ce1cg          nan   31.26         24         84                                                                                    
ara            nan   20.39         10         77                                                                                    
pbr322         nan   19.54         93        102                                                                                    
ompa           nan   18.98         53         78                                                                                    
gale           nan   17.91         45         65                                                                                    
bglr1          nan   17.35         79        101                                                                                    
tnaa           nan   16.14         24        101                                                                                    
deop2          nan   16.11         10         28                                                                                    
crp            nan   16.08         66         84                                                                                    
ilv            nan   15.89          6         62                                                                                    
male           nan   15.48         17         36                                                                                    
lac            nan   15.11         12         32                                                                                    
tdc            nan   13.53         79         99                                                                                    
gale           nan   13.28          1         41                                                                                    
pbr322         nan   13.14         17         23                                                                                    
uxu1           nan   12.93         20         46                                                                                    
malk           nan   11.66         88        104                                                                                    
malk           nan   11.52          6         40                                                                                    
lac            nan   11.21         95        105                                                                                    
malk           nan   11.02         52         64                                                                                    
deop2          nan   10.89         63         75                                                                                    
gale           nan   10.19         67         71                                                                                    
cya            nan   10.19         24         28                                                                                    
 -----------------------------------------------------------------------------------------------------------------------------------


Derived parameters for E-value calculations
 type of distribution: Extreme Value
 source of distribution: Actual sequence scores
 status: Too few (23 < 200) scores to estimate E-values.
 number of matches: 23
 db length: 1890

Program parameters for mhmmscan
  HMM file: mhmm/crp0.linear.mhmm
  Sequence file: common/crp0.fasta
  Paths: single
  Minimum match score: 10
  Partial motif matches are: allowed
  E-value threshold for scores: 10
  Background: nrdb
  Score matrix for pseudocount frequencies: PAM 1
  Beta (weight on pseudocount frequencies):   1.00
  Zero spacer emission log-odds: false
  Fancy output format: false

Actual command line:
  mhmmscan --text mhmm/crp0.linear.mhmm common/crp0.fasta 

CPU: cantor
Total time 0.01 secs.
Overhead 0.00 secs.
18 sequences
0.3 millisec/seq
2.4 microsec/character
