HMM length of domain: 23 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	13.8	0.5	0.00096	0.057	2	23	79	100
2	3.5	0.3	1.8	1.1e+02	3	23	286	308
3	3.0	4.2	2.5	1.5e+02	2	23	344	366
4	17.6	2.8	6e-05	0.0036	3	23	374	394
5	12.2	0.1	0.003	0.18	2	23	402	424
6	15.6	2.3	0.00027	0.016	1	23	430	452
7	7.0	3.2	0.13	8.1	1	23	458	480
8	10.0	4.2	0.015	0.92	1	23	486	509
9	7.4	3.5	0.1	6.2	1	23	518	540

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00096
                    EETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   2 kCpdCgksFkrksnLkrHirtH 23 
                    +Cp+C+ +F + + L++H+r H
  KWMTBOMO03240  79 QCPGCTDVFETEETLRTHLRNH 100
                    8********************6 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 1.8
                    ET..TTTEEESSHHHHHHHHHCC CS
        zf-C2H2   3 Cp..dCgksFkrksnLkrHirtH 23 
                    C+  +C  + ++  nL  H+++H
  KWMTBOMO03240 286 CSiaGCQIRLRDENNLSYHRKSH 308
                    88889****************99 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 2.5
                    EETTTT.EEESSHHHHHHHHHCC CS
        zf-C2H2   2 kCpdCg.ksFkrksnLkrHirtH 23 
                    +C++Cg k++k   + + H+++H
  KWMTBOMO03240 344 TCEICGfKTYKKHRLHNIHMKIH 366
                    7********************99 PP

  == domain 4  score: 17.6 bits;  conditional E-value: 6e-05
                    ETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   3 CpdCgksFkrksnLkrHirtH 23 
                    Cp+C+ksFk+  +L +H  tH
  KWMTBOMO03240 374 CPICSKSFKNANQLSKHKLTH 394
                    *******************99 PP

  == domain 5  score: 12.2 bits;  conditional E-value: 0.003
                    EETTTTEEESSHHHHHHHHHC.C CS
        zf-C2H2   2 kCpdCgksFkrksnLkrHirt.H 23 
                    kCp+C++ F++  +L+ H    H
  KWMTBOMO03240 402 KCPICPREFSNGRQLREHVTAvH 424
                    8*****************86555 PP

  == domain 6  score: 15.6 bits;  conditional E-value: 0.00027
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    ykC +C+++  rk ++k H+r+H
  KWMTBOMO03240 430 YKCQHCDYTAARKGEMKLHMRSH 452
                    9*********************9 PP

  == domain 7  score: 7.0 bits;  conditional E-value: 0.13
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    y C++C+++  +   ++rH ++H
  KWMTBOMO03240 458 YSCNICSYRSADHNAMRRHKKMH 480
                    89*******************99 PP

  == domain 8  score: 10.0 bits;  conditional E-value: 0.015
                    EEETTTTEEESSHHHHHHHHHC.C CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                    ykC++C+++  ++ ++  H+++ H
  KWMTBOMO03240 486 YKCKHCPYTSIQSTSFAYHMMSrH 509
                    9********************999 PP

  == domain 9  score: 7.4 bits;  conditional E-value: 0.1
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    ++Cp+C+ +  +k+ +++H+  H
  KWMTBOMO03240 518 HRCPYCSFKSINKDKYVTHLTNH 540
                    79*****************9988 PP