# cmsearch :: search a sequence database with an RNA CM
# INFERNAL 1.0 (January 2009)
# Copyright (C) 2009 HHMI Janelia Farm Research Campus
# Freely distributed under the GNU General Public License (GPLv3)
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# command:    cmsearch my.cm tosearch.300Kb.db
# date:       Tue May 19 11:36:34 2009
# num seqs:   1
# dbsize(Mb): 0.600000
#
# Pre-search info for CM 1: trna.5-1
#
#                                  cutoffs            predictions     
#                            -------------------  --------------------
# rnd  mod  alg  cfg   beta     E value   bit sc     surv     run time
# ---  ---  ---  ---  -----  ----------  -------  -------  -----------
    1   cm  cyk  loc  1e-07     100.010     3.84   0.0183  00:02:34.47
    2   cm  ins  loc  1e-15       1.000    11.92   0.0001  00:00:13.89
# ---  ---  ---  ---  -----  ----------  -------  -------  -----------
  all    -    -    -      -           -        -        -  00:02:48.36
#

CM: trna.5-1
>example

  Plus strand results:

 Query = 1 - 72, Target = 101 - 173
 Score = 78.06, E = 3.133e-21, P = 2.906e-26, GC =  53

           (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______
         1 gCcgacAUaGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUu 59      
           GC::A::UAGC:CAGU GG AG:GCGCCAG:CUG+++A:CUGGAGGUCC:G:GUUCGAU 
       101 GCGGAUUUAGCUCAGUuGGGAGAGCGCCAGACUGAAGAUCUGGAGGUCCUGUGUUCGAUC 160     

           >>>>>))))))):
        60 CcccGUgucgGca 72      
           C:C:G::U::GCA
       161 CACAGAAUUCGCA 173     


 Query = 1 - 72, Target = 70822 - 70891
 Score = 12.47, E = 0.6752, P = 6.263e-06, GC =  53

           (((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,~~~~~~)))))))
         1 gCcgacAUaGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUC*[17]*UgucgGc 71      
            C:G :AU+GCG:A+UGG  :CGCGC    C  UCAA +++GA +UC      U: C:G 
     70822 UCUGCUAUGGCGUAAUGGCCACGCGC----CCAUCAACAAAGAUAUC*[19]*UAACAGG 70890   

           :
        72 a 72      
           A
     70891 A 70891   


  Minus strand results:

 Query = 1 - 72, Target = 15124 - 15083
 Score = 12.93, E = 0.4841, P = 4.491e-06, GC =  48

           (((((((,,~~~~~~,,,,,<<<<<_______>>>>>))))))):
         1 gCcgacAUa*[33]*AGgUCCgggGUUCGAUuCcccGUgucgGca 72      
           GCC: :AUA      A G CC::GG UCG  UCC::GU: :GGC+
     15124 GCCAGUAUA*[ 5]*AUGCCCUAGGAUCG--UCCUAGUAAUGGCG 15083   


#
# Post-search info for CM 1: trna.5-1
#
#                              number of hits       surv fraction  
#                            -------------------  -----------------
# rnd  mod  alg  cfg   beta    expected   actual  expected   actual
# ---  ---  ---  ---  -----  ----------  -------  --------  -------
    1   cm  cyk  loc  1e-07     100.010       70    0.0183   0.0152
    2   cm  ins  loc  1e-15       1.000        3    0.0001   0.0003
#
# expected time    actual time
# -------------  -------------
    00:02:48.36    00:02:42.00
//
#
# CPU time: 157.69u 1.65s 00:02:39.34 Elapsed: 00:02:43