t/data/cmsearch_output.txt

   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:                         RF00174.cm
   7 # target sequence database:              NC_000913.fna
   8 # CM configuration:                      glocal
   9 # number of worker threads:              16
  10 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  11
  12 Query:       Cobalamin  [CLEN=191]
  13 Accession:   RF00174
  14 Hit scores:
  15  rank     E-value  score  bias  sequence                        start     end   mdl trunc   gc  description
  16  ----   --------- ------ -----  ----------------------------- ------- -------   --- ----- ----  -----------
  17   (1) !   8.7e-16   98.2   0.0  gi|556503834|ref|NC_000913.3| 4163384 4163574 +  cm    no 0.54  Escherichia coli str. K-12 substr. MG1655, com
  18  ------ inclusion threshold ------
  19   (2) ?      0.63    8.4   0.0  gi|556503834|ref|NC_000913.3| 4593356 4593565 +  cm    no 0.53  Escherichia coli str. K-12 substr. MG1655, com
  20
  21
  22 Hit alignments:
  23 >> gi|556503834|ref|NC_000913.3|  Escherichia coli str. K-12 substr. MG1655, complete genome
  24  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  25  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  26   (1) !   8.7e-16   98.2   0.0  cm        1      191 []     4163384     4163574 + .. 0.98    no 0.54
  27
  28                                                                v              v                                  NC
  29                                         :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS
  30                       Cobalamin       1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72
  31                                          U +A  ++ +   UG::GGU C : U          : GUUAA AGGGAA:CC:GUG++AAUC:GG:GCUG
  32   gi|556503834|ref|NC_000913.3| 4163384 CUGUAGCAUCCACUUGCCGGU-CCUGU----------GAGUUAAUAGGGAAUCCAGUGCGAAUCUGGAGCUG 4163444
  33                                         *********************.98888..........99********************************* PP
  34
  35                                         v    v            v                                                      NC
  36                                         <____>>>,<<<---<<<<------<<<<<<-----......<<<-<<<<<<______>>>>>>--->>>>> CS
  37                       Cobalamin      73 cCCCCgCaACuGUAAgcGgagagcaccccccAauAa......GCCACUggcccgcaagggccGGGAAGGCgg 138
  38                                           C C CA+C:GUAAG:: AG+ ++::::::  + +      G:CACU::C   +++  G::GGGAAG:C::
  39   gi|556503834|ref|NC_000913.3| 4163445 A-CGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACUGCC--AUUC--GGUGGGAAGUCAU 4163511
  40                                         *.*********************************9***************..5555..************* PP
  41
  42                                                                 v                                       NC
  43                                         >>>>----------..........>>>>---->>>,,,,)))]]]]]]::::::::::::::: CS
  44                       Cobalamin     139 ggggaaggaaugac..........cCgcgAGcCaGGAGACCuGCCaucaguuuuugaaucucc 191
  45                                         ::::   +A+U+ C           ::C+AGCC:G+AGACCUGCC::C ++  U G AUCU
  46   gi|556503834|ref|NC_000913.3| 4163512 CAUCUCUUAGUAUCuuagauacccCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG 4163574
  47                                         **********9998************************************************* PP
  48
  49 >> gi|556503834|ref|NC_000913.3|  Escherichia coli str. K-12 substr. MG1655, complete genome
  50  rank     E-value  score  bias mdl mdl from   mdl to       seq from      seq to       acc trunc   gc
  51  ----   --------- ------ ----- --- -------- --------    ----------- -----------      ---- ----- ----
  52   (2) ?      0.63    8.4   0.0  cm        1      191 []     4593356     4593565 + .. 0.72    no 0.53
  53
  54                                                        v                                    v             v   v  NC
  55                                         :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<< CS
  56                       Cobalamin       1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuG 72
  57                                           A AUU+A+++    :UGG  :C +U ++  G     G: +AA : GGAA:  G         C  :+  G
  58   gi|556503834|ref|NC_000913.3| 4593356 GGAGAUUAAUCUUUACGUGGG-UCGUUGAUCGG---CUGACGAACCAGGAAGAUGU-------ACGCCAGUG 4593416
  59                                         *********************.88877554444...5777779*********9996.......7999***** PP
  60
  61                                                v       v  v       vvvvvv     vvv    vvv                          NC
  62                                         <____>>>,<<<---<<<<.------<<<<<<-----<<<-<<<<<<_____.................... CS
  63                       Cobalamin      73 cCCCCgCaACuGUAAgcGg.agagcaccccccAauAaGCCACUggcccgcaa.................... 123
  64                                         CCCCCGC +C GU+A ::     GCA ++ ++ A   GCCA   G+C G
  65   gi|556503834|ref|NC_000913.3| 4593417 CCCCCGCUGCGGUGACGCAa-CCGCAGAUGAUUAGU-GCCA---GACGG---aaugagugggugguaucaac 4593480
  66                                         ***************88873.333333333333333.4544...33333...44566655444444444444 PP
  67
  68                                                   vvv      vvvvvvvvv                                             NC
  69                                         ........._>>>>>>--->>>>>>>>>----------.................................. CS
  70                       Cobalamin     124 .........gggccGGGAAGGCggggggaaggaaugac.................................. 152
  71
  72   gi|556503834|ref|NC_000913.3| 4593481 aauaaaacc-----------------------------aguaaugaucggcgcaaaagaggcgcagaugaag 4593523
  73                                         444444444.............................5666666666666666666666666777777777 PP
  74
  75                                           v  v                    v                NC
  76                                         ..>>>>----.>>>,,,,)))]]]]]]::::::::::::::: CS
  77                       Cobalamin     153 ..cCgcgAGc.CaGGAGACCuGCCaucaguuuuugaaucucc 191
  78                                            :: +AG+ C GGA AC : CCA:  + + + + AU
  79   gi|556503834|ref|NC_000913.3| 4593524 cuGGCAAAGUuCUGGAUACUGCCCACCGACGCAGUCAUGCGA 4593565
  80                                         76788899966******************************* PP
  81
  82
  83
  84 Internal CM pipeline statistics summary:
  85 ----------------------------------------
  86 Query model(s):                                                  1  (191 consensus positions)
  87 Target sequences:                                                1  (9283304 residues searched)
  88 Target sequences re-searched for truncated hits:                 1  (1840 residues re-searched)
  89 Windows   passing  local HMM SSV           filter:            7160  (0.4322); expected (0.35)
  90 Windows   passing  local HMM Viterbi       filter:                  (off)
  91 Windows   passing  local HMM Viterbi  bias filter:                  (off)
  92 Windows   passing  local HMM Forward       filter:             171  (0.01188); expected (0.005)
  93 Windows   passing  local HMM Forward  bias filter:             139  (0.0095); expected (0.005)
  94 Windows   passing glocal HMM Forward       filter:              76  (0.005795); expected (0.005)
  95 Windows   passing glocal HMM Forward  bias filter:              69  (0.005313); expected (0.005)
  96 Envelopes passing glocal HMM envelope defn filter:              70  (0.002021); expected (0.005)
  97 Envelopes passing glocal CM  CYK           filter:               2  (4.534e-05); expected (0.0001)
  98 Total CM hits reported:                                          2  (4.319e-05); includes 0 truncated hit(s)
  99
 100 # CPU time: 11.74u 1.00s 00:00:12.74 Elapsed: 00:00:02.27
 101 //
 102 [ok]