# cmsearch :: search CM(s) against a sequence database
# INFERNAL 1.1.1 (July 2014)
# Copyright (C) 2014 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query CM file:                         multimodel.c.cm
# target sequence database:              multiseqs.fa
# number of worker threads:              4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       tRNA5  [CLEN=72]
Hit scores:
 rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
 ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
  (1) !   2.9e-21   71.5   0.0  mrum-tRNA.1         1     72 +  cm    no 0.50  -
  (2) !     2e-20   68.8   0.0  mrum-tRNA.2         1     73 +  cm    no 0.67  -
  (3) !   6.1e-19   64.1   0.0  mrum-tRNA.3         1     74 +  cm    no 0.59  -
  (4) !     2e-18   62.5   0.0  mrum-tRNA.4         1     75 +  cm    no 0.61  -
  (5) !   2.1e-18   62.4   0.0  AAGA01015927.1    229    302 +  cm    no 0.62  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
  (6) !   3.6e-18   61.7   0.0  mrum-tRNA.5         1     74 +  cm    no 0.53  -
  (7) !   2.2e-17   59.2   0.0  mrum-tRNA.6         1     73 +  cm    no 0.51  -
  (8) !   2.2e-17   59.2   0.0  mrum-tRNA.7         1     75 +  cm    no 0.60  -
  (9) !   2.4e-17   59.1   0.0  mrum-tRNA.8         1     74 +  cm    no 0.59  -
 (10) !   2.7e-17   58.9   0.0  mrum-tRNA.9         1    110 +  cm    no 0.61  -
 (11) !   8.7e-17   57.3   0.0  mrum-tRNA.10        1     72 +  cm    no 0.42  -
 (12) !   1.4e-15   53.5   0.0  AAGA01015927.1    314    386 +  cm    no 0.59  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence


Hit alignments:
>> mrum-tRNA.1  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   2.9e-21   71.5   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.50

                   v                                             v             v     v    NC
                 (((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G: G::AUAGC:CA+UGG AG:GCG:::G:CUG+CA :C:::AGGU : GGGUUCGAUUCCC :U::C :CA
  mrum-tRNA.1  1 GGAGCUAUAGCUCAAUGGCAGAGCGUUUGGCUGACAUCCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA 72
                 ************************************************************************ PP

>> mrum-tRNA.2  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (2) !     2e-20   68.8   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.67

                                                                                           NC
                 (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G::::C UAGC:CAGU GG AG:GCGC:::CCU+ CAAG:::GAGG CC:GGGUUC A UCCC:G G::::CA
  mrum-tRNA.2  1 GGGCCCGUAGCUCAGUuGGGAGAGCGCUGCCCUUGCAAGGCAGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA 73
                 ************************************************************************* PP

>> mrum-tRNA.3  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (3) !   6.1e-19   64.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59

                                                                                            NC
                 (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 G::::CAUAGC::AG   GGUA::GCGC :G:CU + AA:C: GA GUC::GGGUUCGA UCCC::UG::::CA
  mrum-tRNA.3  1 GGGCCCAUAGCUUAGCcaGGUAGAGCGCUCGGCUCAUAACCGGGAUGUCAUGGGUUCGAAUCCCAUUGGGCCCA 74
                 ************************************************************************** PP

>> mrum-tRNA.4  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (4) !     2e-18   62.5   0.0  cm        1       72 []           1          75 + [] 1.00    no 0.61

                            v            v                                                   NC
                 (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 :::::::U+GC CAG   GGU AG GCGC::G:CUG+ AA:C::GAGGUCC:GGGUUCGA UCCC:G:::::::A
  mrum-tRNA.4  1 AGGCUAGUGGCACAGCcuGGUcAGCGCGCACGGCUGAUAACCGUGAGGUCCUGGGUUCGAAUCCCAGCUAGCCUA 75
                 ***************999********************************************************* PP

>> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (5) !   2.1e-18   62.4   0.0  cm        1       72 []         229         302 + .. 1.00    no 0.62

