# nhmmer :: search a DNA model or alignment against a DNA database
# HMMER 3.1b1 (May 2013); http://hmmer.org/
# Copyright (C) 2013 Howard Hughes Medical Institute.
# Freely distributed under the GNU General Public License (GPLv3).
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query file:                      ../HMMs/A_HA_H7_CDS_nucleotide.hmm
# target sequence database:        tmp.fa
# number of worker threads:        4
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       A_HA_H7_CDS_nucleotide  [M=1683]
Scores for complete hits:
    E-value  score  bias  Sequence  start    end  Description
    ------- ------ -----  --------  -----  -----  -----------
    3.2e-48  148.2   5.7  seq1          1    151  Description of seq1
    3.9e-15   38.6   0.4  seq2         59      1  Description of seq2


Annotation for each hit  (and alignments):
>> seq1  Description of seq1
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
 !  148.2   5.7   3.2e-48       258       411 ..         1       151 []         1       151 []       151    0.98

  Alignment:
  score: 148.2 bits
  A_HA_H7_CDS_nucleotide 258 attcctagaattttcagctgatttaattattgagaggcgagaaggaagtaatgatgtctgttatcctgggaaattcgtaaatgaaga 344
                             attcctagaattttcagc+gatttaattattgagaggcgagaaggaagt   gatgtctgttatcctgggaaattcgt+aatgaaga
                    seq1   1 ATTCCTAGAATTTTCAGCCGATTTAATTATTGAGAGGCGAGAAGGAAGT---GATGTCTGTTATCCTGGGAAATTCGTGAATGAAGA 84 
                             689*******************************************777...*********************************** PP

  A_HA_H7_CDS_nucleotide 345 agctctgaggcaaattctcagggggtcaggcggaattgacaaggagacaatgggattcacatatagc 411
                             agctctgaggcaaattctcaggg+gtcaggcggaattgacaaggagacaatgggattcac+ta+agc
                    seq1  85 AGCTCTGAGGCAAATTCTCAGGGAGTCAGGCGGAATTGACAAGGAGACAATGGGATTCACCTACAGC 151
                             ****************************************************************986 PP

>> seq2  Description of seq2
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to    sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- --------- ---------    ----
 !   38.6   0.4   3.9e-15        34        92 ..        59         1 ..        60         1 ..        60    0.97

  Alignment:
  score: 38.6 bits
  A_HA_H7_CDS_nucleotide 34 gtgatgattgcaacaaatgcagacaaaatctgccttgggcaccatgctgtgtcaaacgg 92
                            g+gat+att+c+acaaatgcagacaa atctgccttgggca+catgc+gtgtcaaacgg
                    seq2 59 GCGATCATTCCGACAAATGCAGACAAGATCTGCCTTGGGCATCATGCCGTGTCAAACGG 1 
                            6899****************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                              1  (1683 nodes)
Target sequences:                            2  (422 residues searched)
Residues passing SSV filter:               211  (0.5); expected (0.02)
Residues passing bias filter:              211  (0.5); expected (0.02)
Residues passing Vit filter:               211  (0.5); expected (0.003)
Residues passing Fwd filter:               211  (0.5); expected (3e-05)
Total number of hits:                        2  (0.498)
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.30
# Mc/sec: 2.37
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