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	2.0	0.1	5.5	3.3e+02	1	9	8	16
2	2.3	0.0	4.2	2.5e+02	3	23	39	59
3	6.3	0.2	0.24	14	3	23	164	185
4	22.8	1.6	1.3e-06	7.9e-05	1	23	198	221
5	17.8	5.3	5.2e-05	0.0031	2	23	262	283
6	12.7	4.9	0.0022	0.13	1	23	289	311
7	19.7	3.0	1.3e-05	0.0008	1	23	317	339
8	18.1	3.4	4.2e-05	0.0025	1	23	345	367
9	6.9	3.8	0.15	8.8	1	20	373	392

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 5.5
                   EEETTTTEE CS
        zf-C2H2  1 ykCpdCgks 9 
                   ++Cp+C+ s
  KWMTBOMO09123  8 FPCPVCTLS 16
                   89****943 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 4.2
                   ETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2  3 CpdCgksFkrksnLkrHirtH 23
                   Cp+C +     + L+ H+ +H
  KWMTBOMO09123 39 CPVCQEEIIGLDKLTIHLFSH 59
                   9*****99999******9988 PP

  == domain 3  score: 6.3 bits;  conditional E-value: 0.24
                    ETTTTEEESSHHHHHHHHHC.C CS
        zf-C2H2   3 CpdCgksFkrksnLkrHirt.H 23 
                    C++Cg  F +   Lk+H++  H
  KWMTBOMO09123 164 CNICGLQFVDENILKVHRCLiH 185
                    *****************99888 PP

  == domain 4  score: 22.8 bits;  conditional E-value: 1.3e-06
                    EEETTTTEEESSHHHHHHHHHC.C CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirt.H 23 
                    y+C+ C+k+Fk + +L++H+r+ H
  KWMTBOMO09123 198 YQCHLCPKKFKMRGSLMVHLRVaH 221
                    9********************999 PP

  == domain 5  score: 17.8 bits;  conditional E-value: 5.2e-05
                    EETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   2 kCpdCgksFkrksnLkrHirtH 23 
                    +C++C k+F++k+ Lk+H r H
  KWMTBOMO09123 262 QCDVCRKCFTTKYFLKKHKRLH 283
                    8*******************99 PP

  == domain 6  score: 12.7 bits;  conditional E-value: 0.0022
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    y C+ C+k+F+ + ++ +H+  H
  KWMTBOMO09123 289 YACTQCNKTFTFQQSYHKHLLYH 311
                    88******************998 PP

  == domain 7  score: 19.7 bits;  conditional E-value: 1.3e-05
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    + C++Cg+ Fk  s L +H+r+H
  KWMTBOMO09123 317 HICNYCGRAFKELSTLHNHQRIH 339
                    67********************9 PP

  == domain 8  score: 18.1 bits;  conditional E-value: 4.2e-05
                    EEETTTTEEESSHHHHHHHHHCC CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHirtH 23 
                    + C+ Cgk+F+++ ++ +H+r+H
  KWMTBOMO09123 345 FSCETCGKCFRQRVSYLVHRRIH 367
                    89********************9 PP

  == domain 9  score: 6.9 bits;  conditional E-value: 0.15
                    EEETTTTEEESSHHHHHHHH CS
        zf-C2H2   1 ykCpdCgksFkrksnLkrHi 20 
                    ykC+ C ksF+ k + ++H 
  KWMTBOMO09123 373 YKCTACEKSFRYKVSQRTHK 392
                    9************9999995 PP