                                                                                                NC
                     (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
           tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                     G::::::UA:::CAGU GGU AG:::+CC:GCCUGUCA+GC:GG GGU  :GGGUUCGA UCCC: ::::::C+
  AAGA01015927.1 229 GGAGCGGUAGUUCAGUcGGUuAGAAUACCUGCCUGUCACGCAGGGGGUUGCGGGUUCGAGUCCCGUCCGUUCCG 302
                     ************************************************************************** PP

>> mrum-tRNA.5  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (6) !   3.6e-18   61.7   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.53

                                                                                            NC
                 (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 :CCG:C:UAGC:CA+U  GG AG:GCG:::G:CUGU++A:C:::A GU :::GGUUC A UCC::::G:CGG:A
  mrum-tRNA.5  1 CCCGACUUAGCUCAAUuuGGCAGAGCGUUGGACUGUAGAUCCAAAUGUUGCUGGUUCAAGUCCGGCAGUCGGGA 74
                 ************************************************************************** PP

>> mrum-tRNA.6  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (7) !   2.2e-17   59.2   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.51

                                                                                            NC
                 (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC::::AU+G G:A+U GG  A:C C+:C:G:CU+UC+A:C:G:  +  C:GGGUUC A UCCC:GU::::GCA
  mrum-tRNA.6  1 GCUUCUAUGGGGUAAUcGGCaAACCCAUCGGACUUUCGAUCCGAUAA-UCCGGGUUCAAAUCCCGGUAGAAGCA 73
                 ***********************************************.9************************* PP

>> mrum-tRNA.7  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (8) !   2.2e-17   59.2   0.0  cm        1       72 []           1          75 + [] 0.99    no 0.60

                                                                                              NC
                 (((((((,,<<<<___..___.._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu..AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC::::AU+::G:AGU  GG   A:C:: :C:GCCU+UC+AGC:G:AG+ C :GGGUUCGA UCCC: U::::GCA
  mrum-tRNA.7  1 GCUCCGAUGGUGUAGUccGGCcaAUCAUUUCGGCCUUUCGAGCCGAAGA-CUCGGGUUCGAAUCCCGGUCGGAGCA 75
                 ********************9999*************************.************************** PP

>> mrum-tRNA.8  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (9) !   2.4e-17   59.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59

                             v          v                                                    NC
                 (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                 GC:G:::UAG:: AG   GGU A ::C C:A:CCUG CA+G:U:GAG+ CC:GGGUUC A UCCC:G:::C:GCA
  mrum-tRNA.8  1 GCGGUGUUAGUCCAGCcuGGUuAAGACUCUAGCCUGCCACGUUAGAGA-CCCGGGUUCAAAUCCCGGACGCCGCA 74
                 ***************999******************************.************************** PP

>> mrum-tRNA.9  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (10) !   2.7e-17   58.9   0.0  cm        1       72 []           1         110 + [] 0.98    no 0.61

                                                                                               NC
                  (((((((,,<<<<___.___._>>>>,<<<<<___~~~~~~>>>>>,,,,,<<<<<_______>>>>>))))))): CS
        tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUg*[ 4]*gcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                  GCCGG::U+GC:CAG  GGU AG:GCGC::G:CU       :C::GAG+UC::GGGUUCGA UCCC::::CCGGCA
  mrum-tRNA.9   1 GCCGGGGUGGCUCAGCuGGUuAGAGCGCACGGCUC*[40]*CCGUGAGAUCGCGGGUUCGAAUCCCGCCCCCGGCA 110
                  ********************************995...*..*********************************** PP

>> mrum-tRNA.10  
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (11) !   8.7e-17   57.3   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.42

                                            v               v                               NC
                  (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
         tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
                  G:::::AUAG:::A+  GGUA:::C+ C G:CUGU AA:C G AG+  :G :GUUCGA UC: C:U:::::C+
  mrum-tRNA.10  1 GGUUCUAUAGUUUAACaGGUAAAACAACUGGCUGUUAACCGGCAGA-UAGGAGUUCGAAUCUUCUUAGAACCG 72
                  **********************************************.9************************* PP

>> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 (12) !   1.4e-15   53.5   0.0  cm        1       72 []         314         386 + .. 1.00    no 0.59

