# 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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