HMM length of domain: 57 aa

c-Evalue (conditional Evalue): It is an attempt to measure the statistical significance of each domain, given that we’ve already decided that the target sequence is a true homolog. It is the expected number of additional domains we’d find with a domain score this big in the set of sequences reported in the top hits list, if those sequences consisted only of random nonhomologous sequence outside the region that sufficed to define them as homologs.
i-Evalue (independent Evalue): The significance of the sequence in the whole database search, if this were the only domain we had identified. 
Domain annotation for each sequence:
#	score	bias	c-Evalue	i-Evalue	hmmfrom	hmm to	alifrom	ali to
--	-----	----	--------	--------	-------	------	-------	------
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
1	0.2	0.1	3.3	6.3e+02	3	22	238	257
2	45.7	0.7	2.1e-14	4.1e-12	5	56	291	342

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 3.3
                    -SSSS-HHHHHHHHHHHHHS CS
       Homeobox   3 kRttftkeqleeLeelFeen 22 
                    +R ++ k q   Le++++e 
  KWMTBOMO13953 238 QRSSHAKLQALWLEAHYQEA 257
                    56677777777788888764 PP

  == domain 2  score: 45.7 bits;  conditional E-value: 2.1e-14
                    SSS-HHHHHHHHHHHHHSSS-SHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
       Homeobox   5 ttftkeqleeLeelFeenrypsaeereeLAkklgLeerqVkvWFqNrRakek 56 
                    ++f++     L e + +++yp+ ++++eLA+ +gL+ +qV +WF+NrR++++
  KWMTBOMO13953 291 HCFKERTRSLLREWYLQDPYPNPTKKRELAAATGLTPTQVGNWFKNRRQRDR 342
                    56788888899999************************************98 PP