t/data/cmsearch.multi.out

   1 # cmsearch :: search CM(s) against a sequence database
   2 # INFERNAL 1.1.1 (July 2014)
   3 # Copyright (C) 2014 Howard Hughes Medical Institute.
   4 # Freely distributed under the GNU General Public License (GPLv3).
   5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   6 # query CM file:                         multimodel.c.cm
   7 # target sequence database:              multiseqs.fa
   8 # number of worker threads:              4
   9 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  10
  11 Query:       tRNA5  [CLEN=72]
  12 Hit scores:
  13  rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
  14  ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
  15   (1) !   2.9e-21   71.5   0.0  mrum-tRNA.1         1     72 +  cm    no 0.50  -
  16   (2) !     2e-20   68.8   0.0  mrum-tRNA.2         1     73 +  cm    no 0.67  -
  17   (3) !   6.1e-19   64.1   0.0  mrum-tRNA.3         1     74 +  cm    no 0.59  -
  18   (4) !     2e-18   62.5   0.0  mrum-tRNA.4         1     75 +  cm    no 0.61  -
  19   (5) !   2.1e-18   62.4   0.0  AAGA01015927.1    229    302 +  cm    no 0.62  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
  20   (6) !   3.6e-18   61.7   0.0  mrum-tRNA.5         1     74 +  cm    no 0.53  -
  21   (7) !   2.2e-17   59.2   0.0  mrum-tRNA.6         1     73 +  cm    no 0.51  -
  22   (8) !   2.2e-17   59.2   0.0  mrum-tRNA.7         1     75 +  cm    no 0.60  -
  23   (9) !   2.4e-17   59.1   0.0  mrum-tRNA.8         1     74 +  cm    no 0.59  -
  24  (10) !   2.7e-17   58.9   0.0  mrum-tRNA.9         1    110 +  cm    no 0.61  -
  25  (11) !   8.7e-17   57.3   0.0  mrum-tRNA.10        1     72 +  cm    no 0.42  -
  26  (12) !   1.4e-15   53.5   0.0  AAGA01015927.1    314    386 +  cm    no 0.59  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
  27
  28
  29 Hit alignments:
  30 >> mrum-tRNA.1
  31  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  32  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  33   (1) !   2.9e-21   71.5   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.50
  34
  35                    v                                             v             v     v    NC
  36                  (((((((,,<<<<_______>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  37         tRNA5  1 gCcggcAUAGcgcAgUGGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  38                  G: G::AUAGC:CA+UGG AG:GCG:::G:CUG+CA :C:::AGGU : GGGUUCGAUUCCC :U::C :CA
  39   mrum-tRNA.1  1 GGAGCUAUAGCUCAAUGGCAGAGCGUUUGGCUGACAUCCAAAAGGUUAUGGGUUCGAUUCCCUUUAGCCCCA 72
  40                  ************************************************************************ PP
  41
  42 >> mrum-tRNA.2
  43  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  44  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  45   (2) !     2e-20   68.8   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.67
  46
  47                                                                                            NC
  48                  (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  49         tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  50                  G::::C UAGC:CAGU GG AG:GCGC:::CCU+ CAAG:::GAGG CC:GGGUUC A UCCC:G G::::CA
  51   mrum-tRNA.2  1 GGGCCCGUAGCUCAGUuGGGAGAGCGCUGCCCUUGCAAGGCAGAGGCCCCGGGUUCAAAUCCCGGUGGGUCCA 73
  52                  ************************************************************************* PP
  53
  54 >> mrum-tRNA.3
  55  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  56  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  57   (3) !   6.1e-19   64.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59
  58
  59                                                                                             NC
  60                  (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  61         tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  62                  G::::CAUAGC::AG   GGUA::GCGC :G:CU + AA:C: GA GUC::GGGUUCGA UCCC::UG::::CA
  63   mrum-tRNA.3  1 GGGCCCAUAGCUUAGCcaGGUAGAGCGCUCGGCUCAUAACCGGGAUGUCAUGGGUUCGAAUCCCAUUGGGCCCA 74
