# 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.tbl
# 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, 


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

>> ENA|BK006948|BK006948.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XV, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) ?      0.49   19.8   0.0  cm        1      193 []      737498      737324 - .. 0.96    no 0.39

                                                                                                                  NC
                                 ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<~~~~~~>>>>>>,<<<<<<<___>>>>> CS
                       U2      1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAG*[ 8]*CUGauAuggcccccAuuggggg 82    
                                 AU+CC U U+ GCC U  GGC +A AU AAGU UA UA C GUUCU:A::A        U::U:  ::::::A U:::::
  ENA|BK006948|BK006948.2 737498 AUCCCAUAUUUGCCAUC-GGCAUAUAUUAAGUAUAUUAGCAGUUCUAAUUAC*[88]*GUAGUUGGAAGGAUACUAUCCU 737338
                                 **************999.*******************************996...*..6999999999999999999999 PP

                                                                                   NC
                                 >>,,,,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~::::::: CS
                       U2     83 ccaauuauaUUAaauuaAUUUUUggaacua*[34]**[40]*Acccuuu 193   
                                 : A+                                      A CC++U
  ENA|BK006948|BK006948.2 737337 UUAU--------------------------*[ 2]**[ 1]*AUCCCCU 737324
                                 9987.............................6.....9..******* PP

>> ENA|BK006947|BK006947.3  TPA_inf: Saccharomyces cerevisiae S288C chromosome XIV, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (3) ?       5.7   15.3   0.0  cm        1      193 []      266059      266208 + .. 0.91    no 0.39

                                             v          v                                                     v   NC
                                 ::::::.<<<.-<<<<____>>>>->>>,,,,.,,,,,,~~~~~~,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<< CS
                       U2      1 AUacCU.UCu.cgGCcUUUUgGCuaaGAUCAA.GUGUAG*[48]*aauuauaUUAaauuaAUUUUUggaacuaGuggggg 119   
                                 AU     UCU + G C  UUG C  AGAU A  GUGUAG        UUAUAU   +UU AU UUU G   +A:: : G:
  ENA|BK006947|BK006947.3 266059 AUGUUGaUCUaUCGUCAAUUGACCCAGAUGAUaGUGUAG*[ 1]*-GUUAUAUAGUUUUGAUAUUUUGGCGAAAAGUUGA 266132
                                 *****9****999****************9988999987...5...3377778888888888888888888888888888 PP

                                                          v      v  v     v v             v v      v  v        NC
                                 <----.<<<<<__>>>>>-..->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>::::::: CS
                       U2    120 cauuu.uggGCUUGCccau..ugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193   
                                 :A+U+ U :GCUUGC: AU  +::C : ::   G:  :AC: G   U GCA UA+   C :GU+:  :C    +U +
  ENA|BK006947|BK006947.3 266133 GAAUAuUGCGCUUGCGUAUauAUUCCAUUUGAGGUGGCACUAGAGCUCGCAUUAU-UACCAGUAGUGGCAGGAUUGC 266208
                                 888888**************99999******************************.99******************* PP

>> ENA|BK006949|BK006949.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome XVI, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (4) ?       6.6   15.1   0.4  cm        1      193 []      443393      443253 - .. 0.71    no 0.32

                                                                                         v  v   v  v              NC
                                 ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~,<<<<<<<___>>>>>>>,,,..,,,,, CS
                       U2      1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]*uggcccccAuugggggccaau..uauaU 92    
                                   A  U C:+G  C    G  UA:G UCAAG  UAGUAU UGUUCU       ::: C  A+   G :::++U       
  ENA|BK006949|BK006949.2 443393 CCAUUUACAUGAACCCCAGUUUAUGUUCAAG--UAGUAUAUGUUCU*[ 4]*-UCAACGCAAACUGCUGAUUUcaCC--- 443322
                                 ***************999************6..7**********98...4...222222222222222222222222... PP

                                                         v           v  v         v      v   v    v               NC
                                 ,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________ CS
                       U2     93 UAaauuaAUUUUUggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUacc 172   
                                                     :U : :::+U U     UU+      ::: : A:A+ ::: G+C: : :A U CAC AC 
  ENA|BK006949|BK006949.2 443321 --------------------AUUGAAUAUUGU-----UUA------UAUAUGAUAUAUACCGUCAAAUUACUUCACGAC- 443274
                                 ....................222222222222.....221......3333345599***********************. PP

                                    v     v   v        NC
                                 >>>>>>-->>>>>>::::::: CS
                       U2    173 gccagguucagcccAcccuuu 193   
                                 : : :G++C :::  +  U+ 
  ENA|BK006949|BK006949.2 443273 AGUGUGAACUGUGAUAAAUCA 443253
                                 ********************* PP

>> ENA|BK006939|BK006939.2  TPA_inf: Saccharomyces cerevisiae S288C chromosome V, complete sequence.
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (5) ?       7.1   14.9   0.0  cm        1      193 []      190882      191043 + .. 0.92    no 0.41

                                             v        v                                                           NC
                                 ::::::<<<.-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
                       U2      1 AUacCUUCu.cgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105   
                                 AU CC U : +: C: UUU:G : : AUCA                             AA ++U+UUAAAU AA UUUU
  ENA|BK006939|BK006939.2 190882 AUUCCAUGAuUUCCUGUUUAGCU-UCAUCA-----------------*[ 4]**[ 4]*AACAUUUUUAAAUGAAAUUUU 190939
                                 *******9955678899999976.799997....................9.....9..77699**************** PP

                                            vv v                             v vv              v                  NC
                                 ,,,,,,,<<<<<<<<----.<<<<<_._>>>>>-.........->>>>>>>>,,<<<<<<-<<<<<<__________... CS
                       U2    106 ggaacuaGugggggcauuu.uggGCU.UGCccau.........ugcccccaCacggguugaccuggcaUUGCAcUac... 171   
                                  +  + +GU::  : AUU  :G:GCU UGC:C:          + :  ::ACA+ :: :: : ::::  U CAC AC   
  ENA|BK006939|BK006939.2 190940 AAUGUCUGUUUCCUUAUUGaAGAGCUuUGCUCUGgauuuuccaACAUUAAACAUGCCGCCGAGGCCUCCUCCACCACcac 191019
                                 ***********9999998899999964799999999999999999999**************************999888 PP

                                        v                 NC
                                 .._>>>>>>-->>>>>>::::::: CS
                       U2    172 ..cgccagguucagcccAcccuuu 193   
                                   +:::: :UU:: ::  + CU+U
  ENA|BK006939|BK006939.2 191020 caUUGGCAUUUGGUGGUGAACUAU 191043
                                 988********************* 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:                                          5  (3.063e-05); includes 0 truncated hit(s)

# CPU time: 66.56u 2.31s 00:01:08.87 Elapsed: 00:00:03.41
//
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