t/data/nhmmer-3.1.out

   1 # nhmmer :: search a DNA model or alignment against a DNA database
   2 # HMMER 3.1b1 (May 2013); http://hmmer.org/
   3 # Copyright (C) 2013 Howard Hughes Medical Institute.
   4 # Freely distributed under the GNU General Public License (GPLv3).
   5 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
   6 # query file:                      ../HMMs/A_HA_H7_CDS_nucleotide.hmm
   7 # target sequence database:        tmp.fa
   8 # number of worker threads:        4
   9 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
  10
  11 Query:       A_HA_H7_CDS_nucleotide  [M=1683]
  12 Scores for complete hits:
  13     E-value  score  bias  Sequence  start    end  Description
  14     ------- ------ -----  --------  -----  -----  -----------
  15     3.2e-48  148.2   5.7  seq1          1    151  Description of seq1
  16     3.9e-15   38.6   0.4  seq2         59      1  Description of seq2
  17
  18
  19 Annotation for each hit  (and alignments):
  20 >> seq1  Description of seq1
  21     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
  22    ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
  23  !  148.2   5.7   3.2e-48       258       411 ..         1       151 []         1       151 []       151    0.98
  24
  25   Alignment:
  26   score: 148.2 bits
  27   A_HA_H7_CDS_nucleotide 258 attcctagaattttcagctgatttaattattgagaggcgagaaggaagtaatgatgtctgttatcctgggaaattcgtaaatgaaga 344
  28                              attcctagaattttcagc+gatttaattattgagaggcgagaaggaagt   gatgtctgttatcctgggaaattcgt+aatgaaga
  29                     seq1   1 ATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGT---GATGTCTGTTATCCTGGGAAATTCGTGAATGAAGA 84
  30                              689*******************************************777...*********************************** PP
  31
  32   A_HA_H7_CDS_nucleotide 345 agctctgaggcaaattctcagggggtcaggcggaattgacaaggagacaatgggattcacatatagc 411
  33                              agctctgaggcaaattctcaggg+gtcaggcggaattgacaaggagacaatgggattcac+ta+agc
  34                     seq1  85 AGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGC 151
  35                              ****************************************************************986 PP
  36
  37 >> seq2  Description of seq2
  38     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
  39    ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
  40  !   38.6   0.4   3.9e-15        34        92 ..        59         1 ..        60         1 ..        60    0.97
  41
  42   Alignment:
  43   score: 38.6 bits
  44   A_HA_H7_CDS_nucleotide 34 gtgatgattgcaacaaatgcagacaaaatctgccttgggcaccatgctgtgtcaaacgg 92
  45                             g+gat+att+c+acaaatgcagacaa atctgccttgggca+catgc+gtgtcaaacgg
  46                     seq2 59 GCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGG 1
  47                             6899****************************************************986 PP
  48
  49
  50
  51 Internal pipeline statistics summary:
  52 -------------------------------------
  53 Query model(s):                              1  (1683 nodes)
  54 Target sequences:                            2  (422 residues searched)
  55 Residues passing SSV filter:               211  (0.5); expected (0.02)
  56 Residues passing bias filter:              211  (0.5); expected (0.02)
  57 Residues passing Vit filter:               211  (0.5); expected (0.003)
  58 Residues passing Fwd filter:               211  (0.5); expected (3e-05)
  59 Total number of hits:                        2  (0.498)
  60 # CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.30
  61 # Mc/sec: 2.37
  62 //
  63 [ok]