  64                  ************************************************************************** PP
  65
  66 >> mrum-tRNA.4
  67  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  68  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  69   (4) !     2e-18   62.5   0.0  cm        1       72 []           1          75 + [] 1.00    no 0.61
  70
  71                             v            v                                                   NC
  72                  (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  73         tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  74                  :::::::U+GC CAG   GGU AG GCGC::G:CUG+ AA:C::GAGGUCC:GGGUUCGA UCCC:G:::::::A
  75   mrum-tRNA.4  1 AGGCUAGUGGCACAGCcuGGUcAGCGCGCACGGCUGAUAACCGUGAGGUCCUGGGUUCGAAUCCCAGCUAGCCUA 75
  76                  ***************999********************************************************* PP
  77
  78 >> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
  79  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  80  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  81   (5) !   2.1e-18   62.4   0.0  cm        1       72 []         229         302 + .. 1.00    no 0.62
  82
  83                                                                                                 NC
  84                      (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  85            tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  86                      G::::::UA:::CAGU GGU AG:::+CC:GCCUGUCA+GC:GG GGU  :GGGUUCGA UCCC: ::::::C+
  87   AAGA01015927.1 229 GGAGCGGUAGUUCAGUcGGUuAGAAUACCUGCCUGUCACGCAGGGGGUUGCGGGUUCGAGUCCCGUCCGUUCCG 302
  88                      ************************************************************************** PP
  89
  90 >> mrum-tRNA.5
  91  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  92  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  93   (6) !   3.6e-18   61.7   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.53
  94
  95                                                                                             NC
  96                  (((((((,,<<<<___..____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
  97         tRNA5  1 gCcggcAUAGcgcAgU..GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
  98                  :CCG:C:UAGC:CA+U  GG AG:GCG:::G:CUGU++A:C:::A GU :::GGUUC A UCC::::G:CGG:A
  99   mrum-tRNA.5  1 CCCGACUUAGCUCAAUuuGGCAGAGCGUUGGACUGUAGAUCCAAAUGUUGCUGGUUCAAGUCCGGCAGUCGGGA 74
 100                  ************************************************************************** PP
 101
 102 >> mrum-tRNA.6
 103  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 104  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 105   (7) !   2.2e-17   59.2   0.0  cm        1       72 []           1          73 + [] 1.00    no 0.51
 106
 107                                                                                             NC
 108                  (((((((,,<<<<___.___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 109         tRNA5  1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 110                  GC::::AU+G G:A+U GG  A:C C+:C:G:CU+UC+A:C:G:  +  C:GGGUUC A UCCC:GU::::GCA
 111   mrum-tRNA.6  1 GCUUCUAUGGGGUAAUcGGCaAACCCAUCGGACUUUCGAUCCGAUAA-UCCGGGUUCAAAUCCCGGUAGAAGCA 73
 112                  ***********************************************.9************************* PP
 113
 114 >> mrum-tRNA.7
 115  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 116  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 117   (8) !   2.2e-17   59.2   0.0  cm        1       72 []           1          75 + [] 0.99    no 0.60
 118
 119                                                                                               NC
 120                  (((((((,,<<<<___..___.._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 121         tRNA5  1 gCcggcAUAGcgcAgU..GGu..AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 122                  GC::::AU+::G:AGU  GG   A:C:: :C:GCCU+UC+AGC:G:AG+ C :GGGUUCGA UCCC: U::::GCA
 123   mrum-tRNA.7  1 GCUCCGAUGGUGUAGUccGGCcaAUCAUUUCGGCCUUUCGAGCCGAAGA-CUCGGGUUCGAAUCCCGGUCGGAGCA 75