                                                                                               NC
                     (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
           tRNA5   1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72 
                     :::GGC:UAG :CA+U GGUAG: C+CC:G:CU  +AA:C:GG  GU : G:GUUCGA UC:C ::GCC:::+
  AAGA01015927.1 314 AGGGGCGUAGUUCAAUuGGUAGAGCACCGGUCUCCAAAACCGGGUGUUGGGAGUUCGAGUCUCUCCGCCCCUG 386
                     ************************************************************************* PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (72 consensus positions)
Target sequences:                                               13  (12958 residues searched)
Target sequences re-searched for truncated hits:                13  (5412 residues re-searched)
Windows   passing  local HMM SSV           filter:              81  (0.3848); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:              50  (0.2035); expected (0.02)
Windows   passing  local HMM Forward  bias filter:              48  (0.195); expected (0.02)
Windows   passing glocal HMM Forward       filter:              42  (0.1794); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:              42  (0.1794); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:              43  (0.1724); expected (0.02)
Envelopes passing  local CM  CYK           filter:              40  (0.1612); expected (0.0001)
Total CM hits reported:                                         12  (0.05003); includes 0 truncated hit(s)

# CPU time: 0.42u 0.01s 00:00:00.43 Elapsed: 00:00:00.44
//
Query:       Cobalamin  [CLEN=191]
Accession:   RF00174
Description: Cobalamin riboswitch
Hit scores:
 rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
 ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
  (1) !   1.4e-08   30.0   0.0  AAFY01022046.1    934    832 -  cm    5' 0.48  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence


Hit alignments:
>> AAFY01022046.1  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
 rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  (1) !   1.4e-08   30.0   0.0  cm       32      191 ~]         934         832 - ~. 0.92    5' 0.48

                                 ???              v           v      v    v                                     ???? NC
                     ~~~~~~______>>>,,,,,(((,,,<.<<<<_______>>>>>,,<<<____>>>,<<<---<<<<~~~~~~>>>>---->>>,,,,)))]]]] CS
       Cobalamin   1 <[31]*agugaaggguuAAaaGGGAAc.ccGGUGaaAaUCCgggGCuGcCCCCgCaACuGUAAgcGg*[61]*cCgcgAGcCaGGAGACCuGCCa 174
                             +G+     + AA: GGAA: : GGUG AAAUCC ::+C:G CCC  C:ACUGUAA:C:        :G:+AG+CAG A AC :  C 
  AAFY01022046.1 934 <[ 0]*GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCACUGUAACCAG*[ 4]*UUGGAAGUCAG-AUACUCUUCU 849
                     ......44455566666899******989************************************97...7..79*********.9********* PP

                     ??                NC
                     ]]::::::::::::::: CS
       Cobalamin 175 ucaguuuuugaaucucc 191
                       ++++   GAA+CU C
  AAFY01022046.1 848 AUUAAGGCGGAAACUAC 832
                     ***************** PP



Internal CM pipeline statistics summary:
----------------------------------------
Query model(s):                                                  1  (191 consensus positions)
Target sequences:                                               13  (12958 residues searched)
Target sequences re-searched for truncated hits:                13  (10152 residues re-searched)
Windows   passing  local HMM SSV           filter:              10  (0.207); expected (0.35)
Windows   passing  local HMM Viterbi       filter:                  (off)
Windows   passing  local HMM Viterbi  bias filter:                  (off)
Windows   passing  local HMM Forward       filter:               2  (0.03116); expected (0.02)
Windows   passing  local HMM Forward  bias filter:               2  (0.03116); expected (0.02)
Windows   passing glocal HMM Forward       filter:               1  (0.01558); expected (0.02)
Windows   passing glocal HMM Forward  bias filter:               1  (0.01558); expected (0.02)
Envelopes passing glocal HMM envelope defn filter:               1  (0.008784); expected (0.02)
Envelopes passing  local CM  CYK           filter:               1  (0.005712); expected (0.0001)
Total CM hits reported:                                          1  (0.008914); includes 1 truncated hit(s)

# CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.17
//
[ok]
