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# 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
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