# 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
# tabular output of hits:                U2_Yeast-threshold.tbl
# sequence reporting threshold:          score >= 46
# 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,


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) !   5.9e-20   98.7   0.1  cm        1      193 []      681858      681747 - .. 0.91    no 0.33

                                                                                                      v           NC
                                 ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>> CS
                       U2      1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuuggg 80    
                                 AU+   UCU+:GCCUUUUGGC:+AGAUCAAGUGUAGUAUCUGUUCUU:UCAGU+UAA+A+CUGA:AUG: CC:CA+UG:G
  ENA|BK006936|BK006936.2 681858 AUC---UCUUUGCCUUUUGGCUUAGAUCAAGUGUAGUAUCUGUUCUUUUCAGUGUAACAACUGAAAUGA-CCUCAAUGAG 681783
                                 ***...************************************************************999.********** PP

                                  v                                                   NC
                                 >>>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~::::::: CS
                       U2     81 ggccaau.uauaUUAaauuaAUUUUUggaacua*[34]**[40]*Acccuuu 193   
                                 G+:CA+U   U+UUAA+UU                          AC +UUU
  ENA|BK006936|BK006936.2 681782 GCUCAUUaCCUUUUAAUUUG-------------*[ 6]**[ 3]*ACAUUUU 681747
                                 ******86555555555443................7.....9..******* PP



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:                                          1  (4.636e-06); includes 0 truncated hit(s)

# CPU time: 64.67u 2.16s 00:01:06.83 Elapsed: 00:00:03.09
//
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