 124                  ********************9999*************************.************************** PP
 125
 126 >> mrum-tRNA.8
 127  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 128  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 129   (9) !   2.4e-17   59.1   0.0  cm        1       72 []           1          74 + [] 1.00    no 0.59
 130
 131                              v          v                                                    NC
 132                  (((((((,,<<<<___..___._>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 133         tRNA5  1 gCcggcAUAGcgcAgU..GGu.AgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 134                  GC:G:::UAG:: AG   GGU A ::C C:A:CCUG CA+G:U:GAG+ CC:GGGUUC A UCCC:G:::C:GCA
 135   mrum-tRNA.8  1 GCGGUGUUAGUCCAGCcuGGUuAAGACUCUAGCCUGCCACGUUAGAGA-CCCGGGUUCAAAUCCCGGACGCCGCA 74
 136                  ***************999******************************.************************** PP
 137
 138 >> mrum-tRNA.9
 139  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 140  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 141  (10) !   2.7e-17   58.9   0.0  cm        1       72 []           1         110 + [] 0.98    no 0.61
 142
 143                                                                                                NC
 144                   (((((((,,<<<<___.___._>>>>,<<<<<___~~~~~~>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 145         tRNA5   1 gCcggcAUAGcgcAgU.GGu.AgcgCgccagccUg*[ 4]*gcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 146                   GCCGG::U+GC:CAG  GGU AG:GCGC::G:CU       :C::GAG+UC::GGGUUCGA UCCC::::CCGGCA
 147   mrum-tRNA.9   1 GCCGGGGUGGCUCAGCuGGUuAGAGCGCACGGCUC*[40]*CCGUGAGAUCGCGGGUUCGAAUCCCGCCCCCGGCA 110
 148                   ********************************995...*..*********************************** PP
 149
 150 >> mrum-tRNA.10
 151  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 152  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 153  (11) !   8.7e-17   57.3   0.0  cm        1       72 []           1          72 + [] 1.00    no 0.42
 154
 155                                             v               v                               NC
 156                   (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 157          tRNA5  1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 158                   G:::::AUAG:::A+  GGUA:::C+ C G:CUGU AA:C G AG+  :G :GUUCGA UC: C:U:::::C+
 159   mrum-tRNA.10  1 GGUUCUAUAGUUUAACaGGUAAAACAACUGGCUGUUAACCGGCAGA-UAGGAGUUCGAAUCUUCUUAGAACCG 72
 160                   **********************************************.9************************* PP
 161
 162 >> AAGA01015927.1  Metagenome sequence AHAI1002.g1, whole genome shotgun sequence
 163  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 164  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 165  (12) !   1.4e-15   53.5   0.0  cm        1       72 []         314         386 + .. 1.00    no 0.59
 166
 167                                                                                                NC
 168                      (((((((,,<<<<___.____>>>>,<<<<<_______>>>>>,,,,,<<<<<_______>>>>>))))))): CS
 169            tRNA5   1 gCcggcAUAGcgcAgU.GGuAgcgCgccagccUgucAagcuggAGgUCCgggGUUCGAUUCcccGUgccgGca 72
 170                      :::GGC:UAG :CA+U GGUAG: C+CC:G:CU  +AA:C:GG  GU : G:GUUCGA UC:C ::GCC:::+
 171   AAGA01015927.1 314 AGGGGCGUAGUUCAAUuGGUAGAGCACCGGUCUCCAAAACCGGGUGUUGGGAGUUCGAGUCUCUCCGCCCCUG 386
 172                      ************************************************************************* PP
 173
 174
 175
 176 Internal CM pipeline statistics summary:
 177 ----------------------------------------
 178 Query model(s):                                                  1  (72 consensus positions)
 179 Target sequences:                                               13  (12958 residues searched)
 180 Target sequences re-searched for truncated hits:                13  (5412 residues re-searched)
 181 Windows   passing  local HMM SSV           filter:              81  (0.3848); expected (0.35)
 182 Windows   passing  local HMM Viterbi       filter:                  (off)
