# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.4 (Dec 2020)
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         RF00004.cm
# target sequence database:              GCA_000146045.2.fasta
# sequence reporting threshold:          score >= 46
# HMM-only mode (for all models):        on [CM will not be used]
# number of worker threads:              56
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       U2  [CLEN=193]
Accession:   RF00004
Description: U2 spliceosomal RNA
Hit scores:
 rank     E-value  score  bias  sequence                 start    end   mdl trunc   gc  description
 ----   --------- ------ -----  ----------------------- ------ ------   --- ----- ----  -----------
  (1) !   1.5e-19   73.1   2.7  ENA|BK006936|BK006936.2 681855 681762 - hmm     - 0.35  TPA_inf: Saccharomyces cerevisiae S288C chromosome II,


Hit alignments:
>> ENA|BK006936|BK006936.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome II, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   1.5e-19   73.1   2.7 hmm        7      100 ..      681855      681762 - .. 0.74     - 0.35

                                 <<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,, CS
                       U2      7 UCucgGCcUUUUGGCUaaGAUCAAGUGUAGUAUCUGUUCUUuuCAGUuUAAuAuCUGauAuugucucuAuugggggccaa 86    
                                 UCu+ GCcUUUUGGCU+aGAUCAAGUGUAGUAUCUGUUCUUuuCAGU+UAA+A+CUGa+Au+ +cuc Au g+gg  ca+
  ENA|BK006936|BK006936.2 681855 UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGACCUCAAU-GAGGCUCAU 681777
                                 999*********************************************************7777666666.777776666 PP

                                 ,.,,,,,,,,,,,,, CS
                       U2     87 u.uauaUUAaauuaA 100   
                                 u   u+UUAa+uu  
  ENA|BK006936|BK006936.2 681776 UaCCUUUUAAUUUGU 681762
                                 544444444433221 PP



Internal HMM-only pipeline statistics summary: (--hmmonly used)
---------------------------------------------------------------
Query model(s):                                          1  (193 consensus positions)
Target sequences:                                       16  (24142652 residues searched)
Windows passing local HMM SSV      filter:           14742  (0.1733); expected (0.02)
Windows passing local HMM MSV bias filter:            3067  (0.03652); expected (0.02)
Windows passing local HMM Viterbi  filter:             143  (0.001824); expected (0.001)
Windows passing local HMM Forward  filter:              29  (0.000422); expected (1e-05)
Total HMM hits reported:                                 1  (3.894e-06)

# CPU time: 1.51u 0.14s 00:00:01.65 Elapsed: 00:00:00.27
//
[ok]
