# cmscan :: search sequence(s) against a CM database
# INFERNAL 1.1.5 (Sep 2023)
# Copyright (C) 2023 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:                   BK006935_6_7.fasta
# target CM database:                    IRES_5S_U2.cm
# tabular output of hits:                IRES_5S_U2_Yeast-cmscan.tbl
# number of worker threads:              4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       ENA|BK006935|BK006935.2  [L=230218]
Hit scores:
 rank     E-value  score  bias  modelname  start    end   mdl trunc   gc  description
 ----   --------- ------ -----  --------- ------ ------   --- ----- ----  -----------
 ------ inclusion threshold ------
  (1) ?      0.91   13.5   0.0  U2         52929  53083 +  cm    no 0.44  U2 spliceosomal RNA
  (2) ?       1.3   12.8   5.3  U2        196571 196389 -  cm    no 0.33  U2 spliceosomal RNA


Hit alignments:
>> U2  U2 spliceosomal RNA
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) ?      0.91   13.5   0.0  cm        1      193 []       52929       53083 + .. 0.80    no 0.44

                                             v        v                                                            NC
                                ::::::.<<<-<<<<..____>>>>->>>,,,,,,,,,,,,,,,,,,,,~~~~~~~~~~~~,,,,,,,,,,,,,,,,,,,,, CS
                       U2     1 AUacCU.UCucgGCc..UUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCU*[20]**[18]*aauuauaUUAaauuaAUUUUU 105  
                                 U +C  UC:C:G    UUUU  C:A:GAUCAAG G AG  UCUGU               ++U+AUA   AAUU AUU   
  ENA|BK006935|BK006935.2 52929 CUGGCAaUCCCGGAGugUUUUUGCCAGGAUCAAGAGCAGCUUCUGU---*[ 2]**[ 1]*UUUAAUAAACAAUUCAUUAAG 52998
                                **********8875544888999*************9999999987......7.....4..333555555566788888888 PP

                                                   vv v    v vv                 v    v               v     v       NC
                                ,,,,,,,<<<<<<<<----<<<<<__>>>>>-->>>>>>>>,,<<<<<<-<<<<<<___________>>>>>>-->>>>>>: CS
                       U2   106 ggaacuaGugggggcauuuuggGCUUGCccauugcccccaCacggguugaccuggcaUUGCAcUaccgccagguucagcccA 187  
                                GGAACU+: ::: :    U++:   U  :   U : ::: :  ::::U   C  G: U  CA U+C :C  G U  A::::A
  ENA|BK006935|BK006935.2 52999 GGAACUUAGCCAUCUGGAUGAUAUGUGCA--GUGGGUGGUUCACAAAUA-GCUCGUCUGCCAGUUCAUCUGGUUGGAUUUGA 53077
                                88888888888888877664333333322..358999999999999999.8888999*********99999999******** PP

                                       NC
                                :::::: CS
                       U2   188 cccuuu 193  
                                C C+UU
  ENA|BK006935|BK006935.2 53078 CACCUU 53083
                                ****** PP

>> U2  U2 spliceosomal RNA
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) ?       1.3   12.8   5.3  cm        1      193 []      196571      196389 - .. 0.77    no 0.33

                                           vvvv    vvvv                         v                v    v           NC
                                 ::::::<<<-<<<<____>>>>->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<~~~~~~>> CS
                       U2      1 AUacCUUCucgGCcUUUUgGCuaaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggccc*[ 7]*gg 81    
                                 AU C UUC:C    U UU+++ +:GAU A  U U G A    UUCU:  CAG +UAAUAUCUG  : GG ::      ::
  ENA|BK006935|BK006935.2 196571 AUUCUUUCCCA---UCUUUAUAUGGAUAAUAUUUUGAA----UUCUAUGCAGAGUAAUAUCUGUUU-GGUAU*[19]*AU 196487
                                 **********5...44444555*******999999999....6********************999.65444...7..33 PP

