# 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
# show alignments in output:             no
# 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) !   5.9e-20   98.7   0.1  ENA|BK006936|BK006936.2 681858 681747 -  cm    no 0.33  TPA_inf: Saccharomyces cerevisiae S288C chromosome II,
 ------ inclusion threshold ------
  (2) ?      0.49   19.8   0.0  ENA|BK006948|BK006948.2 737498 737324 -  cm    no 0.39  TPA_inf: Saccharomyces cerevisiae S288C chromosome XV,
  (3) ?       5.7   15.3   0.0  ENA|BK006947|BK006947.3 266059 266208 +  cm    no 0.39  TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV
  (4) ?       6.6   15.1   0.4  ENA|BK006949|BK006949.2 443393 443253 -  cm    no 0.32  TPA_inf: Saccharomyces cerevisiae S288C chromosome XVI
  (5) ?       7.1   14.9   0.0  ENA|BK006939|BK006939.2 190882 191043 +  cm    no 0.41  TPA_inf: Saccharomyces cerevisiae S288C chromosome V, 


Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (193 consensus positions)
Target sequences:                                               16  (24142652 residues searched)
Target sequences re-searched for truncated hits:                16  (15424 residues re-searched)
Windows   passing  local HMM SSV           filter:           72732  (0.7978); expected (0.35)
Windows   passing  local HMM Viterbi       filter:           24175  (0.3233); expected (0.15)
Windows   passing  local HMM Viterbi  bias filter:            6671  (0.09669); expected (0.15)
Windows   passing  local HMM Forward       filter:            2037  (0.03161); expected (0.003)
Windows   passing  local HMM Forward  bias filter:            1133  (0.01757); expected (0.003)
Windows   passing glocal HMM Forward       filter:             596  (0.01251); expected (0.003)
Windows   passing glocal HMM Forward  bias filter:             438  (0.009175); expected (0.003)
Envelopes passing glocal HMM envelope defn filter:             460  (0.00429); expected (0.003)
Envelopes passing  local CM  CYK           filter:              38  (0.000201); expected (0.0001)
Total CM hits reported:                                          5  (3.063e-05); includes 0 truncated hit(s)

# CPU time: 66.25u 2.12s 00:01:08.37 Elapsed: 00:00:03.14
//
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