 183 Windows   passing  local HMM Viterbi  bias filter:                  (off)
 184 Windows   passing  local HMM Forward       filter:              50  (0.2035); expected (0.02)
 185 Windows   passing  local HMM Forward  bias filter:              48  (0.195); expected (0.02)
 186 Windows   passing glocal HMM Forward       filter:              42  (0.1794); expected (0.02)
 187 Windows   passing glocal HMM Forward  bias filter:              42  (0.1794); expected (0.02)
 188 Envelopes passing glocal HMM envelope defn filter:              43  (0.1724); expected (0.02)
 189 Envelopes passing  local CM  CYK           filter:              40  (0.1612); expected (0.0001)
 190 Total CM hits reported:                                         12  (0.05003); includes 0 truncated hit(s)
 191
 192 # CPU time: 0.42u 0.01s 00:00:00.43 Elapsed: 00:00:00.44
 193 //
 194 Query:       Cobalamin  [CLEN=191]
 195 Accession:   RF00174
 196 Description: Cobalamin riboswitch
 197 Hit scores:
 198  rank     E-value  score  bias  sequence        start    end   mdl trunc   gc  description
 199  ----   --------- ------ -----  -------------- ------ ------   --- ----- ----  -----------
 200   (1) !   1.4e-08   30.0   0.0  AAFY01022046.1    934    832 -  cm    5' 0.48  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
 201
 202
 203 Hit alignments:
 204 >> AAFY01022046.1  Metagenome sequence AGZO15064.g2, whole genome shotgun sequence
 205  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
 206  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
 207   (1) !   1.4e-08   30.0   0.0  cm       32      191 ~]         934         832 - ~. 0.92    5' 0.48
 208
 209                                  ???              v           v      v    v                                     ???? NC
 210                      ~~~~~~______>>>,,,,,(((,,,<.<<<<_______>>>>>,,<<<____>>>,<<<---<<<<~~~~~~>>>>---->>>,,,,)))]]]] CS
 211        Cobalamin   1 <[31]*agugaaggguuAAaaGGGAAc.ccGGUGaaAaUCCgggGCuGcCCCCgCaACuGUAAgcGg*[61]*cCgcgAGcCaGGAGACCuGCCa 174
 212                              +G+     + AA: GGAA: : GGUG AAAUCC ::+C:G CCC  C:ACUGUAA:C:        :G:+AG+CAG A AC :  C
 213   AAFY01022046.1 934 <[ 0]*GUAGGCAAAAGGAAGAGGAAGgAUGGUGGAAAUCCUUCACGGGCCCGGCCACUGUAACCAG*[ 4]*UUGGAAGUCAG-AUACUCUUCU 849
 214                      ......44455566666899******989************************************97...7..79*********.9********* PP
 215
 216                      ??                NC
 217                      ]]::::::::::::::: CS
 218        Cobalamin 175 ucaguuuuugaaucucc 191
 219                        ++++   GAA+CU C
 220   AAFY01022046.1 848 AUUAAGGCGGAAACUAC 832
 221                      ***************** PP
 222
 223
 224
 225 Internal CM pipeline statistics summary:
 226 ----------------------------------------
 227 Query model(s):                                                  1  (191 consensus positions)
 228 Target sequences:                                               13  (12958 residues searched)
 229 Target sequences re-searched for truncated hits:                13  (10152 residues re-searched)
 230 Windows   passing  local HMM SSV           filter:              10  (0.207); expected (0.35)
 231 Windows   passing  local HMM Viterbi       filter:                  (off)
 232 Windows   passing  local HMM Viterbi  bias filter:                  (off)
 233 Windows   passing  local HMM Forward       filter:               2  (0.03116); expected (0.02)
 234 Windows   passing  local HMM Forward  bias filter:               2  (0.03116); expected (0.02)
 235 Windows   passing glocal HMM Forward       filter:               1  (0.01558); expected (0.02)
 236 Windows   passing glocal HMM Forward  bias filter:               1  (0.01558); expected (0.02)
 237 Envelopes passing glocal HMM envelope defn filter:               1  (0.008784); expected (0.02)
 238 Envelopes passing  local CM  CYK           filter:               1  (0.005712); expected (0.0001)
 239 Total CM hits reported:                                          1  (0.008914); includes 1 truncated hit(s)
 240
 241 # CPU time: 0.16u 0.01s 00:00:00.17 Elapsed: 00:00:00.17
 242 //
 243 [ok]