                                 v                                 vvvv                           vvvv       v v  NC
                                 >>>,,,.,,,,,,,,,,,,,,,,,,,,,,,,,<<<<<<<<----<<<<<_~~~~~~>>>>>-->>>>>>>>,,<<<<<<- CS
                       U2     82 gccaau.uauaUUAaauuaAUUUUUggaacuaGugggggcauuuuggGCU*[ 1]*GCccauugcccccaCacggguuga 155   
                                  CC++  UA A UA +UU+ UUUUU G +++ ::                               ++ +::A+G:: : A
  ENA|BK006935|BK006935.2 196486 CCCUUGuUAGAGUAGUUUUUUUUUUUGGUUAGUG---------------G*[10]*---------AAGUCAAUGAAAGCA 196427
                                 3444445666666666666666666666665544...............2...3...........34467899******* PP

                                   v                 v    v v           NC
                                 <<<<<<___________>>>>>>-->>>>>>::::::: CS
                       U2    156 ccuggcaUUGCAcUaccgccagguucagcccAcccuuu 193   
                                 ::  :: U GCA  +++::  ::UU : ::CA CC+  
  ENA|BK006935|BK006935.2 196426 UAAGUUUUAGCAUCUUUAAUAUAUUUCGUUCAGCCCGG 196389
                                 ************************************** PP



Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s):                                               1  (460436 residues searched)
Query sequences re-searched for truncated hits:                  1  (1166.7 residues re-searched, avg per model)
Target model(s):                                                 3  (664 consensus positions)
Windows   passing  local HMM SSV           filter:            1951  (0.3874); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:             932  (0.1928); expected (0.02)
Windows   passing  local HMM Forward  bias filter:             386  (0.09111); expected (0.02)
Windows   passing glocal HMM Forward       filter:             129  (0.06346); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:              75  (0.03339); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:              84  (0.01354); expected (0.02)
Envelopes passing  local CM  CYK           filter:               3  (0.0002665); expected (0.0001)
Total CM hits reported:                                          2  (0.0002441); includes 0 truncated hit(s)

# CPU time: 8.73u 0.20s 00:00:08.93 Elapsed: 00:00:08.28
//
Query:       ENA|BK006936|BK006936.2  [L=813184]
Hit scores:
 rank     E-value  score  bias  modelname  start    end   mdl trunc   gc  description
 ----   --------- ------ -----  --------- ------ ------   --- ----- ----  -----------
  (1) !   1.2e-20   98.7   0.1  U2        681858 681747 -  cm    no 0.33  U2 spliceosomal RNA


Hit alignments:
>> U2  U2 spliceosomal RNA
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   1.2e-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 sequence(s):                                               1  (1626368 residues searched)
Query sequences re-searched for truncated hits:                  1  (1166.7 residues re-searched, avg per model)
Target model(s):                                                 3  (664 consensus positions)
Windows   passing  local HMM SSV           filter:            6996  (0.3917); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:            1952  (0.1271); expected (0.005)
Windows   passing  local HMM Forward  bias filter:             311  (0.02308); expected (0.005)
Windows   passing glocal HMM Forward       filter:             162  (0.01766); expected (0.005)
Windows   passing glocal HMM Forward  bias filter:             104  (0.01062); expected (0.005)
Envelopes passing glocal HMM envelope defn filter:             109  (0.004945); expected (0.005)
Envelopes passing  local CM  CYK           filter:               7  (0.0001391); expected (0.0001)
Total CM hits reported:                                          1  (2.294e-05); includes 0 truncated hit(s)

# CPU time: 10.01u 0.30s 00:00:10.31 Elapsed: 00:00:09.27
//
Query:       ENA|BK006937|BK006937.2  [L=316620]
Hit scores:
 rank     E-value  score  bias  modelname  start    end   mdl trunc   gc  description
 ----   --------- ------ -----  --------- ------ ------   --- ----- ----  -----------
 ------ inclusion threshold ------
  (1) ?       2.4   14.1   0.3  5S_rRNA      761    644 -  cm    no 0.41  5S ribosomal RNA
  (2) ?       4.7   11.1   0.1  U2        229986 229885 -  cm    no 0.32  U2 spliceosomal RNA


Hit alignments:
>> 5S_rRNA  5S ribosomal RNA
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) ?       2.4   14.1   0.3  cm        1      119 []         761         644 - .. 0.90    no 0.41

                              v             v  v                 v        v                 v   v                    NC
                              (((((((((,,,,<<-<<.<<<.---<<--<<<<.<<______>>-->>>>-->>---->>>>>-->><<<-<<----<-<<---- CS
                  5S_rRNA   1 gccuGcggcCAUAccagc.gcg.aAagcACcgGa.uCCCAUCcGaACuCcgAAguUAAGcgcgcUugggCcagggUAGUAcuagGa 83 
                               : :: ::: AUAC +   ::     G: C::::  CC AUC+G   ::::AA:U AAG ::  U+ GGC:  :G  GUA :+GGA
  ENA|BK006937|BK006937.2 761 GAGAUGGUAUAUACUGUAgCAUcCGUGUGCGUAUgACCGAUCAGA--AUACAAGUGAAGGUGAGUAUGGCAUGUG--GUAGUGGGA 680
                              **************9753244314478889999889999999999..89**********9999999*********..********* PP

                                                                 v  NC
                              -<<____>>----->>->-->>->>>.))))))))): CS
                  5S_rRNA  84 UGgGuGAcCuCcUGggAAgaccagGu.gccgCaggcc 119
                              U :G G :     G: AAG+: A:GU ::: :: : C
  ENA|BK006937|BK006937.2 679 UUAGAG-UGGUAGGAUAAGUAUAUGUgUAUUAUUUAC 644
                              *99988.689999************************ PP

>> U2  U2 spliceosomal RNA
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) ?       4.7   11.1   0.1  cm        1      193 []      229986      229885 - .. 0.83    no 0.32

                                         v        v                        v              v     v           v     NC
                                 ::::::<<<-~~~~~~->>>,,,,,,,,,,,,,,,,,,,,<<<<<<________>>>>>>,<<<<<<<___>>>>>>>,, CS
                       U2      1 AUacCUUCuc*[12]*aaGAUCAAGUGUAGUAUCUGUUCUUauCAGUuUAAuAuCUGauAuggcccccAuugggggccaa 86    
                                   A CUU  +      +  AUCAAGUGUAG AUCU UU  :A : : UU  +A+: : U: G: ::::A U::::+:CAA
  ENA|BK006937|BK006937.2 229986 UCAACUUGUU*[ 4]*UUCAUCAAGUGUAGAAUCUAUUUCAAAAUACUUCCCAAUGUCUU-GU-AAGGAGUCCUUUACAA 229911
                                 *******876...4..589****************9999888888888888888888888.88.5566666888888899 PP

                                                                 NC
                                 ,,,,,,,,,,,,,,,,,,~~~~~~::::::: CS
                       U2     87 uuauaUUAaauuaAUUUU*[82]*Acccuuu 193   
                                 +U+ AU A     AUUUU      ACC+UU 
  ENA|BK006937|BK006937.2 229910 AUUCAUAACCACGAUUUU*[ 1]*ACCUUUG 229885
                                 888888888888888876...8..******* PP



Internal CM pipeline statistics summary:
----------------------------------------
Query sequence(s):                                               1  (633240 residues searched)
Query sequences re-searched for truncated hits:                  1  (1166.7 residues re-searched, avg per model)
Target model(s):                                                 3  (664 consensus positions)
Windows   passing  local HMM SSV           filter:            2708  (0.3858); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:            1345  (0.2002); expected (0.02)
Windows   passing  local HMM Forward  bias filter:             470  (0.08163); expected (0.02)
Windows   passing glocal HMM Forward       filter:             181  (0.05878); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:              99  (0.03068); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:             111  (0.01272); expected (0.02)
Envelopes passing  local CM  CYK           filter:               6  (0.0003184); expected (0.0001)
Total CM hits reported:                                          2  (0.0001156); includes 0 truncated hit(s)

# CPU time: 10.51u 0.39s 00:00:10.90 Elapsed: 00:00:09.15
//
[ok]
